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

Gene ID: 55756, updated on 10-Dec-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
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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: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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Related articles in PubMed

  1. 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
  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. 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
  4. Inositol hexakisphosphate is required for Integrator function. Lin MH, et al. Nat Commun, 2022 Sep 30. PMID 36180473, Free PMC Article
  5. INTS10-INTS13-INTS14 form a functional module of Integrator that binds nucleic acids and the cleavage module. Sabath K, et al. Nat Commun, 2020 Jul 9. PMID 32647223, Free PMC Article

See all (55) 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)

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
 PubMed 
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
  
is_active_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
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

    UniProtKB/TrEMBL
    B7Z970

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

    UniProtKB/TrEMBL
    B7Z970

  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

    UniProtKB/TrEMBL
    G3XAN1

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

    UniProtKB/TrEMBL
    B7Z970

  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

    UniProtKB/TrEMBL
    B7Z970

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

    UniProtKB/TrEMBL
    B7Z970

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

    UniProtKB/TrEMBL
    B7Z970

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

    UniProtKB/TrEMBL
    G3XAN1

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

    UniProtKB/TrEMBL
    B7Z970

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

    UniProtKB/TrEMBL
    B7Z970

  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

    UniProtKB/TrEMBL
    G3XAN1

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

    UniProtKB/TrEMBL
    B7Z970

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

    UniProtKB/TrEMBL
    B7Z970
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NV88.2 GenPept UniProtKB/Swiss-Prot:Q9NV88

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