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SCAF1 SR-related CTD associated factor 1 [ Homo sapiens (human) ]

Gene ID: 58506, updated on 5-Mar-2024

Summary

Official Symbol
SCAF1provided by HGNC
Official Full Name
SR-related CTD associated factor 1provided by HGNC
Primary source
HGNC:HGNC:30403
See related
Ensembl:ENSG00000126461 MIM:617264; AllianceGenome:HGNC:30403
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
SRA1
Summary
Enables RNA polymerase II C-terminal domain binding activity. Predicted to be involved in RNA splicing; mRNA processing; and transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in fat (RPKM 11.1), brain (RPKM 11.1) and 25 other tissues See more
Orthologs
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Genomic context

See SCAF1 in Genome Data Viewer
Location:
19q13.33
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (49640465..49658642)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (52640497..52658671)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (50145466..50161899)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10923 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10924 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:50095111-50095610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14950 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10925 Neighboring gene proline rich 12 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50135833-50136332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50139452-50140018 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50143247-50143916 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50143917-50144586 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50144587-50145256 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10927 Neighboring gene RAS related Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50158945-50159720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50161341-50162044 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10928 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10929 Neighboring gene interferon regulatory factor 3 Neighboring gene BCL2 like 12 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50175361-50175919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14954 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:50180167-50180898 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:50184019-50184183 Neighboring gene protein arginine methyltransferase 1 Neighboring gene microRNA 5088

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of SR-related CTD-associated factor 1 (SCAF1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ00034

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
 
enables RNA polymerase II C-terminal domain binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables RNA polymerase II C-terminal domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein domain specific binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in RNA splicing IEA
Inferred from Electronic Annotation
more info
 
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
 
involved_in transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
splicing factor, arginine/serine-rich 19
Names
SCAF
SR-related C-terminal domain-associated factor 1
SR-related and CTD-associated factor 1
SR-related-CTD-associated factor
serine arginine-rich pre-mRNA splicing factor SR-A1

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_021228.3NP_067051.2  splicing factor, arginine/serine-rich 19

    See identical proteins and their annotated locations for NP_067051.2

    Status: VALIDATED

    Source sequence(s)
    AC011495
    Consensus CDS
    CCDS33074.1
    UniProtKB/Swiss-Prot
    Q7Z5V7, Q8WVA1, Q9H7N4, Q9NR59
    Related
    ENSP00000353769.2, ENST00000360565.8

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    49640465..49658642
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011527194.4XP_011525496.1  splicing factor, arginine/serine-rich 19 isoform X1

  2. XM_005259122.6XP_005259179.1  splicing factor, arginine/serine-rich 19 isoform X2

    See identical proteins and their annotated locations for XP_005259179.1

    UniProtKB/Swiss-Prot
    Q7Z5V7, Q8WVA1, Q9H7N4, Q9NR59
  3. XM_017027083.3XP_016882572.1  splicing factor, arginine/serine-rich 19 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    52640497..52658671
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054321632.1XP_054177607.1  splicing factor, arginine/serine-rich 19 isoform X1

  2. XM_054321630.1XP_054177605.1  splicing factor, arginine/serine-rich 19 isoform X2

  3. XM_054321631.1XP_054177606.1  splicing factor, arginine/serine-rich 19 isoform X2

  4. XM_054321633.1XP_054177608.1  splicing factor, arginine/serine-rich 19 isoform X3