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

Gene ID: 22828, updated on 3-Nov-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, Nov 2024]
Expression
Ubiquitous expression in testis (RPKM 16.9), bone marrow (RPKM 14.1) and 25 other tissues See more
Orthologs
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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: HPA RNA-seq normal tissues 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

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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

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