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SCAF4 SR-related CTD associated factor 4 [ Homo sapiens (human) ]

Gene ID: 57466, updated on 9-Feb-2020

Summary

Official Symbol
SCAF4provided by HGNC
Official Full Name
SR-related CTD associated factor 4provided by HGNC
Primary source
HGNC:HGNC:19304
See related
Ensembl:ENSG00000156304 MIM:616023
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SRA4; SFRS15
Summary
This gene likely encodes a member of the arginine/serine-rich splicing factor family. A similar protein in Rat appears to bind the large subunit of RNA polymerase II and provide a link between transcription and pre-mRNA splicing. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2009]
Expression
Ubiquitous expression in testis (RPKM 12.8), lymph node (RPKM 10.5) and 25 other tissues See more
Orthologs

Genomic context

See SCAF4 in Genome Data Viewer
Location:
21q22.11
Exon count:
20
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 21 NC_000021.9 (31668987..31732118, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (33043313..33104431, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102724449 Neighboring gene superoxide dismutase 1 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 2 Neighboring gene tumor protein, translationally-controlled 1 pseudogene 1 Neighboring gene hormonally up-regulated Neu-associated kinase

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ23364, KIAA1172, DKFZp434E098

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II C-terminal domain phosphoserine binding IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
SR-related and CTD-associated factor 4
Names
CTD-binding SR-like protein rA4
SR-like CTD-associated factor 4
pre-mRNA splicing SR protein rA4
splicing factor serine alanine 15
splicing factor, arginine/serine-rich 15

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_047173.1 RefSeqGene

    Range
    5001..66119
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001145444.1NP_001138916.1  SR-related and CTD-associated factor 4 isoform 2

    See identical proteins and their annotated locations for NP_001138916.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AF023142, AK308406, BC014921, BC031898, DA016102
    Consensus CDS
    CCDS54482.1
    UniProtKB/Swiss-Prot
    O95104
    Related
    ENSP00000402377.2, ENST00000434667.3
    Conserved Domains (4) summary
    cd12461
    Location:489569
    RRM_SCAF4; RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins
    pfam08648
    Location:9781095
    DUF1777; Protein of unknown function (DUF1777)
    cl02544
    Location:6119
    VHS_ENTH_ANTH; VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal ...
    cl26386
    Location:118266
    DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III
  2. NM_001145445.1NP_001138917.1  SR-related and CTD-associated factor 4 isoform 3

    See identical proteins and their annotated locations for NP_001138917.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. This results in a shorter protein (isoform 3) compared to isoform 1.
    Source sequence(s)
    AF023142, AL834304, BC014921, BC031898, DA016102
    Consensus CDS
    CCDS46644.1
    UniProtKB/Swiss-Prot
    O95104
    Related
    ENSP00000382703.1, ENST00000399804.5
    Conserved Domains (4) summary
    smart00582
    Location:6134
    RPR; domain present in proteins, which are involved in regulation of nuclear pre-mRNA
    cd12461
    Location:504584
    RRM_SCAF4; RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins
    pfam08648
    Location:9711088
    DUF1777; Protein of unknown function (DUF1777)
    cl26386
    Location:133281
    DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III
  3. NM_020706.2NP_065757.1  SR-related and CTD-associated factor 4 isoform 1

    See identical proteins and their annotated locations for NP_065757.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AF023142, BC014921, BC031898, DA016102
    Consensus CDS
    CCDS33537.1
    UniProtKB/Swiss-Prot
    O95104
    Related
    ENSP00000286835.7, ENST00000286835.12
    Conserved Domains (4) summary
    smart00582
    Location:6134
    RPR; domain present in proteins, which are involved in regulation of nuclear pre-mRNA
    cd12461
    Location:504584
    RRM_SCAF4; RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins
    pfam08648
    Location:9931110
    DUF1777; Protein of unknown function (DUF1777)
    cl26386
    Location:133281
    DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p13 Primary Assembly

    Range
    31668987..31732118 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006724036.3XP_006724099.1  SR-related and CTD-associated factor 4 isoform X4

    Conserved Domains (5) summary
    smart00582
    Location:6134
    RPR; domain present in proteins, which are involved in regulation of nuclear pre-mRNA
    COG0724
    Location:495579
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12461
    Location:500580
    RRM_SCAF4; RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins
    pfam08648
    Location:9691094
    DUF1777; Protein of unknown function (DUF1777)
    pfam12871
    Location:9661030
    PRP38_assoc; Pre-mRNA-splicing factor 38-associated hydrophilic C-term
  2. XM_006724035.3XP_006724098.1  SR-related and CTD-associated factor 4 isoform X2

    Conserved Domains (5) summary
    smart00582
    Location:6134
    RPR; domain present in proteins, which are involved in regulation of nuclear pre-mRNA
    COG0724
    Location:495579
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12461
    Location:500580
    RRM_SCAF4; RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins
    pfam08648
    Location:9911116
    DUF1777; Protein of unknown function (DUF1777)
    pfam12871
    Location:9881052
    PRP38_assoc; Pre-mRNA-splicing factor 38-associated hydrophilic C-term
  3. XM_005261017.3XP_005261074.1  SR-related and CTD-associated factor 4 isoform X5

    See identical proteins and their annotated locations for XP_005261074.1

    Conserved Domains (5) summary
    smart00582
    Location:6134
    RPR; domain present in proteins, which are involved in regulation of nuclear pre-mRNA
    COG0724
    Location:440524
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12461
    Location:445525
    RRM_SCAF4; RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins
    pfam08648
    Location:9361061
    DUF1777; Protein of unknown function (DUF1777)
    pfam12871
    Location:933997
    PRP38_assoc; Pre-mRNA-splicing factor 38-associated hydrophilic C-term
  4. XM_017028417.1XP_016883906.1  SR-related and CTD-associated factor 4 isoform X6

  5. XM_017028416.2XP_016883905.1  SR-related and CTD-associated factor 4 isoform X3

  6. XM_017028415.2XP_016883904.1  SR-related and CTD-associated factor 4 isoform X1

    Conserved Domains (5) summary
    smart00582
    Location:6134
    RPR; domain present in proteins, which are involved in regulation of nuclear pre-mRNA
    COG0724
    Location:498582
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12461
    Location:503583
    RRM_SCAF4; RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins
    pfam08648
    Location:9941119
    DUF1777; Protein of unknown function (DUF1777)
    pfam12871
    Location:9911055
    PRP38_assoc; Pre-mRNA-splicing factor 38-associated hydrophilic C-term
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