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Conserved domains on  [gi|564386147|ref|XP_006252025|]
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apoptotic chromatin condensation inducer in the nucleus isoform X19 [Rattus norvegicus]

Protein Classification

RNA-binding protein( domain architecture ID 10880477)

RNA-binding protein containing an RNA recognition motif (RRM) similar to apoptotic chromatin condensation inducer in the nucleus (acinus), a caspase-3-activated nuclear factor that induces apoptotic chromatin condensation after cleavage by caspase-3 without inducing DNA fragmentation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_ACINU cd12432
RNA recognition motif (RRM) found in apoptotic chromatin condensation inducer in the nucleus ...
 253-339 7.72e-50

RNA recognition motif (RRM) found in apoptotic chromatin condensation inducer in the nucleus (acinus) and similar proteins; This subfamily corresponds to the RRM of Acinus, a caspase-3-activated nuclear factor that induces apoptotic chromatin condensation after cleavage by caspase-3 without inducing DNA fragmentation. It is essential for apoptotic chromatin condensation and may also participate in nuclear structural changes occurring in normal cells. Acinus contains a P-loop motif and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which indicates Acinus might have ATPase and DNA/RNA-binding activity.


:

Pssm-ID: 409866 [Multi-domain]  Cd Length: 90  Bit Score: 167.00  E-value: 7.72e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564386147 253 SNIVHISNLVRPFTLGQLKELLGRTGTLVEEAFWIDKIKSHCFVTYSTVEEAVATRTALHGVKWPQSNPKFLCADYAEQD 332
Cdd:cd12432    1 SRILHIDNLVRPFTLGQLKELLSETGTGVIEGFWMDKIKSHCYVTYSSEEEAVATREALHGVVWPSSNGKRLKVEFVTEE 80


                 ....*..
gi 564386147 333 ELDYHRG 339
Cdd:cd12432   81 ELEELIE 87
RSB_motif pfam16294
RNSP1-SAP18 binding (RSB) motif; The RSB motif on the Acinus protein is the core around which ...
 448-482 4.33e-16

RNSP1-SAP18 binding (RSB) motif; The RSB motif on the Acinus protein is the core around which the ASAP complex is built. The apoptosis and splicing-associated protein complex, ASAP, is made up of three proteins, SAP18 (Sin3-associated protein of 18 kDa), RNA-binding protein S1 (RNPS1) and apoptotic chromatin inducer in the nucleus (Acinus). The ASAP complex appears to be an assembly of proteins at the interface between transcription, splicing and NMD, acting as a hub in the network of protein-interactions that regulate gene-expression.


:

Pssm-ID: 465085  Cd Length: 91  Bit Score: 73.62  E-value: 4.33e-16
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 564386147  448 PPAKLLDDLFRKTKAAPCIYWLPLTESQIVQKEAE 482
Cdd:pfam16294  50 PPAKLLDDLFRKTKATPCIYWLPLTPEQIAEKEAQ 84
 
Name Accession Description Interval E-value
RRM_ACINU cd12432
RNA recognition motif (RRM) found in apoptotic chromatin condensation inducer in the nucleus ...
 253-339 7.72e-50

RNA recognition motif (RRM) found in apoptotic chromatin condensation inducer in the nucleus (acinus) and similar proteins; This subfamily corresponds to the RRM of Acinus, a caspase-3-activated nuclear factor that induces apoptotic chromatin condensation after cleavage by caspase-3 without inducing DNA fragmentation. It is essential for apoptotic chromatin condensation and may also participate in nuclear structural changes occurring in normal cells. Acinus contains a P-loop motif and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which indicates Acinus might have ATPase and DNA/RNA-binding activity.


Pssm-ID: 409866 [Multi-domain]  Cd Length: 90  Bit Score: 167.00  E-value: 7.72e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564386147 253 SNIVHISNLVRPFTLGQLKELLGRTGTLVEEAFWIDKIKSHCFVTYSTVEEAVATRTALHGVKWPQSNPKFLCADYAEQD 332
Cdd:cd12432    1 SRILHIDNLVRPFTLGQLKELLSETGTGVIEGFWMDKIKSHCYVTYSSEEEAVATREALHGVVWPSSNGKRLKVEFVTEE 80


                 ....*..
gi 564386147 333 ELDYHRG 339
Cdd:cd12432   81 ELEELIE 87
RSB_motif pfam16294
RNSP1-SAP18 binding (RSB) motif; The RSB motif on the Acinus protein is the core around which ...
 448-482 4.33e-16

RNSP1-SAP18 binding (RSB) motif; The RSB motif on the Acinus protein is the core around which the ASAP complex is built. The apoptosis and splicing-associated protein complex, ASAP, is made up of three proteins, SAP18 (Sin3-associated protein of 18 kDa), RNA-binding protein S1 (RNPS1) and apoptotic chromatin inducer in the nucleus (Acinus). The ASAP complex appears to be an assembly of proteins at the interface between transcription, splicing and NMD, acting as a hub in the network of protein-interactions that regulate gene-expression.


Pssm-ID: 465085  Cd Length: 91  Bit Score: 73.62  E-value: 4.33e-16
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 564386147  448 PPAKLLDDLFRKTKAAPCIYWLPLTESQIVQKEAE 482
Cdd:pfam16294  50 PPAKLLDDLFRKTKATPCIYWLPLTPEQIAEKEAQ 84
 
Name Accession Description Interval E-value
RRM_ACINU cd12432
RNA recognition motif (RRM) found in apoptotic chromatin condensation inducer in the nucleus ...
 253-339 7.72e-50

RNA recognition motif (RRM) found in apoptotic chromatin condensation inducer in the nucleus (acinus) and similar proteins; This subfamily corresponds to the RRM of Acinus, a caspase-3-activated nuclear factor that induces apoptotic chromatin condensation after cleavage by caspase-3 without inducing DNA fragmentation. It is essential for apoptotic chromatin condensation and may also participate in nuclear structural changes occurring in normal cells. Acinus contains a P-loop motif and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which indicates Acinus might have ATPase and DNA/RNA-binding activity.


Pssm-ID: 409866 [Multi-domain]  Cd Length: 90  Bit Score: 167.00  E-value: 7.72e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564386147 253 SNIVHISNLVRPFTLGQLKELLGRTGTLVEEAFWIDKIKSHCFVTYSTVEEAVATRTALHGVKWPQSNPKFLCADYAEQD 332
Cdd:cd12432    1 SRILHIDNLVRPFTLGQLKELLSETGTGVIEGFWMDKIKSHCYVTYSSEEEAVATREALHGVVWPSSNGKRLKVEFVTEE 80


                 ....*..
gi 564386147 333 ELDYHRG 339
Cdd:cd12432   81 ELEELIE 87
RSB_motif pfam16294
RNSP1-SAP18 binding (RSB) motif; The RSB motif on the Acinus protein is the core around which ...
 448-482 4.33e-16

RNSP1-SAP18 binding (RSB) motif; The RSB motif on the Acinus protein is the core around which the ASAP complex is built. The apoptosis and splicing-associated protein complex, ASAP, is made up of three proteins, SAP18 (Sin3-associated protein of 18 kDa), RNA-binding protein S1 (RNPS1) and apoptotic chromatin inducer in the nucleus (Acinus). The ASAP complex appears to be an assembly of proteins at the interface between transcription, splicing and NMD, acting as a hub in the network of protein-interactions that regulate gene-expression.


Pssm-ID: 465085  Cd Length: 91  Bit Score: 73.62  E-value: 4.33e-16
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 564386147  448 PPAKLLDDLFRKTKAAPCIYWLPLTESQIVQKEAE 482
Cdd:pfam16294  50 PPAKLLDDLFRKTKATPCIYWLPLTPEQIAEKEAQ 84
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 256-315 1.66e-04

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 39.96  E-value: 1.66e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564386147 256 VHISNLVRPFTLGQLKELLGRTGTlVEEAFWID----KIKSHCFVTYSTVEEAVATRTALHGVK 315
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGE-VVSVRIVRdrdgKSKGFAFVEFESPEDAEKALEALNGTE 63
RRM_ALKBH8 cd12431
RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and ...
 253-331 3.50e-04

RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins; This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain.


Pssm-ID: 409865 [Multi-domain]  Cd Length: 80  Bit Score: 39.49  E-value: 3.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564386147 253 SNIVHISN--LVRPFTLGQLKELLGRTGTlveeafwIDKI-----KSHCFVTYSTVEEAVATRTALHG--VKWPQSNPKF 323
Cdd:cd12431    1 TQHLVVANggLGNGVSREQLLEVFEKYGT-------VEDIvmlpgKPYSFVSFKSVEEAAKAYNALNGkeLELPQQNVPL 73


                 ....*...
gi 564386147 324 LCAdYAEQ 331
Cdd:cd12431   74 YLS-FVEK 80
RRM_TRMT2A cd12439
RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and ...
 256-316 1.09e-03

RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins; This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases.


Pssm-ID: 409873 [Multi-domain]  Cd Length: 79  Bit Score: 37.99  E-value: 1.09e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564386147 256 VHISNLVRPFTLGQLKELLGRTGtlveeaFWIDKIK-----SHCFVTYSTVEEAVATRTALHGVKW 316
Cdd:cd12439    8 IEIKNLPKYIGFGQLKKFLQKLG------LKPHKIKligrqTFAFVTFRNEEDRDKALKVLNGHKW 67
RRM3_RBM45 cd12368
RNA recognition motif 3 (RRM3) found in RNA-binding protein 45 (RBM45) and similar proteins; ...
 291-320 9.51e-03

RNA recognition motif 3 (RRM3) found in RNA-binding protein 45 (RBM45) and similar proteins; This subfamily corresponds to the RRM3 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409803 [Multi-domain]  Cd Length: 75  Bit Score: 35.35  E-value: 9.51e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 564386147 291 KSHCFVTYSTVEEAVATRTALHGVKWPQSN 320
Cdd:cd12368   41 KGFAYVTYNNPASAIYAKEKLNGFEYPPGN 70
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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