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    SF1 splicing factor 1 [ Homo sapiens (human) ]

    Gene ID: 7536, updated on 6-Sep-2017
    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]
    Orthologs
    Location:
    11q13.1
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 11 NC_000011.10 (64764604..64779043, 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

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    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

    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

    • 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...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    RNA binding IDA
    Inferred from Direct Assay
    more info
    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
     
    regulation of transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    spliceosomal complex assembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    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 
    Preferred Names
    splicing factor 1
    Names
    mammalian branch point-binding protein
    transcription factor ZFM1
    zinc finger gene in MEN1 locus
    zinc finger protein 162

    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
    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
    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
    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 (3) summary
      smart00343
      Location:278293
      ZnF_C2HC; zinc finger
      cd02395
      Location:137255
      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:18130
      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 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p7 Primary Assembly

      Range
      64764604..64779043 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017018246.1XP_016873735.1  splicing factor 1 isoform X8

    2. 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
    3. 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
    4. 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
    5. 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
    6. 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
    7. 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
    8. XM_017018249.1XP_016873738.1  splicing factor 1 isoform X11

      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 ...
    9. XM_017018250.1XP_016873739.1  splicing factor 1 isoform X11

      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_017018251.1XP_016873740.1  splicing factor 1 isoform X11

      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_017018245.1XP_016873734.1  splicing factor 1 isoform X6

    12. XM_017018248.1XP_016873737.1  splicing factor 1 isoform X10

    13. XM_017018247.1XP_016873736.1  splicing factor 1 isoform X9

    Alternate CHM1_1.1

    Genomic

    1. NC_018922.2 Alternate CHM1_1.1

      Range
      64415846..64430091 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.
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