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INTS6 integrator complex subunit 6 [ Homo sapiens (human) ]

Gene ID: 26512, updated on 21-Dec-2019

Summary

Official Symbol
INTS6provided by HGNC
Official Full Name
integrator complex subunit 6provided by HGNC
Primary source
HGNC:HGNC:14879
See related
Ensembl:ENSG00000102786 MIM:604331
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
HDB; INT6; DBI-1; DDX26; DICE1; DDX26A; Notchl2
Summary
DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. The protein encoded by this gene is a DEAD box protein that is part of a complex that interacts with the C-terminus of RNA polymerase II and is involved in 3' end processing of snRNAs. In addition, this gene is a candidate tumor suppressor and is located in the critical region of loss of heterozygosity (LOH). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2015]
Expression
Broad expression in testis (RPKM 13.0), thyroid (RPKM 3.7) and 25 other tissues See more
Orthologs

Genomic context

See INTS6 in Genome Data Viewer
Location:
13q14.3
Exon count:
22
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (51353171..51453333, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (51927678..52027275, complement)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 124 member A Neighboring gene serpin family E member 3 Neighboring gene microRNA 5693 Neighboring gene INTS6 antisense RNA 1 Neighboring gene ribosomal protein S4X pseudogene 16

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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of integrator complex subunit 6 (INTS6) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp434B105

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transmembrane signaling receptor activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
snRNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
actin cytoskeleton IDA
Inferred from Direct Assay
more info
 
integrator complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 6
Names
DEAD box protein
DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 26
RNA helicase HDB
protein deleted in cancer 1

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.

mRNA and Protein(s)

  1. NM_001039937.2NP_001035026.1  integrator complex subunit 6 isoform b

    See identical proteins and their annotated locations for NP_001035026.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) is missing a segment in the the 5' coding region, and uses an in-frame downstream start codon compared to variant 1. This results in an isoform (b) with a shorter N-terminus compared to isoform a.
    Source sequence(s)
    AF097645, AL137780, AL833524
    Consensus CDS
    CCDS41890.1
    UniProtKB/Swiss-Prot
    Q9UL03
    Related
    ENSP00000381187.2, ENST00000398119.6
    Conserved Domains (2) summary
    cd00198
    Location:8118
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam15300
    Location:796855
    INT_SG_DDX_CT_C; INTS6/SAGE1/DDX26B/CT45 C-terminus
  2. NM_001039938.2NP_001035027.1  integrator complex subunit 6 isoform c

    See identical proteins and their annotated locations for NP_001035027.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) is missing many 3' exons and contains an alternative segment at the 3' end compared to variant 1. This results in a shorter isoform (c) with a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AL354820, AL833524, BC032386
    Consensus CDS
    CCDS45048.1
    UniProtKB/Swiss-Prot
    Q9UL03
    Related
    ENSP00000411245.3, ENST00000442263.4
    Conserved Domains (1) summary
    pfam13519
    Location:4103
    VWA_2; von Willebrand factor type A domain
  3. NM_001306091.2NP_001293020.1  integrator complex subunit 6 isoform 4

    See identical proteins and their annotated locations for NP_001293020.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains two alternate internal exons, and uses an in-frame downstream start codon compared to variant 1. This results in an isoform (4) with a shorter N-terminus compared to isoform a.
    Source sequence(s)
    AA251444, AA262171, AF097645, AK128795, AL833524, AW967611, BC039829, BC094745, BE160101, BG621629, BM699545, BU754174, BX116410, DA182797, FN136361
    Consensus CDS
    CCDS76636.1
    UniProtKB/Swiss-Prot
    Q9UL03
    UniProtKB/TrEMBL
    B3KQH5
    Related
    ENSP00000419871.1, ENST00000497989.5
    Conserved Domains (1) summary
    pfam15300
    Location:631690
    INT_SG_DDX_CT_C; INTS6/SAGE1/DDX26B/CT45 C-terminus
  4. NM_012141.3NP_036273.1  integrator complex subunit 6 isoform a

    See identical proteins and their annotated locations for NP_036273.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AF097645, AL137780, AL354820, AL833524
    Consensus CDS
    CCDS9428.1
    UniProtKB/Swiss-Prot
    Q9UL03
    UniProtKB/TrEMBL
    A0A024RDU0
    Related
    ENSP00000310260.4, ENST00000311234.9
    Conserved Domains (2) summary
    pfam13519
    Location:4131
    VWA_2; von Willebrand factor type A domain
    pfam15300
    Location:807868
    INT_SG_DDX_CT_C; INTS6/SAGE1/DDX26B/CT45 C-terminus

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p13 Primary Assembly

    Range
    51353171..51453333 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011535040.3XP_011533342.1  integrator complex subunit 6 isoform X1

    See identical proteins and their annotated locations for XP_011533342.1

    UniProtKB/Swiss-Prot
    Q9UL03
    UniProtKB/TrEMBL
    A0A024RDU0
    Conserved Domains (2) summary
    pfam13519
    Location:4131
    VWA_2; von Willebrand factor type A domain
    pfam15300
    Location:807868
    INT_SG_DDX_CT_C; INTS6/SAGE1/DDX26B/CT45 C-terminus
  2. XM_011535041.2XP_011533343.1  integrator complex subunit 6 isoform X2

    Related
    ENSP00000419984.1, ENST00000490542.5
    Conserved Domains (1) summary
    pfam15300
    Location:595654
    INT_SG_DDX_CT_C; INTS6/SAGE1/DDX26B/CT45 C-terminus
  3. XM_017020540.2XP_016876029.1  integrator complex subunit 6 isoform X3

    Conserved Domains (1) summary
    pfam15300
    Location:377436
    INT_SG_DDX_CT_C; INTS6/SAGE1/DDX26B/CT45 C-terminus
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