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    INTS9 integrator complex subunit 9 [ Homo sapiens (human) ]

    Gene ID: 55756, updated on 17-Jun-2019

    Summary

    Official Symbol
    INTS9provided by HGNC
    Official Full Name
    integrator complex subunit 9provided by HGNC
    Primary source
    HGNC:HGNC:25592
    See related
    Ensembl:ENSG00000104299 MIM:611352
    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
    INT9; RC74; CPSF2L
    Summary
    This gene encodes a subunit of the Integrator complex. This protein complex binds the C-terminal domain of RNA polymerase II and likely plays a role in small nuclear RNA processing. The encoded protein has similarities to the subunits of the cleavage and polyadenylation specificity factor complex. Alternatively spliced transcript variants have been described.[provided by RefSeq, Feb 2010]
    Expression
    Ubiquitous expression in testis (RPKM 6.2), adrenal (RPKM 5.5) and 25 other tissues See more
    Orthologs

    Genomic context

    See INTS9 in Genome Data Viewer
    Location:
    8p21.1
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 8 NC_000008.11 (28767658..28890226, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (28625175..28747698, complement)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene RNA, 5S ribosomal pseudogene 259 Neighboring gene frizzled class receptor 3 Neighboring gene exostosin like glycosyltransferase 3 Neighboring gene EXTL3 antisense RNA 1 Neighboring gene ribosomal protein L36a pseudogene 32 Neighboring gene homeobox containing 1 Neighboring gene uncharacterized LOC105379346 Neighboring gene RNA, 5S ribosomal pseudogene 260

    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 Apr 4 07:08:55 2018

    Bibliography

    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...
    • RNA polymerase II transcribes snRNA genes, organism-specific biosystem (from REACTOME)
      RNA polymerase II transcribes snRNA genes, organism-specific biosystemSmall nuclear RNAs (snRNAs) play key roles in splicing and some of them, specifically the U1 and U2 snRNAs, are encoded by multicopy snRNA gene clusters containing tandem arrays of genes, about 30 in...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ10871

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    snRNA processing IDA
    Inferred from Direct Assay
    more info
    PubMed 
    snRNA transcription by RNA polymerase II TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    cytosol IDA
    Inferred from Direct Assay
    more info
     
    integrator complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    integrator complex subunit 9
    Names
    protein related to CPSF subunits of 74 kDa

    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_016981.2 RefSeqGene

      Range
      5001..127524
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001145159.2NP_001138631.1  integrator complex subunit 9 isoform 2

      See identical proteins and their annotated locations for NP_001138631.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AA825242, AK300593, BC025267, DC339488
      Consensus CDS
      CCDS55216.1
      UniProtKB/Swiss-Prot
      Q9NV88
      Related
      ENSP00000398208.2, ENST00000416984.6
      Conserved Domains (2) summary
      smart01027
      Location:286404
      Beta-Casp; Beta-Casp domain
      cd16294
      Location:1244
      Int9-like_MBL-fold; integrator subunit 9, and related proteins; MBL-fold metallo-hydrolase domain
    2. NM_001172562.1NP_001166033.1  integrator complex subunit 9 isoform 3

      See identical proteins and their annotated locations for NP_001166033.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AA825242, AK298468
      Consensus CDS
      CCDS55215.1
      UniProtKB/Swiss-Prot
      Q9NV88
      Related
      ENSP00000430943.1, ENST00000521777.5
      Conserved Domains (2) summary
      smart01027
      Location:283401
      Beta-Casp; Beta-Casp domain
      cl23716
      Location:60241
      metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain
    3. NM_001363038.2NP_001349967.1  integrator complex subunit 9 isoform 4

      Status: REVIEWED

      Source sequence(s)
      BC025267, BM931164, DC339488
      Conserved Domains (2) summary
      smart01027
      Location:307425
      Beta-Casp; Beta-Casp domain
      cd16294
      Location:1265
      Int9-like_MBL-fold; integrator subunit 9, and related proteins; MBL-fold metallo-hydrolase domain
    4. NM_018250.4NP_060720.2  integrator complex subunit 9 isoform 1

      See identical proteins and their annotated locations for NP_060720.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      BC025267, DC339488
      Consensus CDS
      CCDS34873.1
      UniProtKB/Swiss-Prot
      Q9NV88
      Related
      ENSP00000429065.1, ENST00000521022.6
      Conserved Domains (2) summary
      smart01027
      Location:307425
      Beta-Casp; Beta-Casp domain
      cd16294
      Location:1265
      Int9-like_MBL-fold; integrator subunit 9, and related proteins; MBL-fold metallo-hydrolase domain

    RNA

    1. NR_026826.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks two alternate internal exons compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AA825242, AK304525, BC025267, DC339488
      Related
      ENST00000523303.5

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p13 Primary Assembly

      Range
      28767658..28890226 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011544575.2XP_011542877.1  integrator complex subunit 9 isoform X3

      See identical proteins and their annotated locations for XP_011542877.1

      Conserved Domains (2) summary
      smart01027
      Location:283401
      Beta-Casp; Beta-Casp domain
      cl23716
      Location:60241
      metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain
    2. XM_011544573.1XP_011542875.1  integrator complex subunit 9 isoform X2

      Conserved Domains (2) summary
      smart01027
      Location:286404
      Beta-Casp; Beta-Casp domain
      cd16294
      Location:1244
      Int9-like_MBL-fold; integrator subunit 9, and related proteins; MBL-fold metallo-hydrolase domain
    3. XM_011544576.2XP_011542878.1  integrator complex subunit 9 isoform X5

      Conserved Domains (2) summary
      smart01027
      Location:262380
      Beta-Casp; Beta-Casp domain
      cl23716
      Location:1220
      metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain
    4. XM_011544574.1XP_011542876.1  integrator complex subunit 9 isoform X3

      See identical proteins and their annotated locations for XP_011542876.1

      Conserved Domains (2) summary
      smart01027
      Location:283401
      Beta-Casp; Beta-Casp domain
      cl23716
      Location:60241
      metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain
    5. XM_006716357.4XP_006716420.1  integrator complex subunit 9 isoform X4

      Conserved Domains (2) summary
      smart01027
      Location:307425
      Beta-Casp; Beta-Casp domain
      cd16294
      Location:1265
      Int9-like_MBL-fold; integrator subunit 9, and related proteins; MBL-fold metallo-hydrolase domain
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