RNA recognition motif (RRM) found in inner nuclear membrane protein Man1 (Man1) and similar proteins; This subfamily corresponds to the RRM of Man1, also termed LEM domain-containing protein 3 (LEMD3), an integral protein of the inner nuclear membrane that binds to nuclear lamins and emerin, thus playing a role in nuclear organization. It is part of a protein complex essential for chromatin organization and cell division. It also functions as an important negative regulator for the transforming growth factor (TGF) beta/activin/Nodal signaling pathway by directly interacting with chromatin-associated proteins and transcriptional regulators, including the R-Smads, Smad1, Smad2, and Smad3. Moreover, Man1 is a unique type of left-right (LR) signaling regulator that acts on the inner nuclear membrane. Man1 plays a crucial role in angiogenesis. The vascular remodeling can be regulated at the inner nuclear membrane through the interaction between Man1 and Smads. Man1 contains an N-terminal LEM domain, two putative transmembrane domains, a MAN1-Src1p C-terminal (MSC) domain, and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The LEM domain interacts with the DNA and chromatin-binding protein Barrier-to-Autointegration Factor, and is also necessary for efficient localization of MAN1 in the inner nuclear membrane. Research has indicated that C-terminal nucleoplasmic region of Man1 exhibits a DNA binding winged helix domain and is responsible for both DNA- and Smad-binding.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665403324 542 CLKIRHMFDSSEVDQANLKQSIVESIIEKVGTRCKICDVQLDVQS--CCVYIRCASEEDAGTIHKEINGWWFDKRLISIK 619
Cdd:cd12286    1 CLKIRNMFDPEMEIGEDWHVRIQEAILEKCSDNGGIVHIAVDKNSreGCVYIKCASPEDAGKAFKALHGCWFDGRLVTVK 80

                         90
                 ....*....|..
gi 665403324 620 FLRLERYLSRFP 631
Cdd:cd12286   81 YLRLERYHSRFP 92

RNA recognition motif (RRM) found in inner nuclear membrane protein Man1 (Man1) and similar proteins; This subfamily corresponds to the RRM of Man1, also termed LEM domain-containing protein 3 (LEMD3), an integral protein of the inner nuclear membrane that binds to nuclear lamins and emerin, thus playing a role in nuclear organization. It is part of a protein complex essential for chromatin organization and cell division. It also functions as an important negative regulator for the transforming growth factor (TGF) beta/activin/Nodal signaling pathway by directly interacting with chromatin-associated proteins and transcriptional regulators, including the R-Smads, Smad1, Smad2, and Smad3. Moreover, Man1 is a unique type of left-right (LR) signaling regulator that acts on the inner nuclear membrane. Man1 plays a crucial role in angiogenesis. The vascular remodeling can be regulated at the inner nuclear membrane through the interaction between Man1 and Smads. Man1 contains an N-terminal LEM domain, two putative transmembrane domains, a MAN1-Src1p C-terminal (MSC) domain, and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The LEM domain interacts with the DNA and chromatin-binding protein Barrier-to-Autointegration Factor, and is also necessary for efficient localization of MAN1 in the inner nuclear membrane. Research has indicated that C-terminal nucleoplasmic region of Man1 exhibits a DNA binding winged helix domain and is responsible for both DNA- and Smad-binding.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665403324 542 CLKIRHMFDSSEVDQANLKQSIVESIIEKVGTRCKICDVQLDVQS--CCVYIRCASEEDAGTIHKEINGWWFDKRLISIK 619
Cdd:cd12286    1 CLKIRNMFDPEMEIGEDWHVRIQEAILEKCSDNGGIVHIAVDKNSreGCVYIKCASPEDAGKAFKALHGCWFDGRLVTVK 80

                         90
                 ....*....|..
gi 665403324 620 FLRLERYLSRFP 631
Cdd:cd12286   81 YLRLERYHSRFP 92

LEM (Lap2/Emerin/Man1) domain found in emerin, lamina-associated polypeptide 2 (LAP2), inner nuclear membrane protein Man1 and similar proteins; The family corresponds to a group of inner nuclear membrane proteins containing LEM domain. Emerin occurs in four phosphorylated forms and plays a role in cell cycle-dependent events. It is absent from the inner nuclear membrane in most patients with X-linked muscular dystrophy. Emerin interacts with A-type and B-type lamins. Man1, also termed LEM domain-containing protein 3 (LEMD3) is an integral protein of the inner nuclear membrane that binds to nuclear lamins and emerin, thus playing a role in nuclear organization. LAP2, also termed thymopoietin (TP), or thymopoietin-related peptide (TPRP), is composed of isoform alpha and isoforms beta/gamma and may be involved in chromatin organization and post-mitotic reassembly. Some LAP2 isoforms are inner nuclear membrane proteins that can bind to nuclear lamins and chromatin, while others are non-membrane nuclear polypeptides. This family also contains LEM domain-containing protein LEMP-1 and LEM2. LEMP-1, also termed cancer/testis antigen 50 (CT50), is encoded by LEMD1, a novel testis-specific gene expressed in colorectal cancers. LEMP-1 may function as a cancer-testis antigen for immunotherapy of colorectal carcinoma (CRC). LEM2, also termed LEMD2, is a novel Man1-related ubiquitously expressed inner nuclear membrane protein required for normal nuclear envelope morphology. Association with lamin A is required for its proper nuclear envelope localization while its binding to lamin C plays an important role in the organization of lamin A/C complexes. Some uncharacterized LEM domain-containing proteins are also included in this family. Unlike other family members, these harbor an ankyrin repeat region that may mediate protein-protein interactions.

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 665403324   9 LSDKELHRKLIQSGFPSTPVTETTRAVLIEKLRKH 43
Cdd:cd12934    1 LSDDELRRELKELGEPPGPITDTTRKVYLKKLAKL 35

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665403324  527 PAFDNSNkiANPPTPCLKIRHMFDSSEVDQANLKQSIVESIIEKVGTRCKICDVQLDVQSCC--VYIRCASEEDAGTIHK 604
Cdd:TIGR01622 388 TSFVPVN--VNLASRCLVLSNMFDPATEEEPNWDKEIEDDVREECSKYGGVVHIYVDDKNSAgdIYLKFDSVQAAEAAIK 465

                          90       100
                  ....*....|....*....|....*..
gi 665403324  605 EINGWWFDKRLISIKFLRLERYLSRFP 631
Cdd:TIGR01622 466 ALNGRYFGGKMITAAFVVDAVYSKSRL 492

RNA recognition motif (RRM) found in inner nuclear membrane protein Man1 (Man1) and similar proteins; This subfamily corresponds to the RRM of Man1, also termed LEM domain-containing protein 3 (LEMD3), an integral protein of the inner nuclear membrane that binds to nuclear lamins and emerin, thus playing a role in nuclear organization. It is part of a protein complex essential for chromatin organization and cell division. It also functions as an important negative regulator for the transforming growth factor (TGF) beta/activin/Nodal signaling pathway by directly interacting with chromatin-associated proteins and transcriptional regulators, including the R-Smads, Smad1, Smad2, and Smad3. Moreover, Man1 is a unique type of left-right (LR) signaling regulator that acts on the inner nuclear membrane. Man1 plays a crucial role in angiogenesis. The vascular remodeling can be regulated at the inner nuclear membrane through the interaction between Man1 and Smads. Man1 contains an N-terminal LEM domain, two putative transmembrane domains, a MAN1-Src1p C-terminal (MSC) domain, and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The LEM domain interacts with the DNA and chromatin-binding protein Barrier-to-Autointegration Factor, and is also necessary for efficient localization of MAN1 in the inner nuclear membrane. Research has indicated that C-terminal nucleoplasmic region of Man1 exhibits a DNA binding winged helix domain and is responsible for both DNA- and Smad-binding.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665403324 542 CLKIRHMFDSSEVDQANLKQSIVESIIEKVGTRCKICDVQLDVQS--CCVYIRCASEEDAGTIHKEINGWWFDKRLISIK 619
Cdd:cd12286    1 CLKIRNMFDPEMEIGEDWHVRIQEAILEKCSDNGGIVHIAVDKNSreGCVYIKCASPEDAGKAFKALHGCWFDGRLVTVK 80

                         90
                 ....*....|..
gi 665403324 620 FLRLERYLSRFP 631
Cdd:cd12286   81 YLRLERYHSRFP 92

RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665403324 540 TPCLKIRHMFDSSEVDQANLKQSIVESIIE---KVGtrcKICDVQLDVQSC--CVYIRCASEEDAGTIHKEINGWWFDKR 614
Cdd:cd12285    1 SRCVILKNMFDPAEETEDNWDDEIKEDVIEecsKYG---PVLHIYVDKNSPqgNVYVKFKTIEAAQKCVQAMNGRWFDGR 77

                 ....*..
gi 665403324 615 LISIKFL 621
Cdd:cd12285   78 QITAAYV 84

LEM domain; The LEM domain is 50 residues long and is composed of two parallel alpha helices. This domain is found in inner nuclear membrane proteins. It is called the LEM domain after LAP2, Emerin and Man1.

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 665403324    8 SLSDKELHRKLIQSGFPSTPVTETTRAVLIEKLRK 42
Cdd:pfam03020   4 QLSDEELREQLKEYGVSPGPITATTRKLYEKKLKK 38

LEM (Lap2/Emerin/Man1) domain found in LEM domain-containing protein 2 (LEM2); This CD corresponds to the LEM domain that is responsible for the interaction with chromatin protein barrier-to-autointegration factor (BAF). LEM2, also termed LEMD2, is a novel Man1-related ubiquitously expressed inner nuclear membrane protein required for normal nuclear envelope morphology. Association with lamin A is required for its proper nuclear envelope localization. It also binds to lamin C and plays an important role in the organization of lamin A/C complexes. LEM2 contains an N-terminal LEM domain, two putative transmembrane domains and a MAN1-Src1p C-terminal (MSC) domain, but lacks the Man1-specific C-terminal RNA recognition motif (RRM).

                         10        20        30
                 ....*....|....*....|....*....|....
gi 665403324   9 LSDKELHRKLIQSGFPSTPVTETTRAVLIEKLRK 42
Cdd:cd12941    1 LTDAELRRELLALGFRPGPITETTRKVYIKKLSC 34

LEM (Lap2/Emerin/Man1) domain found in ankyrin repeat and LEM domain-containing protein 2 (ANKL2); The family includes ANKL2 and similar proteins. Although their biological roles remain unclear, the family members share an N-terminal LEM domain and an ankyrin repeat region. The LEM domain, mainly found in inner nuclear membrane proteins, may be involved in protein- or DNA-binding. The ankyrin repeats are unique motifs mediating protein-protein interactions.

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 665403324   6 LNSLSDKELHRKLIQSGFPSTPVTETTRAVLIEKL 40
Cdd:cd12944    2 LKKLSPDELREELRKAGLKCGPITSTTRFLFEKKL 36