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

Gene ID: 144717, updated on 10-Dec-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
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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
  • 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)

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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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
    UniProtKB/TrEMBL
    B4DRN3

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

    UniProtKB/Swiss-Prot
    J3KP50, Q6PJL9, Q8N4B1, Q96MH8
    UniProtKB/TrEMBL
    B4DRN3

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

    UniProtKB/Swiss-Prot
    J3KP50, Q6PJL9, Q8N4B1, Q96MH8
    UniProtKB/TrEMBL
    B4DRN3

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

    UniProtKB/Swiss-Prot
    J3KP50, Q6PJL9, Q8N4B1, Q96MH8
    UniProtKB/TrEMBL
    B4DRN3
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N4B1.1 GenPept UniProtKB/Swiss-Prot:Q8N4B1

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