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ENTR1 endosome associated trafficking regulator 1 [ Homo sapiens (human) ]

Gene ID: 10807, updated on 26-Oct-2020

Summary

Official Symbol
ENTR1provided by HGNC
Official Full Name
endosome associated trafficking regulator 1provided by HGNC
Primary source
HGNC:HGNC:10667
See related
Ensembl:ENSG00000165689 MIM:618289
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
SDDAG3; NY-CO-3; SDCCAG3
Expression
Ubiquitous expression in testis (RPKM 13.4), lymph node (RPKM 9.3) and 25 other tissues See more
Orthologs

Genomic context

See ENTR1 in Genome Data Viewer
Location:
9q34.3
Exon count:
10
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (136401922..136410614, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (139296374..139305054, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene caspase recruitment domain family member 9 Neighboring gene Sharpr-MPRA regulatory region 3996 Neighboring gene small nuclear RNA activating complex polypeptide 4 Neighboring gene peptidase, mitochondrial processing subunit alpha Neighboring gene inositol polyphosphate-5-phosphatase E

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?

Phenotypes

Associated conditions

Description Tests
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
GeneReviews: Not available
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
GeneReviews: Not available

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Nef nef Genome-wide shRNA screening identifies SDCCAG3, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cell cycle IEA
Inferred from Electronic Annotation
more info
 
cell division IEA
Inferred from Electronic Annotation
more info
 
cell projection organization IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cilium assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of protein localization to cilium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of protein localization to cilium IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein transport IEA
Inferred from Electronic Annotation
more info
 
regulation of cytokinesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of cytokinesis IDA
Inferred from Direct Assay
more info
PubMed 
retrograde transport, endosome to plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retrograde transport, endosome to plasma membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
centrosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
centrosome IDA
Inferred from Direct Assay
more info
PubMed 
ciliary basal body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ciliary basal body IDA
Inferred from Direct Assay
more info
PubMed 
early endosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
early endosome IDA
Inferred from Direct Assay
more info
PubMed 
endosome IDA
Inferred from Direct Assay
more info
PubMed 
midbody IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
midbody IDA
Inferred from Direct Assay
more info
PubMed 
recycling endosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
recycling endosome IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with retromer complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
colocalizes_with retromer complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
endosome-associated-trafficking regulator 1
Names
antigen NY-CO-3
serologically defined colon cancer antigen 3

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_001039707.2NP_001034796.1  endosome-associated-trafficking regulator 1 isoform 1

    See identical proteins and their annotated locations for NP_001034796.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AA742964, AF039688, AK001296, AL559847, AL592301, BC014515, BM549484, BQ723499
    Consensus CDS
    CCDS43904.1
    UniProtKB/Swiss-Prot
    Q96C92
    Related
    ENSP00000349929.3, ENST00000357365.8
    Conserved Domains (1) summary
    pfam10482
    Location:261370
    CtIP_N; Tumour-suppressor protein CtIP N-terminal domain
  2. NM_001039708.2NP_001034797.1  endosome-associated-trafficking regulator 1 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks two alternate in-frame exons in the 5' end compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AA742964, AF039688, AL592301, BM549484
    Consensus CDS
    CCDS43903.1
    UniProtKB/Swiss-Prot
    Q96C92
    Related
    ENSP00000360790.3, ENST00000371725.7
    Conserved Domains (1) summary
    TIGR02168
    Location:188360
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
  3. NM_006643.4NP_006634.3  endosome-associated-trafficking regulator 1 isoform 2

    See identical proteins and their annotated locations for NP_006634.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' end compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AA742964, AF039688, AK001296, AL592301, BC014515, BM549484, BQ723499
    Consensus CDS
    CCDS6999.2
    UniProtKB/Swiss-Prot
    Q96C92
    Related
    ENSP00000298537.7, ENST00000298537.11
    Conserved Domains (1) summary
    pfam10482
    Location:238347
    CtIP_N; Tumour-suppressor protein CtIP N-terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    136401922..136410614 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005266051.3XP_005266108.1  endosome-associated-trafficking regulator 1 isoform X4

    See identical proteins and their annotated locations for XP_005266108.1

    Conserved Domains (1) summary
    TIGR02168
    Location:211383
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
  2. XM_005266050.4XP_005266107.1  endosome-associated-trafficking regulator 1 isoform X2

    Conserved Domains (1) summary
    TIGR02168
    Location:261424
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
  3. XM_017014219.2XP_016869708.1  endosome-associated-trafficking regulator 1 isoform X1

    Conserved Domains (1) summary
    TIGR02168
    Location:310473
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
  4. XM_017014218.2XP_016869707.1  endosome-associated-trafficking regulator 1 isoform X5

    Conserved Domains (1) summary
    TIGR02168
    Location:310482
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
  5. XM_011518157.2XP_011516459.1  endosome-associated-trafficking regulator 1 isoform X3

    Conserved Domains (1) summary
    TIGR02168
    Location:228400
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type

RNA

  1. XR_002956746.1 RNA Sequence

  2. XR_001746168.2 RNA Sequence

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