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

    Gene ID: 55756, updated on 3-Nov-2024

    Summary

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    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; AllianceGenome:HGNC:25592
    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
    mouse all
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    Genomic context

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    See INTS9 in Genome Data Viewer
    Location:
    8p21.1
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (28767661..28889969, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (29045883..29168153, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (28625178..28747486, 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 ReSE screen-validated silencer GRCh37_chr8:28415895-28416077 Neighboring gene NANOG hESC enhancer GRCh37_chr8:28419252-28419778 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:28479657-28480093 Neighboring gene exostosin like glycosyltransferase 3 Neighboring gene Sharpr-MPRA regulatory region 11135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19063 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19064 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19062 Neighboring gene EXTL3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:28583611-28584110 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:28609290-28610234 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:28610235-28611177 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19065 Neighboring gene uncharacterized LOC124902104 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:28647439-28647939 Neighboring gene ribosomal protein L36a pseudogene 32 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19066 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:28728271-28728917 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:28747269-28747825 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:28747826-28748382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27176 Neighboring gene homeobox containing 1 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr8:28834820-28835748 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27177 Neighboring gene uncharacterized LOC105379346 Neighboring gene RNA, 5S ribosomal pseudogene 260

    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. Molecular basis for the interaction between Integrator subunits IntS9 and IntS11 and its functional importance. Wu Y, et al. Proc Natl Acad Sci U S A, 2017 Apr 25. PMID 28396433, Free PMC Article
    2. snRNA 3' end formation requires heterodimeric association of integrator subunits. Albrecht TR, et al. Mol Cell Biol, 2012 Mar. PMID 22252320, Free PMC Article
    3. A CPSF-73 homologue is required for cell cycle progression but not cell growth and interacts with a protein having features of CPSF-100. Dominski Z, et al. Mol Cell Biol, 2005 Feb. PMID 15684398, Free PMC Article
    4. Inositol hexakisphosphate is required for Integrator function. Lin MH, et al. Nat Commun, 2022 Sep 30. PMID 36180473, Free PMC Article
    5. The Human Integrator Complex Facilitates Transcriptional Elongation by Endonucleolytic Cleavage of Nascent Transcripts. Beckedorff F, et al. Cell Rep, 2020 Jul 21. PMID 32697989, Free PMC Article

    See all (53) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. INTS4 is a specific and conserved interaction partner of INTS9/11 that does not interact with either subunit individually.
      Title: Integrator subunit 4 is a 'Symplekin-like' scaffold that associates with INTS9/11 to form the Integrator cleavage module.
    2. Functional studies demonstrate that the IntS9-IntS11 interaction is crucial for the role of INT in snRNA 3'-end processing.
      Title: Molecular basis for the interaction between Integrator subunits IntS9 and IntS11 and its functional importance.
    3. The specific heterodimeric interaction between IntS9 and IntS11 is mediated by a discrete domain present at the extreme C terminus of IntS9 and within the C terminus of IntS11, adjacent to the predicted active site of this endonuclease.
      Title: snRNA 3' end formation requires heterodimeric association of integrator subunits.
    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

    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

    Clone Names

    • FLJ10871

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of transforming growth factor beta receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of transcription elongation by RNA polymerase II NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in snRNA 3'-end processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in snRNA processing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in snRNA processing NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    part_of integrator complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of integrator complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of integrator complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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

    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.

    Genomic

    1. NG_016981.2 RefSeqGene

      Range
      5213..127521
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001145159.3 → NP_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/TrEMBL
      B7Z970
      Related
      ENSP00000398208.2, ENST00000416984.6
      Conserved Domains (2) summary
      smart01027
      Location:286 → 404
      Beta-Casp; Beta-Casp domain
      cd16294
      Location:1 → 244
      Int9-like_MBL-fold; integrator subunit 9, and related proteins; MBL-fold metallo-hydrolase domain

    2. NM_001172562.2 → NP_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, AC040975, AK298468
      Consensus CDS
      CCDS55215.1
      UniProtKB/TrEMBL
      B7Z970
      Related
      ENSP00000430943.1, ENST00000521777.5
      Conserved Domains (2) summary
      smart01027
      Location:283 → 401
      Beta-Casp; Beta-Casp domain
      cl23716
      Location:60 → 241
      metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain

    3. NM_001363038.2 → NP_001349967.1  integrator complex subunit 9 isoform 4

      Status: REVIEWED

      Source sequence(s)
      BC025267, BM931164, DC339488
      UniProtKB/TrEMBL
      B7Z970
      Conserved Domains (2) summary
      smart01027
      Location:307 → 425
      Beta-Casp; Beta-Casp domain
      cd16294
      Location:1 → 265
      Int9-like_MBL-fold; integrator subunit 9, and related proteins; MBL-fold metallo-hydrolase domain

    4. NM_018250.4 → NP_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
      B7Z560, B7Z6M5, O00224, Q8TB16, Q9NV88
      UniProtKB/TrEMBL
      B7Z970
      Related
      ENSP00000429065.1, ENST00000521022.6
      Conserved Domains (2) summary
      smart01027
      Location:307 → 425
      Beta-Casp; Beta-Casp domain
      cd16294
      Location:1 → 265
      Int9-like_MBL-fold; integrator subunit 9, and related proteins; MBL-fold metallo-hydrolase domain

    RNA

    1. NR_026826.3 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
      ENST00000522363.5

    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_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      28767661..28889969 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047421958.1 → XP_047277914.1  integrator complex subunit 9 isoform X9

    2. XM_047421956.1 → XP_047277912.1  integrator complex subunit 9 isoform X7

    3. XM_011544573.2 → XP_011542875.1  integrator complex subunit 9 isoform X1

      UniProtKB/TrEMBL
      B7Z970
      Conserved Domains (2) summary
      smart01027
      Location:286 → 404
      Beta-Casp; Beta-Casp domain
      cd16294
      Location:1 → 244
      Int9-like_MBL-fold; integrator subunit 9, and related proteins; MBL-fold metallo-hydrolase domain

    4. XM_047421954.1 → XP_047277910.1  integrator complex subunit 9 isoform X5

    5. XM_047421955.1 → XP_047277911.1  integrator complex subunit 9 isoform X6

    6. XM_011544576.3 → XP_011542878.1  integrator complex subunit 9 isoform X4

      UniProtKB/TrEMBL
      B7Z970
      Conserved Domains (2) summary
      smart01027
      Location:262 → 380
      Beta-Casp; Beta-Casp domain
      cl23716
      Location:1 → 220
      metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain

    7. XM_047421957.1 → XP_047277913.1  integrator complex subunit 9 isoform X8

    8. XM_006716357.5 → XP_006716420.1  integrator complex subunit 9 isoform X3

      UniProtKB/TrEMBL
      G3XAN1
      Conserved Domains (2) summary
      smart01027
      Location:307 → 425
      Beta-Casp; Beta-Casp domain
      cd16294
      Location:1 → 265
      Int9-like_MBL-fold; integrator subunit 9, and related proteins; MBL-fold metallo-hydrolase domain

    9. XM_011544575.3 → XP_011542877.1  integrator complex subunit 9 isoform X2

      See identical proteins and their annotated locations for XP_011542877.1

      UniProtKB/TrEMBL
      B7Z970
      Conserved Domains (2) summary
      smart01027
      Location:283 → 401
      Beta-Casp; Beta-Casp domain
      cl23716
      Location:60 → 241
      metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain

    10. XM_011544574.1 → XP_011542876.1  integrator complex subunit 9 isoform X2

      See identical proteins and their annotated locations for XP_011542876.1

      UniProtKB/TrEMBL
      B7Z970
      Conserved Domains (2) summary
      smart01027
      Location:283 → 401
      Beta-Casp; Beta-Casp domain
      cl23716
      Location:60 → 241
      metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      29045883..29168153 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054360801.1 → XP_054216776.1  integrator complex subunit 9 isoform X9

    2. XM_054360799.1 → XP_054216774.1  integrator complex subunit 9 isoform X7

    3. XM_054360792.1 → XP_054216767.1  integrator complex subunit 9 isoform X1

    4. XM_054360797.1 → XP_054216772.1  integrator complex subunit 9 isoform X5

    5. XM_054360798.1 → XP_054216773.1  integrator complex subunit 9 isoform X6

    6. XM_054360796.1 → XP_054216771.1  integrator complex subunit 9 isoform X4

    7. XM_054360800.1 → XP_054216775.1  integrator complex subunit 9 isoform X8

    8. XM_054360795.1 → XP_054216770.1  integrator complex subunit 9 isoform X3

    9. XM_054360793.1 → XP_054216768.1  integrator complex subunit 9 isoform X2

    10. XM_054360794.1 → XP_054216769.1  integrator complex subunit 9 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NV88.2 GenPept UniProtKB/Swiss-Prot:Q9NV88

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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