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INTS11 integrator complex subunit 11 [ Homo sapiens (human) ]

Gene ID: 54973, updated on 3-Apr-2024

Summary

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Official Symbol
INTS11provided by HGNC
Official Full Name
integrator complex subunit 11provided by HGNC
Primary source
HGNC:HGNC:26052
See related
Ensembl:ENSG00000127054 MIM:611354; AllianceGenome:HGNC:26052
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
RC68; INT11; PSF3L; RC-68; CPSF3L; CPSF73L; NEDMLOB
Summary
The Integrator complex contains at least 12 subunits and associates with the C-terminal domain of RNA polymerase II large subunit (POLR2A; MIM 180660) and mediates the 3-prime end processing of small nuclear RNAs U1 (RNU1; MIM 180680) and U2 (RNU2; MIM 180690). INTS11, or CPSF3L, is the catalytic subunit of the Integrator complex (Baillat et al., 2005 [PubMed 16239144]).[supplied by OMIM, Mar 2008]
Expression
Ubiquitous expression in testis (RPKM 35.0), endometrium (RPKM 21.3) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
1p36.33
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (1311600..1324660, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (743151..756245, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (1246980..1260040, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1232563-1233499 Neighboring gene ArfGAP with coiled-coil, ankyrin repeat and PH domains 3 Neighboring gene microRNA 6726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1237151-1237752 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1237753-1238352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1238353-1238953 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1238954-1239553 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1239554-1240154 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 52 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 53 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 54 Neighboring gene small nucleolar RNA, C/D box 167 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 55 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 56 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 57 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 58 Neighboring gene pseudouridine synthase like 1 Neighboring gene microRNA 6727 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1253662-1254352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1254353-1255043 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1257229-1257737 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1258501-1259010 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 59 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 60 Neighboring gene ceramide-1-phosphate transfer protein Neighboring gene taste 1 receptor member 3 Neighboring gene dishevelled segment polarity protein 1

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. An examination of the metal ion content in the active sites of human endonucleases CPSF73 and INTS11. Huang J, et al. J Biol Chem, 2023 Apr. PMID 36822327, Free PMC Article
  2. NACK and INTEGRATOR act coordinately to activate Notch-mediated transcription in tumorigenesis. Shersher E, et al. Cell Commun Signal, 2021 Sep 22. PMID 34551776, 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. snRNA 3' end formation requires heterodimeric association of integrator subunits. Albrecht TR, et al. Mol Cell Biol, 2012 Mar. PMID 22252320, Free PMC Article
  5. 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

See all (60) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A homozygous variant in INTS11 links mitosis and neurogenesis defects to a severe neurodevelopmental disorder.
    Title: A homozygous variant in INTS11 links mitosis and neurogenesis defects to a severe neurodevelopmental disorder.
  2. An examination of the metal ion content in the active sites of human endonucleases CPSF73 and INTS11.
    Title: An examination of the metal ion content in the active sites of human endonucleases CPSF73 and INTS11.
  3. NACK and INTEGRATOR act coordinately to activate Notch-mediated transcription in tumorigenesis.
    Title: NACK and INTEGRATOR act coordinately to activate Notch-mediated transcription in tumorigenesis.
  4. 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.
  5. 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.
  6. 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.
  7. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  8. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
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

Associated conditions

Description Tests
Neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities
MedGen: C5830596 OMIM: 620428 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel 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

Clone Names

  • FLJ13294, FLJ20542

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA endonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA endonuclease activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
contributes_to protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in regulation of transcription elongation by RNA polymerase II NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in snRNA 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 blood microparticle HDA PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
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 IBA
Inferred from Biological aspect of Ancestor
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 11
Names
CPSF3-like protein
cleavage and polyadenylation specific factor 3-like
cleavage and polyadenylation-specific factor 3-like protein
protein related to CPSF subunits of 68 kDa
related to CPSF subunits 68 kDa
NP_001243385.1
NP_001243389.1
NP_001243391.1
NP_001243392.1
NP_060341.2
XP_011539949.1
XP_011539950.1
XP_011539952.1
XP_054193241.1
XP_054193242.1
XP_054193243.1

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_001256456.2 → NP_001243385.1  integrator complex subunit 11 isoform 1

    See identical proteins and their annotated locations for NP_001243385.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and it encodes the longest protein (isoform 1).
    Source sequence(s)
    AA687684, AK056652, AK291387, AK297350, DC299237
    Consensus CDS
    CCDS57960.1
    UniProtKB/Swiss-Prot
    Q5TA45
    Related
    ENSP00000445001.1, ENST00000540437.5
    Conserved Domains (5) summary
    smart01027
    Location:251 → 369
    Beta-Casp; Beta-Casp domain
    COG1236
    Location:16 → 450
    YSH1; RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]
    pfam07521
    Location:382 → 422
    RMMBL; RNA-metabolizing metallo-beta-lactamase
    cd16291
    Location:16 → 210
    INTS11-like_MBL-fold; Integrator complex subunit 11, and related proteins; MBL-fold metallo-hydrolase domain
    cl02570
    Location:414 → 486
    RhoGAP; RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when ...

  2. NM_001256460.2 → NP_001243389.1  integrator complex subunit 11 isoform 3

    See identical proteins and their annotated locations for NP_001243389.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has multiple differences which results in the use of a downstream start codon, compared to variant 1. The resulting protein (isoform 3) is shorter when it is compared to isoform 1.
    Source sequence(s)
    AA687684, AK291387, AK297350, DC295791, DC299237
    Consensus CDS
    CCDS57959.1
    UniProtKB/TrEMBL
    C9IYS7
    Related
    ENSP00000444672.1, ENST00000545578.5
    Conserved Domains (5) summary
    smart01027
    Location:216 → 334
    Beta-Casp; Beta-Casp domain
    COG1236
    Location:1 → 415
    YSH1; RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]
    pfam07521
    Location:347 → 387
    RMMBL; RNA-metabolizing metallo-beta-lactamase
    cd16291
    Location:1 → 175
    INTS11-like_MBL-fold; Integrator complex subunit 11, and related proteins; MBL-fold metallo-hydrolase domain
    cl02570
    Location:379 → 451
    RhoGAP; RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when ...

  3. NM_001256462.2 → NP_001243391.1  integrator complex subunit 11 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks several exons which results in the use of an upstream start codon, compared to variant 1. The resulting protein (isoform 4) has a shorter and distinct N-terminus when it is compared to isoform 1.
    Source sequence(s)
    AA687684, AK058018, AK291387, DC299237
    Consensus CDS
    CCDS72678.1
    UniProtKB/TrEMBL
    A0A087WYI0, C9IYS7
    Related
    ENSP00000481821.1, ENST00000620829.4
    Conserved Domains (5) summary
    smart01027
    Location:147 → 265
    Beta-Casp; Beta-Casp domain
    COG1236
    Location:48 → 346
    YSH1; RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]
    pfam07521
    Location:278 → 318
    RMMBL; RNA-metabolizing metallo-beta-lactamase
    cl02570
    Location:310 → 382
    RhoGAP; RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when ...
    cl23716
    Location:46 → 106
    metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain

  4. NM_001256463.2 → NP_001243392.1  integrator complex subunit 11 isoform 5

    See identical proteins and their annotated locations for NP_001243392.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) has multiple differences which results in the use of an upstream start codon, compared to variant 1. The resulting protein (isoform 5) is shorter when it is compared to isoform 1.
    Source sequence(s)
    AA687684, AK021939, AK058018, DC299237
    Consensus CDS
    CCDS57961.1
    UniProtKB/TrEMBL
    C9IYS7
    Related
    ENSP00000404886.1, ENST00000419704.5
    Conserved Domains (5) summary
    smart01027
    Location:144 → 262
    Beta-Casp; Beta-Casp domain
    COG1236
    Location:4 → 343
    YSH1; RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]
    pfam07521
    Location:275 → 315
    RMMBL; RNA-metabolizing metallo-beta-lactamase
    cl02570
    Location:307 → 379
    RhoGAP; RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when ...
    cl23716
    Location:6 → 103
    metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain

  5. NM_017871.6 → NP_060341.2  integrator complex subunit 11 isoform 2

    See identical proteins and their annotated locations for NP_060341.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks two alternate exons in the coding region which results in the use of an upstream start codon, compared to variant 1. The resulting protein (isoform 2) has a shorter and distinct N-terminus when it is compared to isoform 1.
    Source sequence(s)
    AA687684, AK023356, AL136813, DC299993
    Consensus CDS
    CCDS21.1
    UniProtKB/Swiss-Prot
    A8K5S2, B3KPR3, B4DM87, G3V1S5, Q5TA45, Q5TA46, Q5TA48, Q5TA52, Q5TA53, Q5TA54, Q7L3D7, Q96HY1, Q9BW36, Q9H0F9, Q9H8R5, Q9HAA6, Q9NWX9
    Related
    ENSP00000413493.2, ENST00000435064.6
    Conserved Domains (2) summary
    COG1236
    Location:4 → 444
    YSH1; RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]
    cd16291
    Location:6 → 204
    INTS11-like_MBL-fold; Integrator complex subunit 11, and related proteins; MBL-fold metallo-hydrolase 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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    1311600..1324660 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541647.2 → XP_011539949.1  integrator complex subunit 11 isoform X1

    Conserved Domains (5) summary
    smart01027
    Location:305 → 423
    Beta-Casp; Beta-Casp domain
    COG1236
    Location:70 → 504
    YSH1; RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]
    pfam07521
    Location:436 → 476
    RMMBL; RNA-metabolizing metallo-beta-lactamase
    cd16291
    Location:70 → 264
    INTS11-like_MBL-fold; Integrator complex subunit 11, and related proteins; MBL-fold metallo-hydrolase domain
    cl02570
    Location:468 → 540
    RhoGAP; RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when ...

  2. XM_011541648.2 → XP_011539950.1  integrator complex subunit 11 isoform X2

    Conserved Domains (5) summary
    smart01027
    Location:267 → 385
    Beta-Casp; Beta-Casp domain
    COG1236
    Location:32 → 466
    YSH1; RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]
    pfam07521
    Location:398 → 438
    RMMBL; RNA-metabolizing metallo-beta-lactamase
    cd16291
    Location:32 → 226
    INTS11-like_MBL-fold; Integrator complex subunit 11, and related proteins; MBL-fold metallo-hydrolase domain
    cl02570
    Location:430 → 502
    RhoGAP; RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when ...

  3. XM_011541650.3 → XP_011539952.1  integrator complex subunit 11 isoform X3

    See identical proteins and their annotated locations for XP_011539952.1

    UniProtKB/TrEMBL
    C9IYS7
    Conserved Domains (5) summary
    smart01027
    Location:121 → 239
    Beta-Casp; Beta-Casp domain
    COG1236
    Location:2 → 320
    YSH1; RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]
    pfam07521
    Location:252 → 292
    RMMBL; RNA-metabolizing metallo-beta-lactamase
    cl02570
    Location:284 → 356
    RhoGAP; RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when ...
    cl23716
    Location:1 → 80
    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_060925.1 Alternate T2T-CHM13v2.0

    Range
    743151..756245 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337266.1 → XP_054193241.1  integrator complex subunit 11 isoform X1

  2. XM_054337267.1 → XP_054193242.1  integrator complex subunit 11 isoform X2

  3. XM_054337268.1 → XP_054193243.1  integrator complex subunit 11 isoform X3

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_032179.1: Suppressed sequence

    Description
    NM_032179.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5TA45.2 GenPept UniProtKB/Swiss-Prot:Q5TA45

Gene LinkOut

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

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