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    Scaf8 SR-related CTD-associated factor 8 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 245926, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Scaf8provided by RGD
    Official Full Name
    SR-related CTD-associated factor 8provided by RGD
    Primary source
    RGD:708362
    See related
    EnsemblRapid:ENSRNOG00000016919 AllianceGenome:RGD:708362
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Rbm16
    Summary
    Enables RNA polymerase binding activity and protein domain specific binding activity. Involved in mRNA processing and transcription by RNA polymerase II. Located in nuclear matrix. Orthologous to human SCAF8 (SR-related CTD associated factor 8). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 221.3), Spleen (RPKM 169.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Scaf8 in Genome Data Viewer
    Location:
    1q11
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (46132972..46321162)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (43727686..43855889)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (44017801..44120619)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120097709 Neighboring gene RNA, U6 small nuclear 859 Neighboring gene TIAM Rac1 associated GEF 2 Neighboring gene transcription factor B1, mitochondrial Neighboring gene claudin 20

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. A nuclear matrix protein interacts with the phosphorylated C-terminal domain of RNA polymerase II. Patturajan M, et al. Mol Cell Biol, 1998 Apr. PMID 9528809, Free PMC Article
    2. SCAF4 and SCAF8, mRNA Anti-Terminator Proteins. Gregersen LH, et al. Cell, 2019 Jun 13. PMID 31104839, Free PMC Article
    3. Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the carboxyl-terminal domain of RNA polymerase II. Becker R, et al. J Biol Chem, 2008 Aug 15. PMID 18550522
    4. The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins. Yuryev A, et al. Proc Natl Acad Sci U S A, 1996 Jul 9. PMID 8692929, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    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 IEA
    Inferred from Electronic Annotation
    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
    		  
    enables RNA polymerase II complex binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables RNA polymerase core enzyme binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein domain specific binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled IEA
    Inferred from Electronic Annotation
    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
    		  
    involved_in positive regulation of DNA-templated transcription, elongation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of DNA-templated transcription, elongation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of DNA-templated transcription, elongation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in termination of RNA polymerase II transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of mRNA cleavage factor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nuclear matrix IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    SR-related and CTD-associated factor 8
    Names
    CTD-binding SR-like protein rA8
    RNA-binding motif protein 16
    SR-like CTD-associated factor 8
    protein SCAF8
    putative RNA-binding protein 16

    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_001428710.1 → NP_001415639.1  SR-related and CTD-associated factor 8 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/TrEMBL
      F1LPT8

    2. NM_001428712.1 → NP_001415641.1  SR-related and CTD-associated factor 8 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/TrEMBL
      A0A0G2K5M7

    3. NM_139094.2 → NP_620794.2  SR-related and CTD-associated factor 8 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/TrEMBL
      F1LPT8

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086019.1 Reference GRCr8

      Range
      46132972..46321162
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006227858.4 → XP_006227920.3  SR-related and CTD-associated factor 8 isoform X8

      UniProtKB/Swiss-Prot
      Q63623
      Conserved Domains (2) summary
      cd17004
      Location:88 → 218
      CID_SCAF8; CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8
      cd12462
      Location:558 → 636
      RRM_SCAF8; RNA recognition motif (RRM) found in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

    2. XM_039098275.2 → XP_038954203.1  SR-related and CTD-associated factor 8 isoform X1

      Related
      ENSRNOP00000073484.3, ENSRNOT00000083425.3
      Conserved Domains (2) summary
      cd17004
      Location:5 → 135
      CID_SCAF8; CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8
      cd12462
      Location:475 → 553
      RRM_SCAF8; RNA recognition motif (RRM) found in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

    3. XM_063280845.1 → XP_063136915.1  SR-related and CTD-associated factor 8 isoform X5

      UniProtKB/TrEMBL
      A0A8I5XWQ5

    4. XM_063280821.1 → XP_063136891.1  SR-related and CTD-associated factor 8 isoform X1

      UniProtKB/TrEMBL
      F1LPT8

    5. XM_039098351.2 → XP_038954279.1  SR-related and CTD-associated factor 8 isoform X5

      UniProtKB/Swiss-Prot
      Q63623
      UniProtKB/TrEMBL
      A0A8I5XWQ5
      Related
      ENSRNOP00000078015.1, ENSRNOT00000109313.2
      Conserved Domains (3) summary
      PHA03247
      Location:635 → 977
      PHA03247; large tegument protein UL36; Provisional
      cd17004
      Location:5 → 135
      CID_SCAF8; CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8
      cd12462
      Location:475 → 553
      RRM_SCAF8; RNA recognition motif (RRM) found in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

    6. XM_039098309.2 → XP_038954237.1  SR-related and CTD-associated factor 8 isoform X2

      UniProtKB/Swiss-Prot
      Q63623
      Conserved Domains (2) summary
      cd17004
      Location:5 → 135
      CID_SCAF8; CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8
      cd12462
      Location:474 → 552
      RRM_SCAF8; RNA recognition motif (RRM) found in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

    7. XM_063280810.1 → XP_063136880.1  SR-related and CTD-associated factor 8 isoform X1

      UniProtKB/TrEMBL
      F1LPT8

    8. XM_063280850.1 → XP_063136920.1  SR-related and CTD-associated factor 8 isoform X6

    9. XM_063280834.1 → XP_063136904.1  SR-related and CTD-associated factor 8 isoform X4

    10. XM_063280830.1 → XP_063136900.1  SR-related and CTD-associated factor 8 isoform X3

      Related
      ENSRNOP00000062541.5, ENSRNOT00000065733.5

    11. XM_039098360.2 → XP_038954288.1  SR-related and CTD-associated factor 8 isoform X7

      UniProtKB/TrEMBL
      A0A8I6A4L7
      Conserved Domains (1) summary
      cd12462
      Location:342 → 420
      RRM_SCAF8; RNA recognition motif (RRM) found in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

    RNA

    1. XR_010062890.1 RNA Sequence

    2. XR_010062896.1 RNA Sequence

    3. XR_010062898.1 RNA Sequence

    4. XR_010062888.1 RNA Sequence

    5. XR_010062883.1 RNA Sequence

    6. XR_010062884.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q63623.1 GenPept UniProtKB/Swiss-Prot:Q63623

    Gene LinkOut

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