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SF1 splicing factor 1 [ Homo sapiens (human) ]

Gene ID: 7536, updated on 6-Nov-2022

Summary

Official Symbol
SF1provided by HGNC
Official Full Name
splicing factor 1provided by HGNC
Primary source
HGNC:HGNC:12950
See related
Ensembl:ENSG00000168066 MIM:601516; AllianceGenome:HGNC:12950
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
BBP; MBBP; ZFM1; ZNF162; D11S636; ZCCHC25
Summary
This gene encodes a nuclear pre-mRNA splicing factor. The encoded protein specifically recognizes the intron branch point sequence at the 3' splice site, together with the large subunit of U2 auxiliary factor (U2AF), and is required for the early stages of spliceosome assembly. It also plays a role in nuclear pre-mRNA retention and transcriptional repression. The encoded protein contains an N-terminal U2AF ligand motif, a central hnRNP K homology motif and quaking 2 region which bind a key branch-site adenosine within the branch point sequence, a zinc knuckles domain, and a C-terminal proline-rich domain. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2016]
Annotation information
Note: SF1 (Gene ID: 7536) and NR5A1 (Gene ID: 2516) share the SF1 symbol/alias in common. SF1 is a widely used alternative name for nuclear receptor subfamily 5 group A member 1 (NR5A1), which can be confused with the official symbol for SF1 (splicing factor 1). [01 Jun 2018]
Expression
Ubiquitous expression in bone marrow (RPKM 62.1), testis (RPKM 36.4) and 25 other tissues See more
Orthologs
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Genomic context

See SF1 in Genome Data Viewer
Location:
11q13.1
Exon count:
14
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (64764606..64778542, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (64757911..64771848, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (64532078..64546014, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene RAS guanyl releasing protein 2 Neighboring gene glycogen phosphorylase, muscle associated Neighboring gene mitogen-activated protein kinase kinase kinase kinase 2 Neighboring gene menin 1

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?

Phenotypes

EBI GWAS Catalog

Description
Genome-wide association study for serum urate concentrations and gout among African Americans identifies genomic risk loci and a novel URAT1 loss-of-function allele.
EBI GWAS Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
capsid gag The interaction of HIV-1 CA with human cellular splicing factor 1 (SF1) is identified by yeast two-hybrid screen PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables RNA binding TAS
Traceable Author Statement
more info
PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables pre-mRNA branch point binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables transcription corepressor activity TAS
Traceable Author Statement
more info
PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
part_of U2AF complex IPI
Inferred from Physical Interaction
more info
PubMed 
located_in nuclear body IEA
Inferred from Electronic Annotation
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus IC
Inferred by Curator
more info
PubMed 
located_in nucleus NAS
Non-traceable Author Statement
more info
PubMed 
located_in ribosome NAS
Non-traceable Author Statement
more info
PubMed 
part_of spliceosomal complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of spliceosomal complex IPI
Inferred from Physical Interaction
more info
PubMed 

General protein information

Preferred Names
splicing factor 1
Names
mammalian branch point-binding protein
transcription factor ZFM1
zinc finger gene in MEN1 locus
zinc finger protein 162

NCBI Reference Sequences (RefSeq)

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_021399.1 RefSeqGene

    Range
    5001..19241
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_617

mRNA and Protein(s)

  1. NM_001178030.2NP_001171501.1  splicing factor 1 isoform 6

    See identical proteins and their annotated locations for NP_001171501.1

    Status: REVIEWED

    Source sequence(s)
    AP001462
    Consensus CDS
    CCDS53661.1
    UniProtKB/Swiss-Prot
    Q15637
    Related
    ENSP00000366604.1, ENST00000377387.5
    Conserved Domains (2) summary
    smart00343
    Location:403418
    ZnF_C2HC; zinc finger
    COG5176
    Location:142382
    MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]
  2. NM_001178031.3NP_001171502.1  splicing factor 1 isoform 5

    See identical proteins and their annotated locations for NP_001171502.1

    Status: REVIEWED

    Source sequence(s)
    AK293753, AP001462, BC000773, DC317188, DC341853
    Consensus CDS
    CCDS53660.1
    UniProtKB/Swiss-Prot
    Q15637
    Related
    ENSP00000396793.2, ENST00000433274.6
    Conserved Domains (2) summary
    smart00343
    Location:252267
    ZnF_C2HC; zinc finger
    COG5176
    Location:10231
    MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]
  3. NM_001346363.2NP_001333292.1  splicing factor 1 isoform 9

    Status: REVIEWED

    Source sequence(s)
    AK293753, AP001462, BC000773, BC020217, BE745705, DC341853
    UniProtKB/Swiss-Prot
    Q15637
    Conserved Domains (2) summary
    smart00343
    Location:278293
    ZnF_C2HC; zinc finger
    COG5176
    Location:17257
    MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]
  4. NM_001346364.2NP_001333293.1  splicing factor 1 isoform 10

    Status: REVIEWED

    Source sequence(s)
    AK293753, AP001462, BC020217, BC069273, BE745705, DC341853
    UniProtKB/Swiss-Prot
    Q15637
    Conserved Domains (2) summary
    smart00343
    Location:278293
    ZnF_C2HC; zinc finger
    COG5176
    Location:17257
    MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]
  5. NM_001346409.2NP_001333338.1  splicing factor 1 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AK301803, AP001462, BC069273
    UniProtKB/TrEMBL
    B4DX42, E7ESU3
    Conserved Domains (2) summary
    smart00343
    Location:163178
    ZnF_C2HC; zinc finger
    cd22382
    Location:20112
    KH-I_SF1; type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins
  6. NM_001346410.2NP_001333339.1  splicing factor 1 isoform 8

    Status: REVIEWED

    Source sequence(s)
    AP001462, BC032676, BC069273
    Conserved Domains (2) summary
    smart00343
    Location:163178
    ZnF_C2HC; zinc finger
    cd22382
    Location:20112
    KH-I_SF1; type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins
  7. NM_001378956.1NP_001365885.1  splicing factor 1 isoform 11

    Status: REVIEWED

    Source sequence(s)
    AP001462
    Conserved Domains (2) summary
    smart00343
    Location:403418
    ZnF_C2HC; zinc finger
    COG5176
    Location:142382
    MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]
  8. NM_001378957.1NP_001365886.1  splicing factor 1 isoform 12

    Status: REVIEWED

    Source sequence(s)
    AP001462
    Consensus CDS
    CCDS91502.1
    UniProtKB/TrEMBL
    A0A7P0T9U7
    Related
    ENSP00000505779.1, ENST00000681407.1
    Conserved Domains (2) summary
    smart00343
    Location:403418
    ZnF_C2HC; zinc finger
    COG5176
    Location:142382
    MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]
  9. NM_004630.4NP_004621.2  splicing factor 1 isoform 1

    See identical proteins and their annotated locations for NP_004621.2

    Status: REVIEWED

    Source sequence(s)
    BC069273, DC368015, DC370979, Y08765
    Consensus CDS
    CCDS31599.1
    UniProtKB/Swiss-Prot
    Q15637, Q9UEI0
    UniProtKB/TrEMBL
    A0A024R572
    Related
    ENSP00000366607.3, ENST00000377390.8
    Conserved Domains (2) summary
    smart00343
    Location:278293
    ZnF_C2HC; zinc finger
    COG5176
    Location:17257
    MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]
  10. NM_201995.3NP_973724.1  splicing factor 1 isoform 2

    See identical proteins and their annotated locations for NP_973724.1

    Status: REVIEWED

    Source sequence(s)
    AP001462
    Consensus CDS
    CCDS8080.1
    UniProtKB/Swiss-Prot
    Q15637
    UniProtKB/TrEMBL
    A0A024R5D9
    Related
    ENSP00000334414.5, ENST00000334944.9
    Conserved Domains (2) summary
    smart00343
    Location:278293
    ZnF_C2HC; zinc finger
    COG5176
    Location:17257
    MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]
  11. NM_201997.3NP_973726.2  splicing factor 1 isoform 4

    See identical proteins and their annotated locations for NP_973726.2

    Status: REVIEWED

    Source sequence(s)
    AP001462
    Consensus CDS
    CCDS44642.2
    UniProtKB/TrEMBL
    A0A024R566
    Related
    ENSP00000366611.3, ENST00000377394.7
    Conserved Domains (2) summary
    smart00343
    Location:278293
    ZnF_C2HC; zinc finger
    COG5176
    Location:17257
    MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]
  12. NM_201998.3NP_973727.1  splicing factor 1 isoform 3

    See identical proteins and their annotated locations for NP_973727.1

    Status: REVIEWED

    Source sequence(s)
    BC020217, BC069273
    Consensus CDS
    CCDS8081.1
    UniProtKB/Swiss-Prot
    Q15637
    UniProtKB/TrEMBL
    A0A024R588
    Related
    ENSP00000227503.9, ENST00000227503.13
    Conserved Domains (2) summary
    smart00343
    Location:278293
    ZnF_C2HC; zinc finger
    COG5176
    Location:17257
    MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    64764606..64778542 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047427551.1XP_047283507.1  splicing factor 1 isoform X6

  2. XM_047427550.1XP_047283506.1  splicing factor 1 isoform X5

  3. XM_017018246.2XP_016873735.2  splicing factor 1 isoform X2

  4. XM_047427549.1XP_047283505.1  splicing factor 1 isoform X1

  5. XM_011545248.2XP_011543550.2  splicing factor 1 isoform X4

  6. XM_011545247.2XP_011543549.2  splicing factor 1 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    64757911..64771848 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_033649.1: Suppressed sequence

    Description
    NR_033649.1: This RefSeq was removed because it is now thought that this transcript does encode a protein.
  2. NR_033650.1: Suppressed sequence

    Description
    NR_033650.1: This RefSeq was removed because it is now thought that this transcript does encode a protein.