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    PHETA1 PH domain containing endocytic trafficking adaptor 1 [ Homo sapiens (human) ]

    Gene ID: 144717, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PHETA1provided by HGNC
    Official Full Name
    PH domain containing endocytic trafficking adaptor 1provided by HGNC
    Primary source
    HGNC:HGNC:26509
    See related
    Ensembl:ENSG00000198324 MIM:614239; AllianceGenome:HGNC:26509
    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
    SES1; FAM109A; IPIP27A
    Summary
    This gene encodes a protein that localizes to the endosome and interacts with the enzyme, inositol polyphosphate 5-phosphatase OCRL-1. Alternate splicing results in multiple transcript variants. [provided by RefSeq, May 2010]
    Expression
    Ubiquitous expression in small intestine (RPKM 9.7), duodenum (RPKM 9.3) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PHETA1 in Genome Data Viewer
    Location:
    12q24.12
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (111360679..111369095, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (111341175..111349591, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (111798483..111806899, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene cut like homeobox 2 Neighboring gene uncharacterized LOC105369983 Neighboring gene microRNA 6760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:111791286-111791786 Neighboring gene RNA, 5S ribosomal pseudogene 373 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:111799560-111800216 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4865 Neighboring gene long intergenic non-protein coding RNA 2356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7031 Neighboring gene heat shock protein family A (Hsp70) member 8 pseudogene 14 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4866 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4867 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4868 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:111851003-111851850 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:111855471-111856170 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:111863315-111863890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7032 Neighboring gene uncharacterized LOC124903019 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7033 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7034 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:111873559-111874138 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:111874139-111874718 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:111876422-111876935 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:111877948-111878492 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:111880447-111880633 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7035 Neighboring gene SH2B adaptor protein 3

    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. Two closely related endocytic proteins that share a common OCRL-binding motif with APPL1. Swan LE, et al. Proc Natl Acad Sci U S A, 2010 Feb 23. PMID 20133602, Free PMC Article
    2. Deficiency in the endocytic adaptor proteins PHETA1/2 impairs renal and craniofacial development. Ates KM, et al. Dis Model Mech, 2020 May 26. PMID 32152089, Free PMC Article
    3. The PH domain proteins IPIP27A and B link OCRL1 to receptor recycling in the endocytic pathway. Noakes CJ, et al. Mol Biol Cell, 2011 Mar 1. PMID 21233288, Free PMC Article
    4. A role of OCRL in clathrin-coated pit dynamics and uncoating revealed by studies of Lowe syndrome cells. Nández R, et al. Elife, 2014 Aug 8. PMID 25107275, Free PMC Article
    5. POH1 contributes to hyperactivation of TGF-β signaling and facilitates hepatocellular carcinoma metastasis through deubiquitinating TGF-β receptors and caveolin-1. Wang B, et al. EBioMedicine, 2019 Mar. PMID 30745168, Free PMC Article

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Deficiency in the endocytic adaptor proteins PHETA1/2 impairs renal and craniofacial development.
      Title: Deficiency in the endocytic adaptor proteins PHETA1/2 impairs renal and craniofacial development.
    2. Two novel OCRL1-binding proteins, termed inositol polyphosphate phosphatase interacting protein of 27 kDa (IPIP27)A and B (also known as Ses1 and 2), that also bind the related 5-phosphatase Inpp5b, were identified.
      Title: The PH domain proteins IPIP27A and B link OCRL1 to receptor recycling in the endocytic pathway.
    3. Two closely related endocytic proteins, Ses1 and Ses2, which interact with OCRL, were identified. The interaction is mediated by a short amino acid motif similar to that used by the rab-5 effector APPL1.
      Title: Two closely related endocytic proteins that share a common OCRL-binding motif with APPL1.
    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

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ32356

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endosome organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endosome organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in receptor recycling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in receptor recycling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in retrograde transport, endosome to Golgi IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retrograde transport, endosome to Golgi IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in clathrin-coated vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 
    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 
    is_active_in trans-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in trans-Golgi network IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    sesquipedalian-1
    Names
    27 kDa inositol polyphosphate phosphatase-interacting protein A
    family with sequence similarity 109 member A
    inositol polyphosphate phosphatase-interacting protein A
    protein FAM109A

    NCBI Reference Sequences (RefSeq)

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    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.

    Genomic

    1. NG_021347.1 RefSeqGene

      Range
      5027..13443
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001177996.3 → NP_001171467.1  sesquipedalian-1 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC005805, CX758147, DB055268
      Consensus CDS
      CCDS53833.1
      UniProtKB/TrEMBL
      B4DRN3
      Related
      ENSP00000354461.3, ENST00000361483.4
      Conserved Domains (2) summary
      cd13288
      Location:24 → 143
      PH_Ses; Sesquipedalian family Pleckstrin homology (PH) domain
      pfam00169
      Location:35 → 125
      PH; PH domain

    2. NM_001177997.3 → NP_001171468.1  sesquipedalian-1 isoform 2

      See identical proteins and their annotated locations for NP_001171468.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC005805, CX758147, DA707326
      Consensus CDS
      CCDS9152.1
      UniProtKB/Swiss-Prot
      J3KP50, Q6PJL9, Q8N4B1, Q96MH8
      UniProtKB/TrEMBL
      B4DRN3
      Conserved Domains (1) summary
      cd13288
      Location:11 → 130
      PH_Ses; Sesquipedalian family Pleckstrin homology (PH) domain

    3. NM_144671.6 → NP_653272.2  sesquipedalian-1 isoform 2

      See identical proteins and their annotated locations for NP_653272.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC005805, BC034809, CX758147
      Consensus CDS
      CCDS9152.1
      UniProtKB/Swiss-Prot
      J3KP50, Q6PJL9, Q8N4B1, Q96MH8
      UniProtKB/TrEMBL
      B4DRN3
      Related
      ENSP00000507123.1, ENST00000683047.1
      Conserved Domains (1) summary
      cd13288
      Location:11 → 130
      PH_Ses; Sesquipedalian family Pleckstrin homology (PH) 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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      111360679..111369095 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017018883.2 → XP_016874372.1  sesquipedalian-1 isoform X1

      UniProtKB/Swiss-Prot
      J3KP50, Q6PJL9, Q8N4B1, Q96MH8
      UniProtKB/TrEMBL
      B4DRN3
      Conserved Domains (1) summary
      cd13288
      Location:11 → 130
      PH_Ses; Sesquipedalian family Pleckstrin homology (PH) domain

    2. XM_006719257.4 → XP_006719320.1  sesquipedalian-1 isoform X1

      See identical proteins and their annotated locations for XP_006719320.1

      UniProtKB/Swiss-Prot
      J3KP50, Q6PJL9, Q8N4B1, Q96MH8
      UniProtKB/TrEMBL
      B4DRN3
      Conserved Domains (1) summary
      cd13288
      Location:11 → 130
      PH_Ses; Sesquipedalian family Pleckstrin homology (PH) domain

    3. XM_011537976.3 → XP_011536278.1  sesquipedalian-1 isoform X1

      See identical proteins and their annotated locations for XP_011536278.1

      UniProtKB/Swiss-Prot
      J3KP50, Q6PJL9, Q8N4B1, Q96MH8
      UniProtKB/TrEMBL
      B4DRN3
      Related
      ENSP00000447353.1, ENST00000547838.2
      Conserved Domains (1) summary
      cd13288
      Location:11 → 130
      PH_Ses; Sesquipedalian family Pleckstrin homology (PH) domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      111341175..111349591 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371215.1 → XP_054227190.1  sesquipedalian-1 isoform X1

      UniProtKB/Swiss-Prot
      J3KP50, Q6PJL9, Q8N4B1, Q96MH8

    2. XM_054371213.1 → XP_054227188.1  sesquipedalian-1 isoform X1

      UniProtKB/Swiss-Prot
      J3KP50, Q6PJL9, Q8N4B1, Q96MH8

    3. XM_054371212.1 → XP_054227187.1  sesquipedalian-1 isoform X1

      UniProtKB/Swiss-Prot
      J3KP50, Q6PJL9, Q8N4B1, Q96MH8

    4. XM_054371214.1 → XP_054227189.1  sesquipedalian-1 isoform X1

      UniProtKB/Swiss-Prot
      J3KP50, Q6PJL9, Q8N4B1, Q96MH8
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N4B1.1 GenPept UniProtKB/Swiss-Prot:Q8N4B1

    Gene LinkOut

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

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