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

Gene ID: 9169, updated on 3-Apr-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, Apr 2022]
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_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (45919131..45992059, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (45878717..45954628, complement)
105.20220307 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
  • 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. 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
  2. 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
  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 (63) 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_2023_10

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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