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

Summary

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

Location:: 1p36.33

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (1311600..1324660, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (743151..756245, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (1246980..1260040, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9.
Title: Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9.
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.
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.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

L17688 (e-PCR)
- UniSTS:74509

GDB:434012 (e-PCR)
- UniSTS:157204

D1S2520 (e-PCR)
- UniSTS:154145

D8S2279 (e-PCR)
- UniSTS:473907

RH76790 (e-PCR)
- UniSTS:91708

L17709 (e-PCR)
- UniSTS:42599

D15S1477 (e-PCR)
- UniSTS:474482

D1S1425 (e-PCR)
- UniSTS:149621

RH36905 (e-PCR)
- UniSTS:87932

D17S610 (e-PCR)
- UniSTS:46230

L17971 (e-PCR)
- UniSTS:43966

RH91825 (e-PCR)
- UniSTS:87779

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 more info	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
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 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

EC 3.1.27.-

NP_001243389.1

EC 3.1.27.-

NP_001243391.1

EC 3.1.27.-

NP_001243392.1

EC 3.1.27.-

NP_060341.2

EC 3.1.27.-

XP_011539949.1

EC 3.1.27.-

XP_011539950.1

EC 3.1.27.-

XP_011539952.1

EC 3.1.27.-

XP_054193241.1

EC 3.1.27.-

XP_054193242.1

EC 3.1.27.-

XP_054193243.1

EC 3.1.27.-

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)

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 ...
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 ...
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
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
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

1311600..1324660 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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 ...
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 ...
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

NC_060925.1 Alternate T2T-CHM13v2.0

Range

743151..756245 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054337266.1 → XP_054193241.1 integrator complex subunit 11 isoform X1
XM_054337267.1 → XP_054193242.1 integrator complex subunit 11 isoform X2
XM_054337268.1 → XP_054193243.1 integrator complex subunit 11 isoform X3

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

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.