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EIPR1 EARP complex and GARP complex interacting protein 1 [ Homo sapiens (human) ]

Gene ID: 7260, updated on 5-Mar-2024

Summary

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Official Symbol
EIPR1provided by HGNC
Official Full Name
EARP complex and GARP complex interacting protein 1provided by HGNC
Primary source
HGNC:HGNC:12383
See related
Ensembl:ENSG00000032389 MIM:608998; AllianceGenome:HGNC:12383
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
TSSC1; EIPR-1
Summary
This gene has been reported in PMID 9403053 as one of several tumor-suppressing subtransferable fragments located in the imprinted gene domain of 11p15.5, an important tumor-suppressor gene region. Alterations in this region have been associated with the Beckwith-Wiedemann syndrome, Wilms tumor, rhabdomyosarcoma, adrenocortical carcinoma, and lung, ovarian, and breast cancer. Alignment of this gene to genomic sequence data suggests that this gene resides on chromosome 2 rather than chromosome 11. [provided by RefSeq, Dec 2008]
Expression
Ubiquitous expression in thyroid (RPKM 8.8), brain (RPKM 8.2) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
2p25.3
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (3188970..3377818, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (3210031..3399939, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (3192741..3381589, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1250 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3105730-3106514 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:3108292-3108999 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3112467-3113140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3118175-3118676 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:3131179-3131343 Neighboring gene uncharacterized LOC107985840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15221 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15223 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3172751-3173696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3182069-3182826 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3183585-3184342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3184343-3185098 Neighboring gene Sharpr-MPRA regulatory region 8446 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:3202367-3202905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3204190-3204746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15224 Neighboring gene MPRA-validated peak3584 silencer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:3237853-3239052 Neighboring gene Sharpr-MPRA regulatory region 3808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15225 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15226 Neighboring gene VISTA enhancer hs1385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3284251-3284751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3289510-3290088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3290089-3290666 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:3310431-3310601 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3323251-3323862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3326607-3327134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3327135-3327662 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:3358809-3358982 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15227 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11108 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3382431-3382947 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3381914-3382430 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15229 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11109 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3402817-3403742 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3403743-3404668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3404669-3405592 Neighboring gene trafficking protein particle complex subunit 12 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3416341-3416841 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3415840-3416340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3434408-3434908 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:3437307-3437557 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3463593-3464106 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3464459-3465326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3475415-3475916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3475917-3476416 Neighboring gene TRAPPC12 antisense RNA 1 Neighboring gene uncharacterized LOC112268321

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. Allele-specific DNA methylation maps in monozygotic twins discordant for psychiatric disorders reveal that disease-associated switching at the EIPR1 regulatory loci modulates neural function. Li Q, et al. Mol Psychiatry, 2021 Nov. PMID 33963283
  2. Subchromosomal assignment1 of the TSSC1 gene to human chromosome band 11p15.5 near the HBB gene cluster. Scelfo R, et al. Cytogenet Cell Genet, 1998. PMID 9925925
  3. Runx2 induces bone osteolysis by transcriptional suppression of TSSC1. Wang DC, et al. Biochem Biophys Res Commun, 2013 Sep 6. PMID 23933319
  4. A 2.5-Mb transcript map of a tumor-suppressing subchromosomal transferable fragment from 11p15.5, and isolation and sequence analysis of three novel genes. Hu RJ, et al. Genomics, 1997 Nov 15. PMID 9403053
  5. TSSC1 is novel component of the endosomal retrieval machinery. Gershlick DC, et al. Mol Biol Cell, 2016 Sep 15. PMID 27440922, Free PMC Article

See all (30) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Allele-specific DNA methylation maps in monozygotic twins discordant for psychiatric disorders reveal that disease-associated switching at the EIPR1 regulatory loci modulates neural function.
    Title: Allele-specific DNA methylation maps in monozygotic twins discordant for psychiatric disorders reveal that disease-associated switching at the EIPR1 regulatory loci modulates neural function.
  2. Fluorescence recovery after photobleaching shows that TSSC1 is required for efficient recruitment of GARP to the TGN. These studies thus demonstrate that TSSC1 plays a critical role in endosomal retrieval pathways as a regulator of both GARP and EARP function.
    Title: TSSC1 is novel component of the endosomal retrieval machinery.
  3. TSSC1 inhibits breast cancer cell invasion. Subsequently, TSSC1 is confirmed as a target of Runx2 and is negatively regulated by Runx2.
    Title: Runx2 induces bone osteolysis by transcriptional suppression of TSSC1.
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

Pathways from PubChem

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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 endocytic recycling ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of endocytic recycling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of retrograde transport, endosome to Golgi IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of insulin secretion ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
part_of EARP complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of GARP complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in trans-Golgi network IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
EARP and GARP complex-interacting protein 1
Names
EARP-interacting protein
Golgi-associated retrograde protein-interacting protein
endosome-associated recycling protein-interacting protein
protein TSSC1
tumor suppressing subtransferable candidate 1
tumor-suppressing STF cDNA 1 protein
tumor-suppressing subchromosomal transferable fragment candidate gene 1 protein
tumor-suppressing subtransferable fragment candidate gene 1

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_001330530.3 → NP_001317459.1  EARP and GARP complex-interacting protein 1 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC019118, AC073502
    Consensus CDS
    CCDS82416.1
    UniProtKB/TrEMBL
    A8MUM1
    Related
    ENSP00000381652.4, ENST00000398659.8
    Conserved Domains (3) summary
    COG2319
    Location:166 → 401
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:165 → 201
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:166 → 401
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  2. NM_001330531.3 → NP_001317460.1  EARP and GARP complex-interacting protein 1 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks two exons and initiates translation from a downstream start codon compared to variant 1. The encoded isoform (3) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    AC019118, AC073502
    Conserved Domains (2) summary
    sd00039
    Location:44 → 80
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:3 → 226
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  3. NM_003310.5 → NP_003301.1  EARP and GARP complex-interacting protein 1 isoform 2

    See identical proteins and their annotated locations for NP_003301.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC019118, AK026522, BC002485, HY008956
    Consensus CDS
    CCDS1651.1
    UniProtKB/Swiss-Prot
    D6W4Y1, O43179, Q53HC9, Q53S19, Q53SG2
    Related
    ENSP00000371559.4, ENST00000382125.9
    Conserved Domains (2) summary
    sd00039
    Location:138 → 174
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:139 → 370
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    3188970..3377818 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011510383.4 → XP_011508685.1  EARP and GARP complex-interacting protein 1 isoform X1

    Conserved Domains (2) summary
    sd00039
    Location:177 → 213
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:178 → 413
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  2. XM_011510385.3 → XP_011508687.1  EARP and GARP complex-interacting protein 1 isoform X2

    Conserved Domains (2) summary
    sd00039
    Location:150 → 186
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:151 → 382
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  3. XM_006711893.3 → XP_006711956.1  EARP and GARP complex-interacting protein 1 isoform X3

    Conserved Domains (2) summary
    sd00039
    Location:38 → 74
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:39 → 270
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    3210031..3399939 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054343651.1 → XP_054199626.1  EARP and GARP complex-interacting protein 1 isoform X1

  2. XM_054343652.1 → XP_054199627.1  EARP and GARP complex-interacting protein 1 isoform X2

  3. XM_054343653.1 → XP_054199628.1  EARP and GARP complex-interacting protein 1 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q53HC9.2 GenPept UniProtKB/Swiss-Prot:Q53HC9

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