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

    Gene ID: 10807, updated on 2-Nov-2024

    Summary

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    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 several cellular components, including endosome; microtubule organizing center; and retromer complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 13.4), lymph node (RPKM 9.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ENTR1 in Genome Data Viewer
    Location:
    9q34.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (136401922..136410614, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (148631256..148639944, complement)
    RS_2024_09 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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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. Endosome associated trafficking regulator 1 promotes tumor growth and invasion of glioblastoma multiforme via inhibiting TNF signaling pathway. Zhang Q, et al. J Neurooncol, 2024 Jan. PMID 38191954
    2. 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
    3. 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
    4. 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
    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 (74) 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

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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

    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

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    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

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    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 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

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

    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_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_2024_08

    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.

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