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    SCAF8 SR-related CTD associated factor 8 [ Homo sapiens (human) ]

    Gene ID: 22828, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SCAF8provided by HGNC
    Official Full Name
    SR-related CTD associated factor 8provided by HGNC
    Primary source
    HGNC:HGNC:20959
    See related
    Ensembl:ENSG00000213079 MIM:616024; AllianceGenome:HGNC:20959
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RBM16
    Summary
    Enables RNA binding activity and RNA polymerase II C-terminal domain phosphoserine binding activity. Involved in negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled and positive regulation of DNA-templated transcription, elongation. Located in nucleoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in testis (RPKM 16.9), bone marrow (RPKM 14.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SCAF8 in Genome Data Viewer
    Location:
    6q25.2
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (154733378..154834244)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (155935375..156036235)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (155054512..155155378)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25297 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:154936496-154937002 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91055 Neighboring gene ribosomal protein L31 pseudogene 29 Neighboring gene Sharpr-MPRA regulatory region 5041 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:155028335-155029534 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:155033393-155033609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17697 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17698 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155054583-155055086 Neighboring gene stathmin 2 pseudogene Neighboring gene MPRA-validated peak6233 silencer Neighboring gene MPRA-validated peak6234 silencer Neighboring gene RNA, U6 small nuclear 824, pseudogene Neighboring gene MPRA-validated peak6235 silencer Neighboring gene Sharpr-MPRA regulatory region 2718 Neighboring gene microRNA 1273c Neighboring gene ReSE screen-validated silencer GRCh37_chr6:155259719-155259894 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:155272494-155272994 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155287362-155288008 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25298 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25299 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155316343-155316950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155316951-155317556 Neighboring gene lysophosphatidylcholine acyltransferase 3 pseudogene Neighboring gene TIAM Rac1 associated GEF 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. The Association of a Genetic Variant in SCAF8-CNKSR3 with Diabetic Kidney Disease and Diabetic Retinopathy in a Chinese Population. Jin L, et al. J Diabetes Res, 2017. PMID 28401168, Free PMC Article
    2. 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
    3. SCAF4 and SCAF8, mRNA Anti-Terminator Proteins. Gregersen LH, et al. Cell, 2019 Jun 13. PMID 31104839, Free PMC Article
    4. Functional analysis of the human CDC5L complex and identification of its components by mass spectrometry. Ajuh P, et al. EMBO J, 2000 Dec 1. PMID 11101529, Free PMC Article
    5. ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation. van der Weegen Y, et al. Nat Cell Biol, 2021 Jun. PMID 34108663, Free PMC Article

    See all (53) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Potential readthrough

    Included gene: TIAM2

    Homology

    Clone Names

    • KIAA1116, KIAA2016

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA polymerase II C-terminal domain phosphoserine binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA polymerase II complex binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase core enzyme binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription, elongation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in termination of RNA polymerase II transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    SR-related and CTD-associated factor 8
    Names
    CDC5L complex-associated protein 7
    RNA-binding motif protein 16
    SR-like CTD-associated factor 8
    protein SCAF8

    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_001286188.1 → NP_001273117.1  SR-related and CTD-associated factor 8 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AK295651, BC070071, BX090356
      Consensus CDS
      CCDS75541.1
      UniProtKB/TrEMBL
      A0A0A0MT33, B7Z3A4
      Related
      ENSP00000413098.2, ENST00000417268.3
      Conserved Domains (3) summary
      PHA03247
      Location:796 → 1159
      PHA03247; large tegument protein UL36; Provisional
      cd12462
      Location:553 → 631
      RRM_SCAF8; RNA recognition motif in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins
      cd17004
      Location:83 → 213
      CID_SCAF8; CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8

    2. NM_001286189.1 → NP_001273118.1  SR-related and CTD-associated factor 8 isoform b

      See identical proteins and their annotated locations for NP_001273118.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses two alternate splice sites that result in the loss of an in-frame segment in the 5' coding region, and it also includes an additional in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
      Source sequence(s)
      AK303001, BC070071, BX090356
      Consensus CDS
      CCDS69226.1
      UniProtKB/TrEMBL
      B7Z3A4
      Related
      ENSP00000356154.4, ENST00000367186.7
      Conserved Domains (3) summary
      PHA03247
      Location:784 → 1147
      PHA03247; large tegument protein UL36; Provisional
      cd12462
      Location:541 → 619
      RRM_SCAF8; RNA recognition motif in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins
      cd17004
      Location:77 → 201
      CID_SCAF8; CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8

    3. NM_001286194.1 → NP_001273123.1  SR-related and CTD-associated factor 8 isoform c

      See identical proteins and their annotated locations for NP_001273123.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses two alternate splice sites that result in the loss of an in-frame segment in the 5' coding region, compared to variant 1. The encoded isoform (c) is shorter than isoform a.
      Source sequence(s)
      AK295651, AK302969, BC070071, BX090356
      UniProtKB/TrEMBL
      B7Z3A4, B7Z876
      Conserved Domains (3) summary
      PHA03247
      Location:763 → 1126
      PHA03247; large tegument protein UL36; Provisional
      cd12462
      Location:520 → 598
      RRM_SCAF8; RNA recognition motif in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins
      cd17004
      Location:50 → 180
      CID_SCAF8; CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8

    4. NM_001286199.2 → NP_001273128.1  SR-related and CTD-associated factor 8 isoform d

      See identical proteins and their annotated locations for NP_001273128.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) contains an alternate 5' exon and it thus differs in its 5' UTR and initiates translation at an downstream in-frame start codon, compared to variant 1. The encoded isoform (d) is shorter at the N-terminus, compared to isoform a. Both variants 4 and 5 encode isoform d.
      Source sequence(s)
      AK295651, BC070071, BX090356
      Consensus CDS
      CCDS5247.1
      UniProtKB/Swiss-Prot
      B7Z888, Q5TBU6, Q6NSK3, Q9BQN8, Q9BX43, Q9UPN6
      UniProtKB/TrEMBL
      B7Z3A4
      Conserved Domains (3) summary
      PHA03247
      Location:718 → 1081
      PHA03247; large tegument protein UL36; Provisional
      cd12462
      Location:475 → 553
      RRM_SCAF8; RNA recognition motif in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins
      cd17004
      Location:5 → 135
      CID_SCAF8; CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8

    5. NM_014892.5 → NP_055707.3  SR-related and CTD-associated factor 8 isoform d

      See identical proteins and their annotated locations for NP_055707.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains an alternate 5' exon and it thus differs in its 5' UTR and initiates translation at an downstream in-frame start codon, compared to variant 1. The encoded isoform (d) is shorter at the N-terminus, compared to isoform a. Both variants 4 and 5 encode isoform d.
      Source sequence(s)
      AB029039, AK295651, BX090356, DA219101
      Consensus CDS
      CCDS5247.1
      UniProtKB/Swiss-Prot
      B7Z888, Q5TBU6, Q6NSK3, Q9BQN8, Q9BX43, Q9UPN6
      UniProtKB/TrEMBL
      B7Z3A4
      Related
      ENSP00000356146.3, ENST00000367178.8
      Conserved Domains (3) summary
      PHA03247
      Location:718 → 1081
      PHA03247; large tegument protein UL36; Provisional
      cd12462
      Location:475 → 553
      RRM_SCAF8; RNA recognition motif in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins
      cd17004
      Location:5 → 135
      CID_SCAF8; CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      154733378..154834244
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      155935375..156036235
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UPN6.1 GenPept UniProtKB/Swiss-Prot:Q9UPN6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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