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    SF1 splicing factor 1 [ Homo sapiens (human) ]

    Gene ID: 7536, updated on 3-Nov-2024

    Summary

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    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
    mouse all
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    Genomic context

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    See SF1 in Genome Data Viewer
    Location:
    11q13.1
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (64764606..64778542, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (64757911..64771848, complement)
    RS_2024_09 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 H3K4me1 hESC enhancer GRCh37_chr11:64506559-64507108 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3482 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3483 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3484 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3485 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3486 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3487 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64520964-64521574 Neighboring gene glycogen phosphorylase, muscle associated Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64525447-64526151 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64526152-64526855 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64526856-64527560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64527561-64528263 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4910 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64530587-64531460 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64532334-64533208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64533209-64534081 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64534082-64534955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3488 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:64545791-64546392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64557481-64557982 Neighboring gene mitogen-activated protein kinase kinase kinase kinase 2 Neighboring gene Sharpr-MPRA regulatory region 11124 Neighboring gene MPRA-validated peak1298 silencer Neighboring gene Sharpr-MPRA regulatory region 2965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4917 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3491 Neighboring gene menin 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 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. SF1 Phosphorylation Enhances Specific Binding to U2AF(65) and Reduces Binding to 3'-Splice-Site RNA. Chatrikhi R, et al. Biophys J, 2016 Dec 20. PMID 28002734, Free PMC Article
    2. Structural basis for recognition of the intron branch site RNA by splicing factor 1. Liu Z, et al. Science, 2001 Nov 2. PMID 11691992
    3. Diverse modes of alternative splicing of human splicing factor SF1 deduced from the exon-intron structure of the gene. Krämer A, et al. Gene, 1998 Apr 28. PMID 9573336
    4. Analysis of in situ pre-mRNA targets of human splicing factor SF1 reveals a function in alternative splicing. Corioni M, et al. Nucleic Acids Res, 2011 Mar. PMID 21062807, Free PMC Article
    5. Structural basis for the interaction between the first SURP domain of the SF3A1 subunit in U2 snRNP and the human splicing factor SF1. Nameki N, et al. Protein Sci, 2022 Oct. PMID 36173164, Free PMC Article

    See all (187) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Structural basis for the interaction between the first SURP domain of the SF3A1 subunit in U2 snRNP and the human splicing factor SF1.
      Title: Structural basis for the interaction between the first SURP domain of the SF3A1 subunit in U2 snRNP and the human splicing factor SF1.
    2. Deoxynivalenol globally affects the selection of 3' splice sites in human cells by suppressing the splicing factors, U2AF1 and SF1.
      Title: Deoxynivalenol globally affects the selection of 3' splice sites in human cells by suppressing the splicing factors, U2AF1 and SF1.
    3. SF1 Phosphorylation Enhances Specific Binding to U2AF(65) and Reduces Binding to 3'-Splice-Site RNA
      Title: SF1 Phosphorylation Enhances Specific Binding to U2AF(65) and Reduces Binding to 3'-Splice-Site RNA.
    4. A novel function of SF1 in the initial recruitment of the U2 snRNP through direct interactions with two U2 snRNP-associated proteins.
      Title: Mammalian splicing factor SF1 interacts with SURP domains of U2 snRNP-associated proteins.
    5. Data suggest that post-translational processing of SF1 (phosphorylation of Ser20) down-regulates nuclear import of SF1 via alterations in kinetic interaction of SF1 nuclear localization signal (NLS) with NLS receptor isoforms.
      Title: Computational identification of post-translational modification-based nuclear import regulations by characterizing nuclear localization signal-import receptor interaction.
    6. We demonstrated that PRPF40B interacts directly with SF1 and associates with U2AF(65
      Title: Prp40 pre-mRNA processing factor 40 homolog B (PRPF40B) associates with SF1 and U2AF65 and modulates alternative pre-mRNA splicing in vivo.
    7. Gomafu indirectly modulates the function of the splicing factors SF1 and Celf3 by sequestering these proteins into separate nuclear bodies.
      Title: Formation of nuclear bodies by the lncRNA Gomafu-associating proteins Celf3 and SF1.
    8. The conserved SPSP motif phosphorylation and the SF1/U2AF interface are essential in vivo.
      Title: Structure of phosphorylated SF1 bound to U2AF⁶⁵ in an essential splicing factor complex.
    9. Findings suggest that Zinc finger motif-1 (ZFM1) is an important factor for the stabilization of a contractile SMC phenotype under basal or mildly activating conditions.
      Title: Zinc finger motif-1 antagonizes PDGF-BB-induced growth and dedifferentiation of vascular smooth muscle cells.
    10. central ;mystery' domain of SF1 crystals belonged to space group C2 and have most probable solvent contents of 64, 52 or 39% with three, four or five molecules per asymmetric unit, respectively
      Title: Purification, crystallization and preliminary X-ray crystallographic analysis of a central domain of human splicing factor 1.
    Submit: New GeneRIF Correction See all GeneRIFs (17)

    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

    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

    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

    HIV-1 interactions

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    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

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    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
    		  
    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
    		  
    Process Evidence Code Pubs
    involved_in Leydig cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA 3'-splice site recognition TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome IC
    Inferred by Curator
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in male sex determination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of smooth muscle cell proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nuclear body organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of steroid biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spliceosomal complex assembly NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    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
    		  
    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

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

    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_021399.1 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_001178030.2 → NP_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:403 → 418
      ZnF_C2HC; zinc finger
      COG5176
      Location:142 → 382
      MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

    2. NM_001178031.3 → NP_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/TrEMBL
      B4DJU4
      Related
      ENSP00000396793.2, ENST00000433274.6
      Conserved Domains (2) summary
      smart00343
      Location:252 → 267
      ZnF_C2HC; zinc finger
      COG5176
      Location:10 → 231
      MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

    3. NM_001346363.2 → NP_001333292.1  splicing factor 1 isoform 9

      Status: REVIEWED

      Source sequence(s)
      AK293753, AP001462, BC000773, BC020217, BE745705, DC341853
      UniProtKB/TrEMBL
      A0A9L9PXR5, H7C561
      Related
      ENSP00000419062.2, ENST00000486867.2
      Conserved Domains (2) summary
      smart00343
      Location:278 → 293
      ZnF_C2HC; zinc finger
      COG5176
      Location:17 → 257
      MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

    4. NM_001346364.2 → NP_001333293.1  splicing factor 1 isoform 10

      Status: REVIEWED

      Source sequence(s)
      AK293753, AP001462, BC020217, BC069273, BE745705, DC341853
      UniProtKB/TrEMBL
      A0A9L9PXR5
      Conserved Domains (2) summary
      smart00343
      Location:278 → 293
      ZnF_C2HC; zinc finger
      COG5176
      Location:17 → 257
      MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

    5. NM_001346409.2 → NP_001333338.1  splicing factor 1 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AK301803, AP001462, BC069273
      UniProtKB/TrEMBL
      B4DSE4, B4DX42, E7ESU3
      Conserved Domains (2) summary
      smart00343
      Location:163 → 178
      ZnF_C2HC; zinc finger
      cd22382
      Location:20 → 112
      KH-I_SF1; type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins

    6. NM_001346410.2 → NP_001333339.1  splicing factor 1 isoform 8

      Status: REVIEWED

      Source sequence(s)
      AP001462, BC032676, BC069273
      Conserved Domains (2) summary
      smart00343
      Location:163 → 178
      ZnF_C2HC; zinc finger
      cd22382
      Location:20 → 112
      KH-I_SF1; type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins

    7. NM_001378956.1 → NP_001365885.1  splicing factor 1 isoform 11

      Status: REVIEWED

      Source sequence(s)
      AP001462
      UniProtKB/TrEMBL
      A0A9L9PXE4
      Related
      ENSP00000516498.1, ENST00000706684.1
      Conserved Domains (2) summary
      smart00343
      Location:403 → 418
      ZnF_C2HC; zinc finger
      COG5176
      Location:142 → 382
      MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

    8. NM_001378957.1 → NP_001365886.1  splicing factor 1 isoform 12

      Status: REVIEWED

      Source sequence(s)
      AP001462
      Consensus CDS
      CCDS91502.1
      UniProtKB/TrEMBL
      A0A7P0T9U7, B4DJU4
      Related
      ENSP00000505779.1, ENST00000681407.1
      Conserved Domains (2) summary
      smart00343
      Location:403 → 418
      ZnF_C2HC; zinc finger
      COG5176
      Location:142 → 382
      MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

    9. NM_004630.4 → NP_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
      B7Z1Q1, C9JJE2, Q14818, Q14819, Q15637, Q15913, Q8IY00, Q92744, Q92745, Q969H7, Q9BW01, Q9UEI0
      UniProtKB/TrEMBL
      B4DJU4
      Related
      ENSP00000366607.3, ENST00000377390.8
      Conserved Domains (2) summary
      smart00343
      Location:278 → 293
      ZnF_C2HC; zinc finger
      COG5176
      Location:17 → 257
      MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

    10. NM_201995.3 → NP_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/TrEMBL
      B4DJU4
      Related
      ENSP00000334414.5, ENST00000334944.9
      Conserved Domains (2) summary
      smart00343
      Location:278 → 293
      ZnF_C2HC; zinc finger
      COG5176
      Location:17 → 257
      MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

    11. NM_201997.3 → NP_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
      A0A9L9PXR5
      Related
      ENSP00000366611.3, ENST00000377394.7
      Conserved Domains (2) summary
      smart00343
      Location:278 → 293
      ZnF_C2HC; zinc finger
      COG5176
      Location:17 → 257
      MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

    12. NM_201998.3 → NP_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/TrEMBL
      B4DSE4
      Related
      ENSP00000227503.9, ENST00000227503.13
      Conserved Domains (2) summary
      smart00343
      Location:278 → 293
      ZnF_C2HC; zinc finger
      COG5176
      Location:17 → 257
      MSL5; Splicing factor (branch point binding protein) [RNA processing and modification]

    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_000011.10 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

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

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

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

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

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

    6. XM_011545247.2 → XP_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)

    mRNA and Protein(s)

    1. XM_054369869.1 → XP_054225844.1  splicing factor 1 isoform X6

    2. XM_054369868.1 → XP_054225843.1  splicing factor 1 isoform X5

    3. XM_054369865.1 → XP_054225840.1  splicing factor 1 isoform X2

    4. XM_054369864.1 → XP_054225839.1  splicing factor 1 isoform X1

    5. XM_054369867.1 → XP_054225842.1  splicing factor 1 isoform X4

    6. XM_054369866.1 → XP_054225841.1  splicing factor 1 isoform X3

    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.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q15637.4 GenPept UniProtKB/Swiss-Prot:Q15637

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