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Scaf4 SR-related CTD-associated factor 4 [ Mus musculus (house mouse) ]

Gene ID: 224432, updated on 27-Nov-2024

Summary

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Official Symbol
Scaf4provided by MGI
Official Full Name
SR-related CTD-associated factor 4provided by MGI
Primary source
MGI:MGI:2146350
See related
Ensembl:ENSMUSG00000022983 AllianceGenome:MGI:2146350
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Sra4; Sfrs15; Srsf15
Summary
Predicted to enable RNA binding activity and RNA polymerase II C-terminal domain phosphoserine binding activity. Predicted to be involved in mRNA processing and negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Is expressed in several structures, including alimentary system; genitourinary system; nervous system; respiratory system; and sensory organ. Orthologous to human SCAF4 (SR-related CTD associated factor 4). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in adrenal adult (RPKM 30.3), thymus adult (RPKM 26.7) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Scaf4 in Genome Data Viewer
Location:
16 C3.3; 16 51.57 cM
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 16 NC_000082.7 (90021504..90082074, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (90228950..90286140, complement)

Chromosome 16 - NC_000082.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_41438 Neighboring gene ferritin light chain 1 pseudogene Neighboring gene STARR-seq mESC enhancer starr_41441 Neighboring gene predicted gene, 35714 Neighboring gene superoxide dismutase 1, soluble Neighboring gene STARR-seq mESC enhancer starr_41449 Neighboring gene STARR-positive B cell enhancer ABC_E9936 Neighboring gene STARR-seq mESC enhancer starr_41451 Neighboring gene STARR-positive B cell enhancer mm9_chr16:90341938-90342239 Neighboring gene STARR-seq mESC enhancer starr_41453 Neighboring gene STARR-seq mESC enhancer starr_41454 Neighboring gene hormonally upregulated Neu-associated kinase Neighboring gene VISTA enhancer mm1672 Neighboring gene predicted gene, 35882

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. ANKRD13a controls early cell-death checkpoint by interacting with RIP1 independent of NF-κB. Won M, et al. Cell Death Differ, 2022 Jun. PMID 34839354, Free PMC Article
  2. A gene expression map of human chromosome 21 orthologues in the mouse. Gitton Y, et al. Nature, 2002 Dec 5. PMID 12466855
  3. Human chromosome 21 gene expression atlas in the mouse. Reymond A, et al. Nature, 2002 Dec 5. PMID 12466854
  4. The sperm-associated antigen 6 interactome and its role in spermatogenesis. Liu Y, et al. Reproduction, 2019 Aug. PMID 31146259, Free PMC Article
  5. The European renal genome project: an integrated approach towards understanding the genetics of kidney development and disease. Willnow T, et al. Organogenesis, 2005 Apr. PMID 19521566, Free PMC Article

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (2) 
  • Gene trapped (1) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA binding ISO
Inferred from Sequence Orthology
more info
  
enables RNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables RNA polymerase II C-terminal domain phosphoserine binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II C-terminal domain phosphoserine binding ISO
Inferred from Sequence Orthology
more info
  
enables RNA polymerase II C-terminal domain phosphoserine binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in mRNA processing ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
SR-related and CTD-associated factor 4
Names
CTD-binding SR-like protein RA4
serine/arginine-rich splicing factor 15
splicing factor, arginine/serine-rich 15

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

  1. NM_001346799.3 → NP_001333728.1  SR-related and CTD-associated factor 4 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC139573
    Consensus CDS
    CCDS84260.1
    UniProtKB/Swiss-Prot
    A0A338P6Z6, Q69ZP8, Q6PFF0, Q7TSH6, Q8R1B3
    Related
    ENSMUSP00000132250.2, ENSMUST00000163419.9
    Conserved Domains (4) summary
    cd12461
    Location:565 → 645
    RRM_SCAF4; RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins
    TIGR01622
    Location:1033 → 1145
    SF-CC1; splicing factor, CC1-like family
    cd17005
    Location:5 → 135
    CID_SFRS15_SCAF4; CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15
    pfam09770
    Location:305 → 476
    PAT1; Topoisomerase II-associated protein PAT1

  2. NM_001358402.2 → NP_001345331.1  SR-related and CTD-associated factor 4 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC139573
    Consensus CDS
    CCDS88967.1
    Related
    ENSMUSP00000156174.2, ENSMUST00000232371.2
    Conserved Domains (4) summary
    cd12461
    Location:566 → 646
    RRM_SCAF4; RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins
    TIGR01622
    Location:1034 → 1146
    SF-CC1; splicing factor, CC1-like family
    cd17005
    Location:5 → 135
    CID_SFRS15_SCAF4; CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15
    pfam09770
    Location:303 → 484
    PAT1; Topoisomerase II-associated protein PAT1

  3. NM_001417087.1 → NP_001404016.1  SR-related and CTD-associated factor 4 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC139573

  4. NM_001417088.1 → NP_001404017.1  SR-related and CTD-associated factor 4 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC139573

  5. NM_001417089.1 → NP_001404018.1  SR-related and CTD-associated factor 4 isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC139573

  6. NM_001417090.1 → NP_001404019.1  SR-related and CTD-associated factor 4 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC139573

  7. NM_001417091.1 → NP_001404020.1  SR-related and CTD-associated factor 4 isoform 8

    Status: VALIDATED

    Source sequence(s)
    AC139573

  8. NM_178923.5 → NP_849254.2  SR-related and CTD-associated factor 4 isoform 1

    See identical proteins and their annotated locations for NP_849254.2

    Status: VALIDATED

    Source sequence(s)
    AC139573
    Consensus CDS
    CCDS37396.1
    UniProtKB/TrEMBL
    Q6PFF0
    Related
    ENSMUSP00000044472.8, ENSMUST00000039280.9
    Conserved Domains (4) summary
    cd12461
    Location:569 → 649
    RRM_SCAF4; RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins
    TIGR01622
    Location:1059 → 1171
    SF-CC1; splicing factor, CC1-like family
    cd17005
    Location:5 → 135
    CID_SFRS15_SCAF4; CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15
    pfam09770
    Location:305 → 476
    PAT1; Topoisomerase II-associated protein PAT1

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000082.7 Reference GRCm39 C57BL/6J

    Range
    90021504..90082074 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006523014.4 → XP_006523077.1  SR-related and CTD-associated factor 4 isoform X6

    Conserved Domains (4) summary
    cd12461
    Location:520 → 600
    RRM_SCAF4; RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins
    TIGR01622
    Location:1010 → 1122
    SF-CC1; splicing factor, CC1-like family
    cd17005
    Location:5 → 135
    CID_SFRS15_SCAF4; CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15
    pfam09770
    Location:253 → 434
    PAT1; Topoisomerase II-associated protein PAT1

  2. XM_011246114.4 → XP_011244416.1  SR-related and CTD-associated factor 4 isoform X2

    Conserved Domains (4) summary
    cd12461
    Location:566 → 646
    RRM_SCAF4; RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins
    TIGR01622
    Location:1056 → 1168
    SF-CC1; splicing factor, CC1-like family
    cd17005
    Location:5 → 135
    CID_SFRS15_SCAF4; CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15
    pfam09770
    Location:303 → 484
    PAT1; Topoisomerase II-associated protein PAT1

  3. XM_017316972.3 → XP_017172461.1  SR-related and CTD-associated factor 4 isoform X7

    Conserved Domains (3) summary
    cd12461
    Location:239 → 319
    RRM_SCAF4; RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins
    TIGR01622
    Location:729 → 841
    SF-CC1; splicing factor, CC1-like family
    pfam09770
    Location:5 → 153
    PAT1; Topoisomerase II-associated protein PAT1
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7TSH6.1 GenPept UniProtKB/Swiss-Prot:Q7TSH6

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