U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 10807, updated on 5-Mar-2024

Summary

Go to the top of the page Help
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; AllianceGenome:HGNC:10667
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
Summary
Involved in several processes, including endocytic recycling; positive regulation of cilium assembly; and positive regulation of protein localization to cilium. Located in endosome; microtubule organizing center; and midbody. Colocalizes with retromer complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 13.4), lymph node (RPKM 9.3) and 25 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
9q34.3
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (136401922..136410614, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (148631256..148639944, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (139296374..139305066, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902309 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20509 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20510 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139258773-139259663 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139259664-139260553 Neighboring gene caspase recruitment domain family member 9 Neighboring gene Sharpr-MPRA regulatory region 3996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139268303-139269016 Neighboring gene small nuclear RNA activating complex polypeptide 4 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:139291906-139293105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20511 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20512 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139294835-139295771 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20513 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139301375-139301963 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29307 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20515 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20516 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29308 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29309 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:139310410-139311609 Neighboring gene peptidase, mitochondrial processing subunit alpha Neighboring gene inositol polyphosphate-5-phosphatase E Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139330456-139330964 Neighboring gene hESC enhancers GRCh37_chr9:139332501-139333134 to GRCh37_chr9:139333770-139334403

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. Serologically defined colon cancer antigen 3 is necessary for the presentation of TNF receptor 1 on cell surface. Neznanov N, et al. DNA Cell Biol, 2005 Dec. PMID 16332174
  2. The serologically defined colon cancer antigen-3 (SDCCAG3) is involved in the regulation of ciliogenesis. Yu F, et al. Sci Rep, 2016 Oct 21. PMID 27767179, Free PMC Article
  3. The serologically defined colon cancer antigen-3 interacts with the protein tyrosine phosphatase PTPN13 and is involved in the regulation of cytokinesis. Hagemann N, et al. Oncogene, 2013 Sep 26. PMID 23108400
  4. Identification of molecular heterogeneity in SNX27-retromer-mediated endosome-to-plasma-membrane recycling. McGough IJ, et al. J Cell Sci, 2014 Nov 15. PMID 25278552, Free PMC Article
  5. Identification of cyclophilin A as a CD99-binding protein by yeast two-hybrid screening. Kim HJ, et al. Immunol Lett, 2004 Sep. PMID 15388255

See all (69) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Endosome associated trafficking regulator 1 promotes tumor growth and invasion of glioblastoma multiforme via inhibiting TNF signaling pathway.
    Title: Endosome associated trafficking regulator 1 promotes tumor growth and invasion of glioblastoma multiforme via inhibiting TNF signaling pathway.
  2. SDCCAG3 has a role in ciliogenesis and in localization of cargo to primary cilia
    Title: The serologically defined colon cancer antigen-3 (SDCCAG3) is involved in the regulation of ciliogenesis.
  3. The novel endosomal protein SDCCAG3 forms a complex with PTPN13 & interacts with GIT1. Interaction of SDCCAG3 with PTPN13 is mediated by the PTPN13 FERM domain & the SDCCAG3 N-terminus. SDCCAG3 expression levels are elevated in colon cancers.
    Title: The serologically defined colon cancer antigen-3 interacts with the protein tyrosine phosphatase PTPN13 and is involved in the regulation of cytokinesis.
  4. SDCCAG3 is important for protein trafficking and presentation of TNFR1 on the cell surface.
    Title: Serologically defined colon cancer antigen 3 is necessary for the presentation of TNF receptor 1 on cell surface.
Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
EBI GWAS Catalog

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

Go to the top of the page Help

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

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

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 cell cycle IEA
Inferred from Electronic Annotation
more info
  
involved_in cell division IEA
Inferred from Electronic Annotation
more info
  
involved_in cell projection organization IEA
Inferred from Electronic Annotation
more info
  
involved_in endocytic recycling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of cilium assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of cilium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of protein localization to cilium IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of protein localization to cilium IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of cytokinesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of cytokinesis IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in centrosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in centrosome IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in ciliary basal body IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in ciliary basal body IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in early endosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in early endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endosome IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in midbody IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in midbody IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in recycling endosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in recycling endosome IDA
Inferred from Direct Assay
more info
 PubMed 
part_of retromer complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

Go to the top of the page Help
Preferred Names
endosome-associated-trafficking regulator 1
Names
antigen NY-CO-3
serologically defined colon cancer antigen 3

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_001039707.2 → NP_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
    A6NCP1, O60525, Q5SXN1, Q5SXN2, Q5SXN3, Q5SXN4, Q5SXN8, Q6V704, Q96C92, Q9NVY5
    Related
    ENSP00000349929.3, ENST00000357365.8
    Conserved Domains (1) summary
    pfam10482
    Location:261 → 370
    CtIP_N; Tumour-suppressor protein CtIP N-terminal domain

  2. NM_001039708.2 → NP_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:188 → 360
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type

  3. NM_006643.4 → NP_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:238 → 347
    CtIP_N; Tumour-suppressor protein CtIP N-terminal 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_000009.12 Reference GRCh38.p14 Primary Assembly

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

mRNA and Protein(s)

  1. XM_047422657.1 → XP_047278613.1  endosome-associated-trafficking regulator 1 isoform X7

  2. XM_047422656.1 → XP_047278612.1  endosome-associated-trafficking regulator 1 isoform X6

  3. XM_005266051.4 → XP_005266108.1  endosome-associated-trafficking regulator 1 isoform X5

    See identical proteins and their annotated locations for XP_005266108.1

    Conserved Domains (1) summary
    TIGR02168
    Location:211 → 383
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type

  4. XM_047422655.1 → XP_047278611.1  endosome-associated-trafficking regulator 1 isoform X3

  5. XM_005266050.5 → XP_005266107.1  endosome-associated-trafficking regulator 1 isoform X2

    Conserved Domains (1) summary
    TIGR02168
    Location:261 → 424
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type

  6. XM_017014218.3 → XP_016869707.1  endosome-associated-trafficking regulator 1 isoform X1

    Conserved Domains (1) summary
    TIGR02168
    Location:310 → 482
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type

  7. XM_011518157.3 → XP_011516459.1  endosome-associated-trafficking regulator 1 isoform X4

    Conserved Domains (1) summary
    TIGR02168
    Location:228 → 400
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type

RNA

  1. XR_002956746.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    148631256..148639944 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054361807.1 → XP_054217782.1  endosome-associated-trafficking regulator 1 isoform X7

  2. XM_054361806.1 → XP_054217781.1  endosome-associated-trafficking regulator 1 isoform X6

  3. XM_054361805.1 → XP_054217780.1  endosome-associated-trafficking regulator 1 isoform X5

  4. XM_054361803.1 → XP_054217778.1  endosome-associated-trafficking regulator 1 isoform X3

  5. XM_054361802.1 → XP_054217777.1  endosome-associated-trafficking regulator 1 isoform X2

  6. XM_054361801.1 → XP_054217776.1  endosome-associated-trafficking regulator 1 isoform X1

  7. XM_054361804.1 → XP_054217779.1  endosome-associated-trafficking regulator 1 isoform X4

RNA

  1. XR_008487931.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96C92.3 GenPept UniProtKB/Swiss-Prot:Q96C92

Gene LinkOut

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

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous