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ERMARD ER membrane associated RNA degradation [ Homo sapiens (human) ]

Gene ID: 55780, updated on 5-Mar-2024

Summary

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Official Symbol
ERMARDprovided by HGNC
Official Full Name
ER membrane associated RNA degradationprovided by HGNC
Primary source
HGNC:HGNC:21056
See related
Ensembl:ENSG00000130023 MIM:615532; AllianceGenome:HGNC:21056
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
PVNH6; C6orf70; dJ266L20.3
Summary
The protein encoded by this gene contains 2 transmembrane domains near the C-terminus and is localized in the endoplasmic reticulum. Knockout of this gene in developing rat brain showed that it may be involved in neuronal migration. Mutations in this gene are associated with periventricular nodular heterotopia-6 (PVNH6). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2013]
Expression
Ubiquitous expression in testis (RPKM 11.2), thyroid (RPKM 6.1) and 25 other tissues See more
Orthologs
all
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Genomic context

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Location:
6q27
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (169751306..169781600)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (171105236..171135403)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (170151718..170181696)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene WD repeat domain 27 Neighboring gene uncharacterized LOC124901471 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170040667-170041282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170047131-170048124 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25463 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:170056229-170057024 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:170057025-170057820 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170061015-170061514 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:170062913-170064112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170068091-170068591 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170067590-170068090 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:170067058-170067246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170092723-170093223 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25464 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25465 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17797 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17798 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17799 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:170124719-170125261 Neighboring gene chromosome 6 open reading frame 120 Neighboring gene MPRA-validated peak6328 silencer Neighboring gene PHD finger protein 10 Neighboring gene dynein light chain Tctex-type 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170171824-170172324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170172325-170172825 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:170183046-170183546 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170200599-170201291 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170201292-170201985 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170201986-170202678 Neighboring gene long intergenic non-protein coding RNA 242 Neighboring gene long intergenic non-protein coding RNA 574 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:170227060-170227735 Neighboring gene zinc finger protein 227-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
  • 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. Periventricular heterotopia in 6q terminal deletion syndrome: role of the C6orf70 gene. Conti V, et al. Brain, 2013 Nov. PMID 24056535
  2. Expressed sequence tag analysis of human RPE/choroid for the NEIBank Project: over 6000 non-redundant transcripts, novel genes and splice variants. Wistow G, et al. Mol Vis, 2002 Jun 15. PMID 12107410
  3. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Anantharaman V, et al. Biol Direct, 2013 Jun 15. PMID 23768067, Free PMC Article
  4. Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. Fei T, et al. Proc Natl Acad Sci U S A, 2017 Jun 27. PMID 28611215, Free PMC Article
  5. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article

See all (7) citations in PubMed

GeneRIFs: Gene References Into Functions

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

Associated conditions

Description Tests
Periventricular nodular heterotopia 6
MedGen: C3809872 OMIM: 615544 GeneReviews: Not available
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Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2013-11-13)

ClinGen Genome Curation Page
Haploinsufficency

Little evidence for dosage pathogenicity (Last evaluated 2013-11-13)

ClinGen Genome Curation PagePubMed

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

  • FLJ11152

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
Component Evidence Code Pubs
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
endoplasmic reticulum membrane-associated RNA degradation protein
Names
transmembrane protein C6orf70

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_033842.1 RefSeqGene

    Range
    5001..34979
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001278531.2 → NP_001265460.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform 2

    See identical proteins and their annotated locations for NP_001265460.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon and contains another alternate in-frame exon 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)
    AA909435, AK001369, AL354892, DA650477
    Consensus CDS
    CCDS64572.1
    UniProtKB/Swiss-Prot
    Q5T6L9
    Related
    ENSP00000355734.1, ENST00000366772.6
    Conserved Domains (1) summary
    pfam13910
    Location:133 → 214
    DUF4209; Domain of unknown function (DUF4209)

  2. NM_001278532.2 → NP_001265461.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform 3

    See identical proteins and their annotated locations for NP_001265461.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon in the 5' end and uses a downstream start codon compared to variant 1. It encodes isoform 3, which has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AA909435, AK002014, AK294090, AL354892, DA650477
    Consensus CDS
    CCDS64574.1
    UniProtKB/Swiss-Prot
    Q5T6L9
    Related
    ENSP00000375945.4, ENST00000392095.8
    Conserved Domains (1) summary
    pfam13910
    Location:7 → 88
    DUF4209; Domain of unknown function (DUF4209)

  3. NM_001278533.2 → NP_001265462.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform 4

    See identical proteins and their annotated locations for NP_001265462.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AA909435, AL354892, BC044812, DA650477
    Consensus CDS
    CCDS64573.1
    UniProtKB/Swiss-Prot
    Q5T6L9
    Related
    ENSP00000397661.2, ENST00000418781.7
    Conserved Domains (1) summary
    pfam13910
    Location:133 → 214
    DUF4209; Domain of unknown function (DUF4209)

  4. NM_001410957.1 → NP_001397886.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform 5

    Status: REVIEWED

    Source sequence(s)
    AL354892
    Consensus CDS
    CCDS94040.1
    UniProtKB/TrEMBL
    K7ERF7
    Related
    ENSP00000468240.1, ENST00000588451.1

  5. NM_018341.3 → NP_060811.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform 1

    See identical proteins and their annotated locations for NP_060811.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AA909435, AK002014, AK294090, AL354892, DA650477
    Consensus CDS
    CCDS34576.1
    UniProtKB/Swiss-Prot
    B4DFH0, F8WAF1, Q3ZCS8, Q5T6L8, Q5T6L9, Q9NUT5, Q9NVU2
    Related
    ENSP00000355735.3, ENST00000366773.8
    Conserved Domains (1) summary
    pfam13910
    Location:133 → 214
    DUF4209; Domain of unknown function (DUF4209)

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    169751306..169781600
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047419020.1 → XP_047274976.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X5

  2. XM_047419021.1 → XP_047274977.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X5

  3. XM_011535938.4 → XP_011534240.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X1

    See identical proteins and their annotated locations for XP_011534240.1

    Conserved Domains (1) summary
    pfam13910
    Location:133 → 214
    DUF4209; Domain of unknown function (DUF4209)

  4. XM_047419018.1 → XP_047274974.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X2

  5. XM_047419023.1 → XP_047274979.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X6

  6. XM_017011030.2 → XP_016866519.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X4

  7. XM_047419019.1 → XP_047274975.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X3

  8. XM_047419025.1 → XP_047274981.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X8

  9. XM_047419024.1 → XP_047274980.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X7

  10. XM_011535940.3 → XP_011534242.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X5

    See identical proteins and their annotated locations for XP_011534242.1

    UniProtKB/Swiss-Prot
    Q5T6L9
    Conserved Domains (1) summary
    pfam13910
    Location:7 → 88
    DUF4209; Domain of unknown function (DUF4209)

  11. XM_017011031.2 → XP_016866520.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X4

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187552.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    26508..56802
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054328674.1 → XP_054184649.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X5

  2. XM_054328669.1 → XP_054184644.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X1

  3. XM_054328670.1 → XP_054184645.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X2

  4. XM_054328679.1 → XP_054184654.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X6

  5. XM_054328672.1 → XP_054184647.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X4

  6. XM_054328675.1 → XP_054184650.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X9

  7. XM_054328671.1 → XP_054184646.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X3

  8. XM_054328681.1 → XP_054184656.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X8

  9. XM_054328680.1 → XP_054184655.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X7

  10. XM_054328678.1 → XP_054184653.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X5

  11. XM_054328677.1 → XP_054184652.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X5

  12. XM_054328676.1 → XP_054184651.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X5

  13. XM_054328673.1 → XP_054184648.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    171105236..171135403
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054355867.1 → XP_054211842.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X5

  2. XM_054355862.1 → XP_054211837.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X1

  3. XM_054355863.1 → XP_054211838.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X2

  4. XM_054355871.1 → XP_054211846.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X6

  5. XM_054355865.1 → XP_054211840.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X4

  6. XM_054355868.1 → XP_054211843.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X10

  7. XM_054355864.1 → XP_054211839.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X3

  8. XM_054355873.1 → XP_054211848.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X8

  9. XM_054355872.1 → XP_054211847.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X7

  10. XM_054355870.1 → XP_054211845.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X5

  11. XM_054355869.1 → XP_054211844.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X5

  12. XM_054355866.1 → XP_054211841.1  endoplasmic reticulum membrane-associated RNA degradation protein isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5T6L9.1 GenPept UniProtKB/Swiss-Prot:Q5T6L9

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