RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins; This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 161077311  490 CSTTLWVGHLSKLVYQEELSDTFGEYGDIVSIDQIVPRGCAFIVMNRRQDAHKAMQALKNHKLQGRAITISWAAGKG 566
Cdd:cd12227     1 CSTTLWVGHLSKKVTQEELKNLFEEYGEIQSIDMIPPRGCAYVCMKTRQDAHRALQKLKNHKLRGKSIKIAWAPNKG 77

RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins; This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 161077311  490 CSTTLWVGHLSKLVYQEELSDTFGEYGDIVSIDQIVPRGCAFIVMNRRQDAHKAMQALKNHKLQGRAITISWAAGKG 566
Cdd:cd12227     1 CSTTLWVGHLSKKVTQEELKNLFEEYGEIQSIDMIPPRGCAYVCMKTRQDAHRALQKLKNHKLRGKSIKIAWAPNKG 77

domain present in proteins, which are involved in regulation of nuclear pre-mRNA;

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 161077311      6 AFNNELSGLYDSRPPISKAkmaaiTKSAMRAIKLYKHVVQSVEKFILKCKPEYKVPGLYVIDSIVRQSRHQYGMD-KDLF 84
Cdd:smart00582    1 AFEQKLESLNNSQESIQTL-----TKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKYGSEfGDEL 75

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|
gi 161077311     85 APRFQRNLTETFANLFRcapEDKSRIIRVLNLWQKNNVFKSEVIQPIFDL 134
Cdd:smart00582   76 GPVFQDALRRVLGAAPE---ELKKKIRRLLNIWEERGIFPPEVLRPLREK 122

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 161077311  491 STTLWVGHLSKLVYQEELSDTFGEYGDIVSIdQIV-------PRGCAFIVMNRRQDAHKAMQALKNHKLQGRAITISWA 562
Cdd:COG0724     1 SMKIYVGNLPYSVTEEDLRELFSEYGEVTSV-KLItdretgrSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEA 78

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 161077311 1187 SQSANSPPQEKLPAEnenfAKPADVTGDPLVAKSQTETSAACTPLYDELPP-----PAVPQTPTQPPKEPQGS-PPRPAP 1260
Cdd:PHA03247 2696 TSLADPPPPPPTPEP----APHALVSATPLPPGPAAARQASPALPAAPAPPavpagPATPGGPARPARPPTTAgPPAPAP 2771

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 161077311 1261 PVIETEAAPHEESVP--APPAELQTEAPSAEEPIAPAASADVVAEADP 1306
Cdd:PHA03247 2772 PAAPAAGPPRRLTRPavASLSESRESLPSPWDPADPPAAVLAPAAALP 2819

Androgen receptor;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 161077311  1180 QKPGERASQSANS--PPQEKLPAENENFAKPADVTGDPLVAKSQTETSAACTPLYDELPPPA---------------VPQ 1242
Cdd:pfam02166   30 QNPGPRHPEAAGGaaPPGARLQHQQQQQQQVPQQPQQQESSPRQPQASVQPQQAGDDGSPPAhnrgpagylaleddeQPQ 109

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 161077311  1243 tPTQPPKEPQGSP-----PRPAPPVIETEAAPHEESVPAPPAELQTEAPSAEE---PIAPAASA------DVVAEA 1304
Cdd:pfam02166  110 -PSQAQPAAECCPengcvPEPGAAAAAGKGLPQQAVAPAAPDDDDSAAPSTLSllgPSFPGLSGcsadlkDILAEA 184

CCR4-NOT transcriptional regulation complex, NOT5 subunit [Transcription];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 161077311 1127 EGNKAASETEPKPKNVETELGSTnTGAPAAATRVDTEEDWDQELQDyearMEAQKPGERAsQSANSPPQEKLPAEnENFA 1206
Cdd:COG5665   235 EWWGDPSLLATPPATPATEEKSS-QQPKSQPTSPSGGTTPPSTNQL----TTSNTPTSTA-KAQPQPPTKKQPAK-EPPS 307

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 161077311 1207 KPADVTGDPLVAKSQTETSAACTPLYDELPPPAVPQTPTQP------PKEPQGSPPRPAPPVIET--------EAAPHEE 1272
Cdd:COG5665   308 DTASGNPSAPSVLINSDSPTSEDPATASVPTTEETTAFTTPssvpstPAEKDTPATDLATPVSPTppetsvdkKVSPDSA 387

                         170       180       190
                  ....*....|....*....|....*....|....
gi 161077311 1273 SVPAPPAElqtEAPSAEEPIAPAASADVVAEADP 1306
Cdd:COG5665   388 TSSTKSEK---EGGTASSPMPPNIAIGAKDDVDA 418

septation protein SepH; Septation protein H (SepH) was firstly characterized in Streptomyces venezuelae, and homologs were identified in Mycobacterium smegmatis. SepH contains a N-terminal DUF3071 domain and a conserved C-terminal region. It binds directly to cell division protein FtsZ to stimulate the assembly of FtsZ protofilaments.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 161077311 1182 PGERASQSANSPPQEKLPAENENFAKPADVTGDPLVAKSQTETSAACTPLYDELPPPAVPqtPTQPPKEPQGSPPRPAPP 1261
Cdd:NF040712  192 FGRPLRPLATVPRLAREPADARPEEVEPAPAAEGAPATDSDPAEAGTPDDLASARRRRAG--VEQPEDEPVGPGAAPAAE 269

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 161077311 1262 VIETEAAPHEESVPAPPAELQTEAPSAEEPIAPAASADVVAEADP 1306
Cdd:NF040712  270 PDEATRDAGEPPAPGAAETPEAAEPPAPAPAAPAAPAAPEAEEPA 314

CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8; SR-related and CTD-associated factor 8 (SCAF8) is also called CDC5L complex-associated protein 7 (CCAP7) or RNA-binding motif protein 16 (RBM16). It may play a role in mRNA processing. SCAF8 contains a CTD-interacting domain (CID) at the amino terminus and a Ser/Arg-rich domain followed by an RNA recognition motif. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 161077311    6 AFNNELSGLYDSRPPISKAKMAAITKSAMRAIKLYKHVVQSVEKFILKCKPEYKVPGLYVIDSIVRQSRHQYGMDKDLFA 85
Cdd:cd17004     2 TFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVFA 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 161077311   86 PRFQRNLTETFANLFRCAPEDKSRIIRVLNLWQKNNVFKSEVIQPIFDLA 135
Cdd:cd17004    82 PRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMA 131

RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins; This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 161077311  490 CSTTLWVGHLSKLVYQEELSDTFGEYGDIVSIDQIVPRGCAFIVMNRRQDAHKAMQALKNHKLQGRAITISWAAGKG 566
Cdd:cd12227     1 CSTTLWVGHLSKKVTQEELKNLFEEYGEIQSIDMIPPRGCAYVCMKTRQDAHRALQKLKNHKLRGKSIKIAWAPNKG 77

CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase II. This domain is known as the CTD-interacting domain (CID).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 161077311     6 AFNNELSGLYDSrppisKAKMAAITKSAMRAIKLYKHVVQSVEKFILKCKPEYKVPGLYVIDSIVRQSRHQYGMDkdlFA 85
Cdd:pfam04818    2 ALEKKLSSLNNS-----QESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRKKGKSE---FA 73

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 161077311    86 PRFQRNLTETFANLFRCAPED-KSRIIRVLNLWQKNNVFKSEVI 128
Cdd:pfam04818   74 DAFEPVLPEAFASAYKKCDEKlKKKLERLLNIWEERNVFSPEVI 117

RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins; The CD corresponds to the RRM of SCAF4 (also termed splicing factor, arginine/serine-rich 15 or SFR15, or CTD-binding SR-like protein RA4) that belongs to a new class of SCAFs (SR-like CTD-associated factors). Although its biological function remains unclear, SCAF4 shows high sequence similarity to SCAF8 that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II) and may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF4 and SCAF8 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 161077311  488 SVCSTTLWVGHLSKLVYQEELSDTFGEYGDIVSIDQIVPRGCAFIVMNRRQDAHKAMQALK--NHKLQGRAITISWAAGK 565
Cdd:cd12461     1 SVCSTTLWVGQLDKRTTQQDVASLLEEFGQIESINMIPPRGCAYIVMVHRQDAYRALQKLSrgNYKVNQKSIKIAWALNK 80

                  .
gi 161077311  566 G 566
Cdd:cd12461    81 G 81

CID (CTD-Interacting Domain) of Nrd1 and similar proteins; This subfamily includes Saccharomyces cerevisiae protein Nrd1, Schizosaccharomyces pombe Rpb7-binding protein Seb1, and similar proteins. Nrd1 cooperates with Nab3 and Sen1, also called the Nrd1-Nab3-Sen1 (NNS) complex, to terminate the transcription by RNA polymerase (Pol) II (RNAPII) of many noncoding RNAs (ncRNAs), including small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), and cryptic unstable transcripts (CUTs). Schizosaccharomyces pombe Seb1 does not function in an NNS-like termination pathway but promotes polyadenylation site selection of coding and noncoding genes. It cotranscriptionally controls alternative polyadenylation. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. Nrd1 CID preferentially interacts with CTD phosphorylated at Ser5. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 161077311    7 FNNELSGLYDSRPP-ISKAKMAAITKSAMRAIKLYKHVVQSVEKFILKCKPEYKVPGLYVIDSIVRQSRHQ---YGMDKD 82
Cdd:cd16984     3 FEATLKSLQALKPPgVSGSKIKKLTDIAVDNVQSESQIVSKLYRYFKKAPPTHKLGVLYVVDSVVRAWIDQakkNGQSID 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 161077311   83 LFAP---------RFQRNLTETFANLFRCAPED-KSRIIRVLNLWQKNNVFKSEVIQPIFD 133
Cdd:cd16984    83 SSAPdgtfaagvyKITELIESLMNDAIQSAPEDqKEKIKKLVDIWEKGNTFPAEMLNSIKQ 143

CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied protein is Saccharomyces cerevisiae Pcf11, also called protein 1 of CF I, an essential subunit of the cleavage factor IA (CFIA) complex which is required for polyadenylation-dependent pre-mRNA 3'-end processing and RNA polymerase (Pol) II (RNAP II) transcription termination. Human Pcf11, also referred to as pre-mRNA cleavage complex 2 protein Pcf11, has been shown to enhance degradation of RNAP II-associated nascent RNA and transcriptional termination. The family also includes plant PCFS4 (Pcf11-similar-4 protein or Polyadenylation and cleavage factor homolog 4) and Caenorhabditis elegans Polyadenylation and cleavage factor homolog 11. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. Pcf11 CID preferentially interacts with CTD phosphorylated at Ser2. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 161077311    7 FNNELSGL-YDSRPPISkakmaAITKSAMRAIKLYKHVVQSVEKFILKCKPEYKVPGLYVIDSIVRQSRHQYgmdKDLFA 85
Cdd:cd16982     4 YRSALAELtFNSKPIIN-----NLTMLAEENIQAAQAIVEAIEERIRKVPPEQKLPALYLLDSIVKNVGGPY---TSLFS 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 161077311   86 PrfqrNLTETFANLFR-CAPEDKSRIIRVLNLW-----QKNNVFKSEVIQPI 131
Cdd:cd16982    76 P----NLVDLFLDAYRlVDEKTRKKLEKLLNTWktvfpNGKLLFPDEVLNKI 123

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 161077311  492 TTLWVGHLSKLVYQEELSDTFGEYGDIVSIDQIVPRGCAFIVMNRRQDAHKAMQALKNHKLQGRAITISW 561
Cdd:cd12346     2 TTVFVGGLDPNVTEEDLRVLFGPFGEIVYVKIPPGKGCGFVQFVNRASAEAAIQKLQGTPIGGSRIRLSW 71

RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 161077311  492 TTLWVGHLSKLVYQEELSDTFGEYGDIVSIDQIVPRGCAFIVMNRRQDAHKAMQALKNhKL--QGRAITISWA 562
Cdd:cd12224     2 TTLYVGGLGDKITEKDLRDHFYQFGEIRSITVVARQQCAFVQFTTRQAAERAAERTFN-KLiiKGRRLKVKWG 73

RNA recognition motif 2 (RRM2) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 161077311  492 TTLWVGHLSKLVYQEELSDTFGEYGDIVS----IDQI--VPRGCAFIVMNRRQDAHKAMQALKNHKLQGRA--ITISWA 562
Cdd:cd12376     1 ANLYVSGLPKTMTQKELEQLFSQYGRIITsrilRDQLtgVSRGVGFIRFDKRIEAEEAIKGLNGQKPEGASepITVKFA 79

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 161077311 1187 SQSANSPPQEKLPAEnenfAKPADVTGDPLVAKSQTETSAACTPLYDELPP-----PAVPQTPTQPPKEPQGS-PPRPAP 1260
Cdd:PHA03247 2696 TSLADPPPPPPTPEP----APHALVSATPLPPGPAAARQASPALPAAPAPPavpagPATPGGPARPARPPTTAgPPAPAP 2771

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 161077311 1261 PVIETEAAPHEESVP--APPAELQTEAPSAEEPIAPAASADVVAEADP 1306
Cdd:PHA03247 2772 PAAPAAGPPRRLTRPavASLSESRESLPSPWDPADPPAAVLAPAAALP 2819

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator/modulator (CoAA) and similar proteins; This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 161077311  494 LWVGHLSKLVYQEELSDTFGEYGDIVSIDqIVpRGCAFIVMNRRQDAHKAMQALKNHKLQGRAITI 559
Cdd:cd12343     2 IFVGNLPDAATSEELRALFEKYGKVTECD-IV-KNYAFVHMEKEEDAEDAIKALNGYEFMGSRINV 65

RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 161077311  492 TTLWVGHLSKLVYQEELSDTFGEYGDIVSI----DQI--VPRGCAFIVMNRRQDAHKAMQALKNHKLQGRAITIS 560
Cdd:cd12651     3 TNLYVTNLPRTITEDELDTIFGAYGNIVQKnllrDKLtgRPRGVAFVRYDKREEAQAAISALNGTIPEGGTQPLS 77

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 161077311  492 TTLWVGHLSKLVYQEELSDTFGEYGDIVSIDQIVPRGCAFIVMNRRQDAHKAMQALKNHKLQGRAITISW 561
Cdd:cd12354     1 TTVYVGNITKGLTEALLQQTFSPFGQILEVRVFPDKGYAFIRFDSHEAATHAIVSVNGTIINGQAVKCSW 70

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; This family is composed of Regulation of nuclear pre-mRNA domain-containing proteins 1A (RPRD1A), 1B (RPRD1B), 2 (RPRD2), yeast Rtt103, and similar proteins. RPRD1A, RPRD1B, and RPRD2 are CID (CTD-Interacting Domain) containing proteins that co-purify with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. Yeast transcription termination factor Rtt103 is a CID containing protein that functions in DNA damage response. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 161077311   38 KLYKHVVQSVEKFILKCKPEYKVPGLYVIDSIVRQSRHQYGMDkdlFAPRFQRNLTETFANLFRCAPED-KSRIIRVLNL 116
Cdd:cd16981    30 KHAKQIVKIWLKELKKAKPERKLTLLYLANDVLQNSRRKGAPE---FVEAFKKVLPEALALVRSEGDESvRKKVLRVLNI 106

                          90
                  ....*....|..
gi 161077311  117 WQKNNVFKSEVI 128
Cdd:cd16981   107 WEERNVFGSEFL 118

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 161077311  494 LWVGHLSKLVYQEELSDTFGEYGDIVSIDQIvpRGCAFIVMNRRQDAHKAMQALKNHKLQGRAITISWA 562
Cdd:cd12251     4 LYVRNLMLSTTEEKLRELFSEYGKVERVKKI--KDYAFVHFEERDDAVKAMEEMNGKELEGSEIEVSLA 70

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 161077311  494 LWVGHLSKLVYQEELSDTFGEYGDIVSiDQIVPRG-------CAFIVMNRRQDAHKAMQALKNHKLQGRAITI 559
Cdd:cd12417     2 LWISGLSDTTKAADLKKIFSKYGKVVS-AKVVTSArtpgsrcYGYVTMASVEEADLCIKSLNKTELHGRVITV 73

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 (RRM5) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 161077311  505 QEELSDTFGEYGDIVSIDqiVP-------RGCAFIVMNRRQDAHKAMQALKNHKLQGRAITISWA 562
Cdd:cd12320    14 RKEIRELFSPFGQLKSVR--LPkkfdgshRGFAFVEFVTKQEAQNAMEALKSTHLYGRHLVLEYA 76

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 161077311  491 STTLWVGHLSKLVYQEELSDTFGEYGDIVSI-----DQIVP---RGCAFIVMNRRQDAHKAMQALKNHKLQGRAITI 559
Cdd:cd21619     1 SNTIYVGNIDMTINEDALEKIFSRYGQVESVrrppiHTDKAdrtTGFGFIKYTDAESAERAMQQADGILLGRRRLVV 77

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 161077311  506 EELSDTFGEYGDIVSIdQIV------PRGCAFIVMNRRQDAHKAMQALKNHKLQGRAITISWA 562
Cdd:cd12414    14 DDLKKLFSKFGKVLEV-TIPkkpdgkLRGFAFVQFTNVADAAKAIKGMNGKKIKGRPVAVDWA 75

sex-lethal family splicing factor; This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 161077311   488 SVCSTTLWVGHLSKLVYQEELSDTFGEYGDIVSIDQI------VPRGCAFIVMNRRQDAHKAMQALKN 549
Cdd:TIGR01659  190 SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILrdkltgTPRGVAFVRFNKREEAQEAISALNN 257

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 161077311  494 LWVGHLSKLVYQEELSDTFGEYGDIVSIDQIV---------PRGCAFIVMNRRQDAHKAMQALKNHKLQGRAITISWA 562
Cdd:cd12355     2 LWIGNLDPRLTEYHLLKLLSKYGKIKKFDFLFhktgplkgqPRGYCFVTFETKEEAEKAIECLNGKLALGKKLVVRWA 79

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 161077311  488 SVCSTTLWVGHLSKLVYQEELSDTFGEYGDIVS----IDQI--VPRGCAFIVMNRRQDAHKAMQALKNHKLQG--RAITI 559
Cdd:cd12775     2 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITsrilVDQVtgVSRGVGFIRFDKRIEAEEAIKGLNGQKPPGatEPITV 81