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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

      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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