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    SCAF11 SR-related CTD associated factor 11 [ Homo sapiens (human) ]

    Gene ID: 9169, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SCAF11provided by HGNC
    Official Full Name
    SR-related CTD associated factor 11provided by HGNC
    Primary source
    HGNC:HGNC:10784
    See related
    Ensembl:ENSG00000139218 MIM:603668; AllianceGenome:HGNC:10784
    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
    SIP1; CASP11; SFRS2IP; SRRP129; SRSF2IP
    Summary
    Enables RNA binding activity. Involved in spliceosomal complex assembly. Located in nuclear body and nucleolus. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 15.2), appendix (RPKM 14.4) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See SCAF11 in Genome Data Viewer
    Location:
    12q12
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (45919131..45992059, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (45878717..45954628, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (46312914..46384357, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene AT-rich interaction domain 2 Neighboring gene RNA, 7SL, cytoplasmic 246, pseudogene Neighboring gene lysine rich nucleolar protein 1 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4377 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6229 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4379 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:46384079-46384792 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6233 Neighboring gene ribosomal protein L13a pseudogene 21 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:46442615-46443116 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:46443117-46443616 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:46464825-46466024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6235 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:46478170-46479369 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6237 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6238 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4381 Neighboring gene solute carrier family 38 member 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:46660317-46661300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6242 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:46662284-46663266

    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. Identification and characterization of the carboxy-terminal region of Sip-1, a novel autoantigen in Behçet's disease. Delunardo F, et al. Arthritis Res Ther, 2006. PMID 16611372, Free PMC Article
    2. Regulation, Activation and Function of Caspase-11 during Health and Disease. Agnew A, et al. Int J Mol Sci, 2021 Feb 3. PMID 33546173, Free PMC Article
    3. CASP4/11 Contributes to NLRP3 Activation and COVID-19 Exacerbation. Rodrigues TS, et al. J Infect Dis, 2023 Jun 15. PMID 36763010
    4. A novel SR-related protein specifically interacts with the carboxy-terminal domain (CTD) of RNA polymerase II through a conserved interaction domain. Tanner S, et al. Biol Chem, 1997 Jun. PMID 9224939
    5. A serine kinase regulates intracellular localization of splicing factors in the cell cycle. Gui JF, et al. Nature, 1994 Jun 23. PMID 8208298

    See all (71) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CASP4/11 Contributes to NLRP3 Activation and COVID-19 Exacerbation.
      Title: CASP4/11 Contributes to NLRP3 Activation and COVID-19 Exacerbation.
    2. Regulation, Activation and Function of Caspase-11 during Health and Disease.
      Title: Regulation, Activation and Function of Caspase-11 during Health and Disease.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    4. Sip1 C-terminal is a novel autoantigen in Behcet's disease. IgM specific to Sip1 C-ter might be useful in clinical practice as an immunological marker of endothelial dysfunction in vasculitis.
      Title: Identification and characterization of the carboxy-terminal region of Sip-1, a novel autoantigen in Behçet's disease.
    Submit: New GeneRIF Correction

    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
    Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for Alzheimer's disease.
    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

    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 metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA splicing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in RNA splicing, via transesterification reactions IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mRNA processing TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in spliceosomal complex assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spliceosomal complex assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    protein SCAF11
    Names
    CTD-associated SR protein 11
    SC35-interacting protein 1
    SFRS2-interacting protein
    SR-related and CTD-associated factor 11
    SRSF2-interacting protein
    renal carcinoma antigen NY-REN-40
    serine/arginine-rich splicing factor 2-interacting protein
    splicing factor, arginine/serine-rich 2-interacting protein
    splicing regulatory protein 129

    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_004719.3 → NP_004710.2  protein SCAF11

      See identical proteins and their annotated locations for NP_004710.2

      Status: VALIDATED

      Source sequence(s)
      AC000015, AC084878, AF030234
      Consensus CDS
      CCDS8748.2
      UniProtKB/Swiss-Prot
      A6NEU9, A6NLW5, Q8IW59, Q99590
      Related
      ENSP00000358374.3, ENST00000369367.8
      Conserved Domains (2) summary
      pfam13639
      Location:39 → 82
      zf-RING_2; Ring finger domain
      cl21589
      Location:728 → 920
      Relaxase; Relaxase/Mobilization nuclease domain

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      45919131..45992059 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047429883.1 → XP_047285839.1  protein SCAF11 isoform X8

    2. XM_047429880.1 → XP_047285836.1  protein SCAF11 isoform X5

    3. XM_047429878.1 → XP_047285834.1  protein SCAF11 isoform X2

    4. XM_005269230.3 → XP_005269287.3  protein SCAF11 isoform X1

    5. XM_047429882.1 → XP_047285838.1  protein SCAF11 isoform X7

    6. XM_047429879.1 → XP_047285835.1  protein SCAF11 isoform X4

      UniProtKB/Swiss-Prot
      A6NEU9, A6NLW5, Q8IW59, Q99590

    7. XM_047429881.1 → XP_047285837.1  protein SCAF11 isoform X6

    8. XM_011538984.3 → XP_011537286.1  protein SCAF11 isoform X3

      Conserved Domains (3) summary
      PHA02929
      Location:1 → 106
      PHA02929; N1R/p28-like protein; Provisional
      pfam13639
      Location:55 → 98
      zf-RING_2; Ring finger domain
      cl21589
      Location:744 → 936
      Relaxase; Relaxase/Mobilization nuclease domain

    9. XM_024449275.2 → XP_024305043.1  protein SCAF11 isoform X9

      UniProtKB/TrEMBL
      B2RA91
      Conserved Domains (2) summary
      pfam09606
      Location:1143 → 1283
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
      cl28310
      Location:706 → 957
      Rho; Transcription termination factor Rho [Transcription]

    10. XM_047429884.1 → XP_047285840.1  protein SCAF11 isoform X10

      UniProtKB/TrEMBL
      F8VXG7
      Related
      ENSP00000448864.1, ENST00000549162.5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      45878717..45954628 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054373830.1 → XP_054229805.1  protein SCAF11 isoform X8

    2. XM_054373827.1 → XP_054229802.1  protein SCAF11 isoform X5

    3. XM_054373823.1 → XP_054229798.1  protein SCAF11 isoform X2

    4. XM_054373822.1 → XP_054229797.1  protein SCAF11 isoform X1

    5. XM_054373829.1 → XP_054229804.1  protein SCAF11 isoform X7

    6. XM_054373826.1 → XP_054229801.1  protein SCAF11 isoform X4

      UniProtKB/Swiss-Prot
      A6NEU9, A6NLW5, Q8IW59, Q99590

    7. XM_054373825.1 → XP_054229800.1  protein SCAF11 isoform X3

    8. XM_054373828.1 → XP_054229803.1  protein SCAF11 isoform X6

    9. XM_054373824.1 → XP_054229799.1  protein SCAF11 isoform X3

    10. XM_054373831.1 → XP_054229806.1  protein SCAF11 isoform X9

    11. XM_054373832.1 → XP_054229807.1  protein SCAF11 isoform X10

      UniProtKB/TrEMBL
      F8VXG7
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99590.2 GenPept UniProtKB/Swiss-Prot:Q99590

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