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

    Gene ID: 57466, updated on 10-Dec-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
    mouse all
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    Genomic context

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    See SCAF4 in Genome Data Viewer
    Location:
    21q22.11
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (31671000..31732118, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (30038984..30100110, complement)
    RS_2024_09 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. SCAF4 variants are associated with epilepsy with neurodevelopmental disorders. Hu Y, et al. Seizure, 2024 Mar. PMID 37891035
    2. Structural basis for the recognition of the S2, S5-phosphorylated RNA polymerase II CTD by the mRNA anti-terminator protein hSCAF4. Zhou M, et al. FEBS Lett, 2022 Jan. PMID 34897689
    3. 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
    4. SCAF4 variants associated with focal epilepsy accompanied by multisystem disorders. Lin H, et al. Seizure, 2024 Mar. PMID 37394306
    5. 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

    See all (75) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Structural basis for the recognition of the S2, S5-phosphorylated RNA polymerase II CTD by the mRNA anti-terminator protein hSCAF4.
      Title: Structural basis for the recognition of the S2, S5-phosphorylated RNA polymerase II CTD by the mRNA anti-terminator protein hSCAF4.
    2. SCAF4 variants are associated with epilepsy with neurodevelopmental disorders.
      Title: SCAF4 variants are associated with epilepsy with neurodevelopmental disorders.
    3. SCAF4 variants associated with focal epilepsy accompanied by multisystem disorders.
      Title: SCAF4 variants associated with focal epilepsy accompanied by multisystem disorders.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: Polymorphisms in innate immunity genes and risk of childhood leukemia.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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: C5882693 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)

    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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    NEW Try the new Transcript table

    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_2024_08

    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

      UniProtKB/TrEMBL
      Q0P607

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

      UniProtKB/TrEMBL
      Q0P607

    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

      UniProtKB/TrEMBL
      Q0P607

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

      UniProtKB/TrEMBL
      Q0P607

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

      UniProtKB/TrEMBL
      Q0P607

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

      UniProtKB/TrEMBL
      Q0P607

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

      UniProtKB/TrEMBL
      Q0P607

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

      UniProtKB/TrEMBL
      Q0P607
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O95104.3 GenPept UniProtKB/Swiss-Prot:O95104

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