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SCAF4 SR-related CTD associated factor 4 [ Homo sapiens (human) ]

Gene ID: 57466, updated on 16-Apr-2024

Summary

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Official Symbol
SCAF4provided by HGNC
Official Full Name
SR-related CTD associated factor 4provided by HGNC
Primary source
HGNC:HGNC:19304
See related
Ensembl:ENSG00000156304 MIM:616023; AllianceGenome:HGNC:19304
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FZS; SRA4; SFRS15
Summary
This gene likely encodes a member of the arginine/serine-rich splicing factor family. A similar protein in Rat appears to bind the large subunit of RNA polymerase II and provide a link between transcription and pre-mRNA splicing. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2009]
Expression
Ubiquitous expression in testis (RPKM 12.8), lymph node (RPKM 10.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
21q22.11
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (31671000..31732118, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (30038984..30100110, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (33043313..33104431, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:33026156-33026706 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:33026707-33027255 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:33033348-33033857 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:33033858-33034366 Neighboring gene small nucleolar RNA SNORA81 Neighboring gene SOD1 divergent transcript Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:33044406-33044964 Neighboring gene superoxide dismutase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:33078369-33078870 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18355 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:33098092-33098592 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr21:33102852-33103493 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13243 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:33104135-33104776 Neighboring gene uncharacterized LOC124905008 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:33104777-33105416 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:33106899-33107074 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:33119263-33119514 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr21:33126139-33126731 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18357 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:33172518-33173018 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:33173019-33173519 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:33200433-33200620 Neighboring gene TPT1 pseudogene 1

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
  • 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. Variants in SCAF4 Cause a Neurodevelopmental Disorder and Are Associated with Impaired mRNA Processing. Fliedner A, et al. Am J Hum Genet, 2020 Sep 3. PMID 32730804, Free PMC Article
  2. Multiple superoxide dismutase 1/splicing factor serine alanine 15 variants are associated with the development and progression of diabetic nephropathy: the Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications Genetics study. Al-Kateb H, et al. Diabetes, 2008 Jan. PMID 17914031, Free PMC Article
  3. SCAF4 and SCAF8, mRNA Anti-Terminator Proteins. Gregersen LH, et al. Cell, 2019 Jun 13. PMID 31104839, Free PMC Article
  4. Single nucleotide polymorphisms at erythropoietin, superoxide dismutase 1, splicing factor, arginine/serin-rich 15 and plasmacytoma variant translocation genes association with diabetic nephropathy. Alwohhaib M, et al. Saudi J Kidney Dis Transpl, 2014 May. PMID 24821155
  5. 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

See all (61) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SCAF4 variants are associated with epilepsy with neurodevelopmental disorders.
    Title: SCAF4 variants are associated with epilepsy with neurodevelopmental disorders.
  2. SCAF4 variants associated with focal epilepsy accompanied by multisystem disorders.
    Title: SCAF4 variants associated with focal epilepsy accompanied by multisystem disorders.
  3. Variants in SCAF4 Cause a Neurodevelopmental Disorder and Are Associated with Impaired mRNA Processing.
    Title: Variants in SCAF4 Cause a Neurodevelopmental Disorder and Are Associated with Impaired mRNA Processing.
  4. Together, SCAF4 and SCAF8 coordinate the transition between elongation and termination, ensuring correct polyA site selection and RNAPII transcriptional termination in human cells.
    Title: SCAF4 and SCAF8, mRNA Anti-Terminator Proteins.
  5. Report frequency of SFRS15 SNPs in diabetic nephropathy.
    Title: Single nucleotide polymorphisms at erythropoietin, superoxide dismutase 1, splicing factor, arginine/serin-rich 15 and plasmacytoma variant translocation genes association with diabetic nephropathy.
  6. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  7. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
    Title: Polymorphisms in innate immunity genes and risk of childhood leukemia.
  8. Describes function of the CTD-interacting domain of human SCAF8, human SCAF4, and similar proteins in S. cerevisiae.
    Title: Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the carboxyl-terminal domain of RNA polymerase II.
  9. Describes identification of rat serine/arginine-rich splicing factors that interact with RNA polymerase II, including rA1, rA4, rA8, and rA9.
    Title: The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins.
  10. Observational study of gene-disease association. (HuGE Navigator)
    Title: Risk of meningioma and common variation in genes related to innate immunity.
Submit: New GeneRIF Correction

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

Associated conditions

Description Tests
Fliedner-Zweier syndrome
MedGen: CN375328 OMIM: 620511 GeneReviews: Not available
not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ23364, KIAA1172, DKFZp434E098

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
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 IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
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 IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
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 4
Names
CTD-binding SR-like protein rA4
SR-like CTD-associated factor 4
pre-mRNA splicing SR protein rA4
splicing factor serine alanine 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.

Genomic

  1. NG_047173.1 RefSeqGene

    Range
    5001..66119
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001145444.1 → NP_001138916.1  SR-related and CTD-associated factor 4 isoform 2

    See identical proteins and their annotated locations for NP_001138916.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AF023142, AK308406, BC014921, BC031898, DA016102
    Consensus CDS
    CCDS54482.1
    UniProtKB/TrEMBL
    Q0P607
    Related
    ENSP00000402377.2, ENST00000434667.3
    Conserved Domains (4) summary
    PRK07994
    Location:118 → 266
    PRK07994; DNA polymerase III subunits gamma and tau; Validated
    PRK12678
    Location:969 → 1038
    PRK12678; transcription termination factor Rho; Provisional
    cd12461
    Location:489 → 569
    RRM_SCAF4; RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins
    cl02544
    Location:5 → 120
    VHS_ENTH_ANTH; VHS, ENTH and ANTH domain superfamily

  2. NM_001145445.1 → NP_001138917.1  SR-related and CTD-associated factor 4 isoform 3

    See identical proteins and their annotated locations for NP_001138917.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. This results in a shorter protein (isoform 3) compared to isoform 1.
    Source sequence(s)
    AF023142, AL834304, BC014921, BC031898, DA016102
    Consensus CDS
    CCDS46644.1
    UniProtKB/TrEMBL
    Q0P607
    Related
    ENSP00000382703.1, ENST00000399804.5
    Conserved Domains (5) summary
    PRK07994
    Location:133 → 281
    PRK07994; DNA polymerase III subunits gamma and tau; Validated
    PRK12678
    Location:962 → 1031
    PRK12678; transcription termination factor Rho; Provisional
    cd12461
    Location:504 → 584
    RRM_SCAF4; RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins
    cd17005
    Location:5 → 135
    CID_SFRS15_SCAF4; CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15
    pfam09770
    Location:330 → 411
    PAT1; Topoisomerase II-associated protein PAT1

  3. NM_020706.2 → NP_065757.1  SR-related and CTD-associated factor 4 isoform 1

    See identical proteins and their annotated locations for NP_065757.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AF023142, BC014921, BC031898, DA016102
    Consensus CDS
    CCDS33537.1
    UniProtKB/Swiss-Prot
    C9JLZ0, O95104, Q0P5W8, Q6P1M5, Q8N3I8, Q9UFM1, Q9ULP8
    UniProtKB/TrEMBL
    Q0P607
    Related
    ENSP00000286835.7, ENST00000286835.12
    Conserved Domains (5) summary
    PRK07994
    Location:133 → 281
    PRK07994; DNA polymerase III subunits gamma and tau; Validated
    PRK12678
    Location:984 → 1053
    PRK12678; transcription termination factor Rho; Provisional
    cd12461
    Location:504 → 584
    RRM_SCAF4; RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins
    cd17005
    Location:5 → 135
    CID_SFRS15_SCAF4; CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15
    pfam09770
    Location:330 → 411
    PAT1; Topoisomerase II-associated protein PAT1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    31671000..31732118 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047440932.1 → XP_047296888.1  SR-related and CTD-associated factor 4 isoform X6

  2. XM_047440931.1 → XP_047296887.1  SR-related and CTD-associated factor 4 isoform X4

  3. XM_017028417.2 → XP_016883906.1  SR-related and CTD-associated factor 4 isoform X5

    UniProtKB/TrEMBL
    Q0P607
    Conserved Domains (4) summary
    PRK12678
    Location:903 → 972
    PRK12678; transcription termination factor Rho; Provisional
    cd12461
    Location:445 → 525
    RRM_SCAF4; RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins
    cd17005
    Location:5 → 135
    CID_SFRS15_SCAF4; CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15
    pfam09770
    Location:271 → 352
    PAT1; Topoisomerase II-associated protein PAT1

  4. XM_005261017.4 → XP_005261074.1  SR-related and CTD-associated factor 4 isoform X3

    See identical proteins and their annotated locations for XP_005261074.1

    UniProtKB/TrEMBL
    Q0P607
    Conserved Domains (3) summary
    PRK12678
    Location:925 → 994
    PRK12678; transcription termination factor Rho; Provisional
    cd17005
    Location:5 → 135
    CID_SFRS15_SCAF4; CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15
    cd12461
    Location:445 → 525
    RRM_SCAF4; RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins

  5. XM_006724036.4 → XP_006724099.1  SR-related and CTD-associated factor 4 isoform X2

    UniProtKB/TrEMBL
    Q0P607
    Conserved Domains (5) summary
    PRK07994
    Location:133 → 281
    PRK07994; DNA polymerase III subunits gamma and tau; Validated
    PRK12678
    Location:958 → 1027
    PRK12678; transcription termination factor Rho; Provisional
    cd12461
    Location:500 → 580
    RRM_SCAF4; RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins
    cd17005
    Location:5 → 135
    CID_SFRS15_SCAF4; CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15
    pfam09770
    Location:330 → 411
    PAT1; Topoisomerase II-associated protein PAT1

  6. XM_006724035.4 → XP_006724098.1  SR-related and CTD-associated factor 4 isoform X1

    UniProtKB/TrEMBL
    Q0P607
    Conserved Domains (5) summary
    PRK07994
    Location:133 → 281
    PRK07994; DNA polymerase III subunits gamma and tau; Validated
    PRK12678
    Location:980 → 1049
    PRK12678; transcription termination factor Rho; Provisional
    cd12461
    Location:500 → 580
    RRM_SCAF4; RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins
    cd17005
    Location:5 → 135
    CID_SFRS15_SCAF4; CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15
    pfam09770
    Location:330 → 411
    PAT1; Topoisomerase II-associated protein PAT1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    30038984..30100110 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054324726.1 → XP_054180701.1  SR-related and CTD-associated factor 4 isoform X6

  2. XM_054324724.1 → XP_054180699.1  SR-related and CTD-associated factor 4 isoform X4

  3. XM_054324725.1 → XP_054180700.1  SR-related and CTD-associated factor 4 isoform X5

  4. XM_054324723.1 → XP_054180698.1  SR-related and CTD-associated factor 4 isoform X3

  5. XM_054324722.1 → XP_054180697.1  SR-related and CTD-associated factor 4 isoform X2

  6. XM_054324721.1 → XP_054180696.1  SR-related and CTD-associated factor 4 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O95104.3 GenPept UniProtKB/Swiss-Prot:O95104

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