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EPDR1 ependymin related 1 [ Homo sapiens (human) ]

Gene ID: 54749, updated on 2-Nov-2024

Summary

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Official Symbol
EPDR1provided by HGNC
Official Full Name
ependymin related 1provided by HGNC
Primary source
HGNC:HGNC:17572
See related
Ensembl:ENSG00000086289 MIM:619734; AllianceGenome:HGNC:17572
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
EPDR; UCC1; MERP1; MERP-1
Summary
The protein encoded by this gene is a type II transmembrane protein that is similar to two families of cell adhesion molecules, the protocadherins and ependymins. This protein may play a role in calcium-dependent cell adhesion. This protein is glycosylated, and the orthologous mouse protein is localized to the lysosome. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 8. [provided by RefSeq, Aug 2011]
Expression
Broad expression in brain (RPKM 25.1), endometrium (RPKM 24.9) and 23 other tissues See more
Orthologs
mouse all
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Genomic context

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See EPDR1 in Genome Data Viewer
Location:
7p14.1
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (37920640..37951936)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (38061675..38093041)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (37960242..37991538)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene NME/NM23 family member 8 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98467 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18107 Neighboring gene secreted frizzled related protein 4 Neighboring gene Sharpr-MPRA regulatory region 10360 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:37987061-37987582 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:37987583-37988102 Neighboring gene Sharpr-MPRA regulatory region 4879 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:38026488-38027240 Neighboring gene MPRA-validated peak6491 silencer Neighboring gene uncharacterized LOC105375236 Neighboring gene MPRA-validated peak6492 silencer Neighboring gene MPRA-validated peak6493 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:38110217-38110835 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18108 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:38214547-38215746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18109 Neighboring gene Sharpr-MPRA regulatory region 13548 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25865 Neighboring gene STARD3 N-terminal like

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Identification of bone mineral density associated genes with shared genetic architectures across multiple tissues: Functional insights for EPDR1, PKDCC, and SPTBN1.
    Title: Identification of bone mineral density associated genes with shared genetic architectures across multiple tissues: Functional insights for EPDR1, PKDCC, and SPTBN1.
  2. EPDR1 is related to stages and metastasize in bladder cancer and can be used as a prognostic biomarker.
    Title: EPDR1 is related to stages and metastasize in bladder cancer and can be used as a prognostic biomarker.
  3. Evaluation of Primary Angle-Closure Glaucoma Susceptibility Loci for Estimating Angle Closure Disease Severity.
    Title: Evaluation of Primary Angle-Closure Glaucoma Susceptibility Loci for Estimating Angle Closure Disease Severity.
  4. EPDR1 correlates with immune cell infiltration in hepatocellular carcinoma and can be used as a prognostic biomarker.
    Title: EPDR1 correlates with immune cell infiltration in hepatocellular carcinoma and can be used as a prognostic biomarker.
  5. EPDR1 up-regulation in human colorectal cancer is related to staging and favours cell proliferation and invasiveness.
    Title: EPDR1 up-regulation in human colorectal cancer is related to staging and favours cell proliferation and invasiveness.
  6. Crystal structures of human lysosomal EPDR1 reveal homology with the superfamily of bacterial lipoprotein transporters, such as LolA.
    Title: Crystal structures of human lysosomal EPDR1 reveal homology with the superfamily of bacterial lipoprotein transporters.
  7. Study results suggest functional involvement of EPDR1 in the etiology of Dupuytren's Disease.
    Title: Dupuytren's disease susceptibility gene, EPDR1, is involved in myofibroblast contractility.
  8. EPDR1 exhibits a pattern of isoform abundance dependent on KRAS G13D and G12D mutations.
    Title: In silico RNA-seq and experimental analyses reveal the differential expression and splicing of EPDR1 and ZNF518B genes in relation to KRAS mutations in colorectal cancer cells.
  9. Results of this study suggest that EPDR1 gene can be added to a growing list of genes associated with Dupuytren's disease development.
    Title: Common variants of the EPDR1 gene and the risk of Dupuytren’s disease.
  10. Shows that the mouse ortholog is a lysosomal protein.
    Title: Demonstration of lysosomal localization for the mammalian ependymin-related protein using classical approaches combined with a novel density shift method.
Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Wnt signaling and Dupuytren's disease.
EBI GWAS Catalog

Variation

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See Variation Viewer (GRCh37.p13)

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 calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables ganglioside GM1 binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables identical protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables phospholipid binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell-matrix adhesion IEA
Inferred from Electronic Annotation
more info
  
involved_in myofibroblast contraction IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in extracellular region IDA
Inferred from Direct Assay
more info
 PubMed 
located_in lysosomal lumen IEA
Inferred from Electronic Annotation
more info
  
is_active_in lysosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in lysosome IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
mammalian ependymin-related protein 1
Names
ependymin related protein 1
mammalian ependymin related protein 1
upregulated in colorectal cancer gene 1 protein

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_001242946.2 → NP_001229875.2  mammalian ependymin-related protein 1 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001229875.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (2, also known as MERP1a) has a distinct and shorter C-terminus, compared to isoform 1.
    Source sequence(s)
    AC018634, AY027862, BC000686, DQ914439
    Consensus CDS
    CCDS59051.1
    UniProtKB/Swiss-Prot
    Q9UM22
    UniProtKB/TrEMBL
    Q96J80
    Related
    ENSP00000409211.1, ENST00000423717.1

  2. NM_001242948.2 → NP_001229877.1  mammalian ependymin-related protein 1 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate 5' exon and thus differs in the 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (3) has a distinct and shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC018634, AK309180, BC000686, DB167672, DB303790
    Consensus CDS
    CCDS59052.1
    UniProtKB/Swiss-Prot
    Q9UM22
    Related
    ENSP00000413359.1, ENST00000425345.1
    Conserved Domains (1) summary
    pfam00811
    Location:31 → 149
    Ependymin; Ependymin

  3. NM_017549.5 → NP_060019.2  mammalian ependymin-related protein 1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_060019.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC018634, AY027862, BC000686, DA938402
    Consensus CDS
    CCDS5454.2
    UniProtKB/Swiss-Prot
    A8K4C0, C9JYS3, Q06BL0, Q99M77, Q9UM22
    Related
    ENSP00000199448.4, ENST00000199448.9
    Conserved Domains (1) summary
    pfam00811
    Location:89 → 210
    Ependymin; Ependymin

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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    37920640..37951936
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    38061675..38093041
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UM22.2 GenPept UniProtKB/Swiss-Prot:Q9UM22

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