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SF1 splicing factor 1 [ Homo sapiens (human) ]

Gene ID: 7536, updated on 4-Nov-2018

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; Vega:OTTHUMG00000066833
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

Genomic context

See SF1 in Genome Data Viewer
Location:
11q13.1
Exon count:
15
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 11 NC_000011.10 (64764604..64778844, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (64532076..64546515, 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI 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.
NHGRI GWA 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 BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
RNA binding TAS
Traceable Author Statement
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
pre-mRNA branch point binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription corepressor activity TAS
Traceable Author Statement
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
Leydig cell differentiation IEA
Inferred from Electronic Annotation
more info
 
mRNA 3'-splice site recognition TAS
Traceable Author Statement
more info
PubMed 
mRNA splicing, via spliceosome IC
Inferred by Curator
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
male sex determination IEA
Inferred from Electronic Annotation
more info
 
negative regulation of nucleic acid-templated transcription IEA
Inferred from Electronic Annotation
more info
 
negative regulation of smooth muscle cell proliferation IEA
Inferred from Electronic Annotation
more info
 
nuclear body organization IEA
Inferred from Electronic Annotation
more info
 
regulation of steroid biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
spliceosomal complex assembly NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
nuclear body IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus NAS
Non-traceable Author Statement
more info
PubMed 
ribosome NAS
Non-traceable Author Statement
more info
PubMed 
spliceosomal complex IDA
Inferred from Direct Assay
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)

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_001178030.1NP_001171501.1  splicing factor 1 isoform 6

    See identical proteins and their annotated locations for NP_001171501.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) has multiple coding region differences, compared to variant 1, one of which results in a frameshift. It encodes isoform 6, which is longer and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AI492561, BC038446, BC069273
    Consensus CDS
    CCDS53661.1
    UniProtKB/Swiss-Prot
    Q15637
    Related
    ENSP00000366604.1, OTTHUMP00000069753, ENST00000377387.5, OTTHUMT00000143243
    Conserved Domains (3) summary
    smart00343
    Location:403418
    ZnF_C2HC; zinc finger
    cd02395
    Location:262380
    SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
    pfam16275
    Location:143255
    SF1-HH; Splicing factor 1 helix-hairpin domain
  2. NM_001178031.2NP_001171502.1  splicing factor 1 isoform 5

    See identical proteins and their annotated locations for NP_001171502.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform 5, which has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AK293753, AP001462, BC000773, DC317188, DC341853
    Consensus CDS
    CCDS53660.1
    UniProtKB/Swiss-Prot
    Q15637
    Related
    ENSP00000396793.2, OTTHUMP00000196697, ENST00000433274.6, OTTHUMT00000157360
    Conserved Domains (1) summary
    cl25681
    Location:10231
    SF1-HH; Splicing factor 1 helix-hairpin domain
  3. NM_001346363.1NP_001333292.1  splicing factor 1 isoform 9

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. It encodes isoform 9, which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK293753, AP001462, BC000773, BC020217, BE745705, DC341853, DC370979
    UniProtKB/Swiss-Prot
    Q15637
    Conserved Domains (1) summary
    cl25681
    Location:17257
    SF1-HH; Splicing factor 1 helix-hairpin domain
  4. NM_001346364.1NP_001333293.1  splicing factor 1 isoform 10

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) has multiple coding region differences, compared to variant 1, one of which results in a frameshift. It encodes isoform 10, which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK293753, AP001462, BC020217, BC069273, BE745705, DC341853, DC370979
    UniProtKB/Swiss-Prot
    Q15637
    Conserved Domains (1) summary
    cl25681
    Location:17257
    SF1-HH; Splicing factor 1 helix-hairpin domain
  5. NM_001346409.1NP_001333338.1  splicing factor 1 isoform 7

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) differs in the 5' and 3' UTRs and has multiple coding region differences, compared to variant 1. These differences cause translation initiation at a downstream start codon and result in an isoform (7) that is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK301803, AP001462, BC069273, DC370979
    UniProtKB/TrEMBL
    B4DX42
    Conserved Domains (2) summary
    smart00343
    Location:163178
    ZnF_C2HC; zinc finger
    cd02395
    Location:22140
    SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
  6. NM_001346410.1NP_001333339.1  splicing factor 1 isoform 8

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) differs in the 5' and 3' UTRs and has multiple coding region differences, one of which results in a frameshift, compared to variant 1. These differences cause translation initiation at a downstream start codon and result in an isoform (8) that is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AP001462, BC032676, BC069273, DC370979
    Conserved Domains (1) summary
    cd02395
    Location:22140
    SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
  7. NM_004630.3NP_004621.2  splicing factor 1 isoform 1

    See identical proteins and their annotated locations for NP_004621.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes isoform (1).
    Source sequence(s)
    AI492561, BC069273, DC368015, DC370979, Y08765
    Consensus CDS
    CCDS31599.1
    UniProtKB/Swiss-Prot
    Q15637
    UniProtKB/TrEMBL
    A0A024R572
    Related
    ENSP00000366607.3, OTTHUMP00000069752, ENST00000377390.7, OTTHUMT00000143242
    Conserved Domains (1) summary
    cl25681
    Location:17257
    SF1-HH; Splicing factor 1 helix-hairpin domain
  8. NM_201995.2NP_973724.1  splicing factor 1 isoform 2

    See identical proteins and their annotated locations for NP_973724.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks a segment in the 3' UTR and coding region which results in a frameshift, compared to variant 1. It encodes isoform 2, which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AI492561, AP001462, BC000773, BC034451, DC370979
    Consensus CDS
    CCDS8080.1
    UniProtKB/Swiss-Prot
    Q15637
    UniProtKB/TrEMBL
    A0A024R5D9
    Related
    ENSP00000334414.5, OTTHUMP00000069749, ENST00000334944.9, OTTHUMT00000143238
    Conserved Domains (1) summary
    cl25681
    Location:17257
    SF1-HH; Splicing factor 1 helix-hairpin domain
  9. NM_201997.2NP_973726.2  splicing factor 1 isoform 4

    See identical proteins and their annotated locations for NP_973726.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has multiple coding region differences, compared to variant 1, one of which results in a frameshift. It encodes isoform 4, which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AI492561, BC069273, DC370979
    Consensus CDS
    CCDS44642.2
    UniProtKB/TrEMBL
    A0A024R566
    Related
    ENSP00000366611.3, OTTHUMP00000069751, ENST00000377394.7, OTTHUMT00000143241
    Conserved Domains (1) summary
    cl25681
    Location:17257
    SF1-HH; Splicing factor 1 helix-hairpin domain
  10. NM_201998.2NP_973727.1  splicing factor 1 isoform 3

    See identical proteins and their annotated locations for NP_973727.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. It encodes isoform 3, which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AI492561, BC020217, BC069273, DC370979
    Consensus CDS
    CCDS8081.1
    UniProtKB/Swiss-Prot
    Q15637
    UniProtKB/TrEMBL
    A0A024R588
    Related
    ENSP00000227503.9, OTTHUMP00000069750, ENST00000227503.13, OTTHUMT00000143239
    Conserved Domains (1) summary
    cl25681
    Location:17257
    SF1-HH; Splicing factor 1 helix-hairpin domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p12 Primary Assembly

    Range
    64764604..64778844 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024448679.1XP_024304447.1  splicing factor 1 isoform X9

    Conserved Domains (2) summary
    smart00343
    Location:278293
    ZnF_C2HC; zinc finger
    cl25681
    Location:17257
    SF1-HH; Splicing factor 1 helix-hairpin domain
  2. XM_017018246.1XP_016873735.1  splicing factor 1 isoform X8

    Conserved Domains (1) summary
    cl25681
    Location:10231
    SF1-HH; Splicing factor 1 helix-hairpin domain
  3. XM_011545246.1XP_011543548.1  splicing factor 1 isoform X4

    See identical proteins and their annotated locations for XP_011543548.1

    Conserved Domains (3) summary
    smart00343
    Location:252267
    ZnF_C2HC; zinc finger
    cd02395
    Location:111229
    SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
    pfam16275
    Location:2104
    SF1-HH; Splicing factor 1 helix-hairpin domain
  4. XM_011545244.1XP_011543546.1  splicing factor 1 isoform X2

    See identical proteins and their annotated locations for XP_011543546.1

    Conserved Domains (3) summary
    smart00343
    Location:252267
    ZnF_C2HC; zinc finger
    cd02395
    Location:111229
    SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
    pfam16275
    Location:2104
    SF1-HH; Splicing factor 1 helix-hairpin domain
  5. XM_017018244.1XP_016873733.1  splicing factor 1 isoform X1

    UniProtKB/Swiss-Prot
    Q15637
    Conserved Domains (1) summary
    cl25681
    Location:10231
    SF1-HH; Splicing factor 1 helix-hairpin domain
  6. XM_011545248.1XP_011543550.1  splicing factor 1 isoform X7

    See identical proteins and their annotated locations for XP_011543550.1

    Conserved Domains (3) summary
    smart00343
    Location:252267
    ZnF_C2HC; zinc finger
    cd02395
    Location:111229
    SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
    pfam16275
    Location:2104
    SF1-HH; Splicing factor 1 helix-hairpin domain
  7. XM_011545247.1XP_011543549.1  splicing factor 1 isoform X5

    See identical proteins and their annotated locations for XP_011543549.1

    Conserved Domains (3) summary
    smart00343
    Location:252267
    ZnF_C2HC; zinc finger
    cd02395
    Location:111229
    SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
    pfam16275
    Location:2104
    SF1-HH; Splicing factor 1 helix-hairpin domain
  8. XM_011545245.1XP_011543547.1  splicing factor 1 isoform X3

    See identical proteins and their annotated locations for XP_011543547.1

    Conserved Domains (3) summary
    smart00343
    Location:252267
    ZnF_C2HC; zinc finger
    cd02395
    Location:111229
    SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
    pfam16275
    Location:2104
    SF1-HH; Splicing factor 1 helix-hairpin domain
  9. XM_017018250.1XP_016873739.1  splicing factor 1 isoform X10

    Conserved Domains (1) summary
    cd02395
    Location:22140
    SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
  10. XM_017018249.2XP_016873738.1  splicing factor 1 isoform X10

    Conserved Domains (1) summary
    cd02395
    Location:22140
    SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
  11. XM_017018251.1XP_016873740.1  splicing factor 1 isoform X10

    Conserved Domains (1) summary
    cd02395
    Location:22140
    SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
  12. XM_017018245.1XP_016873734.1  splicing factor 1 isoform X6

  13. XM_024448680.1XP_024304448.1  splicing factor 1 isoform X11

    Conserved Domains (2) summary
    smart00343
    Location:163178
    ZnF_C2HC; zinc finger
    cd02395
    Location:22140
    SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...

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.
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