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IGDCC4 immunoglobulin superfamily DCC subclass member 4 [ Homo sapiens (human) ]

Gene ID: 57722, updated on 10-Dec-2024

Summary

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Official Symbol
IGDCC4provided by HGNC
Official Full Name
immunoglobulin superfamily DCC subclass member 4provided by HGNC
Primary source
HGNC:HGNC:13770
See related
Ensembl:ENSG00000103742 MIM:616810; AllianceGenome:HGNC:13770
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
NOPE; DDM36
Summary
Predicted to be involved in cell-cell adhesion. Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Dec 2024]
Expression
Broad expression in ovary (RPKM 6.3), placenta (RPKM 5.2) and 17 other tissues See more
Orthologs
mouse all
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Genomic context

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See IGDCC4 in Genome Data Viewer
Location:
15q22.31
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (65381484..65422947, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (63190848..63232315, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (65673822..65715285, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6555 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9595 Neighboring gene RNA, U5B small nuclear 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:65618173-65618716 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:65624736-65625408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:65626438-65627016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:65627017-65627595 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:65628175-65628752 Neighboring gene immunoglobulin superfamily DCC subclass member 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:65647365-65647867 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:65647868-65648370 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:65648371-65648873 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65655395-65656260 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65659717-65660580 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65660581-65661444 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:65677106-65677717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9598 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65702937-65703594 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65707062-65707929 Neighboring gene uncharacterized LOC124903510 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:65710136-65710346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9599 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9600 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:65715563-65716097 Neighboring gene dipeptidyl peptidase 8 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65809274-65809827 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9601 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:65821125-65821625 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6556 Neighboring gene MPRA-validated peak2372 silencer Neighboring gene 3-hydroxyacyl-CoA dehydratase 3 Neighboring gene RNA, U6 small nuclear 19, pseudogene

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. First evaluation of Neighbor of Punc E11 (NOPE) as a novel marker in human hepatocellular carcinoma. Zweerink S, et al. Cancer Biomark, 2021. PMID 32986656
  2. Expression of Neighbor of Punc E11 (NOPE) in early stage esophageal adenocarcinoma is associated with reduced survival. Kütting F, et al. Sci Rep, 2022 Mar 4. PMID 35246597, Free PMC Article
  3. Neighbor of Punc E11, a novel oncofetal marker for hepatocellular carcinoma. Marquardt JU, et al. Int J Cancer, 2011 May 15. PMID 20658536
  4. Cloning and expression of nope, a new mouse gene of the immunoglobulin superfamily related to guidance receptors. Salbaum JM, et al. Genomics, 2000 Feb 15. PMID 10708514
  5. Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Aug 31. PMID 10997877

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Expression of Neighbor of Punc E11 (NOPE) in early stage esophageal adenocarcinoma is associated with reduced survival.
    Title: Expression of Neighbor of Punc E11 (NOPE) in early stage esophageal adenocarcinoma is associated with reduced survival.
  2. First evaluation of Neighbor of Punc E11 (NOPE) as a novel marker in human hepatocellular carcinoma.
    Title: First evaluation of Neighbor of Punc E11 (NOPE) as a novel marker in human hepatocellular carcinoma.
  3. identified Nope as a novel oncofetal surface marker for murine and human HCC. Nope is specifically expressed by epithelial tumor cells but not in preneoplastic stages and is a promising marker
    Title: Neighbor of Punc E11, a novel oncofetal marker for hepatocellular carcinoma.
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

EBI GWAS Catalog

Description
Genome-wide association study of hematological and biochemical traits in a Japanese population.
EBI GWAS Catalog

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

  • FLJ42051, KIAA1628

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in cell-cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
immunoglobulin superfamily DCC subclass member 4
Names
likely ortholog of mouse neighbor of Punc E11
neighbor of Punc E11

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_020962.3 → NP_066013.1  immunoglobulin superfamily DCC subclass member 4 precursor

    See identical proteins and their annotated locations for NP_066013.1

    Status: VALIDATED

    Source sequence(s)
    AB052622, AC105129
    Consensus CDS
    CCDS10206.1
    UniProtKB/Swiss-Prot
    Q8TDY8, Q9HCE4
    Related
    ENSP00000319623.3, ENST00000352385.3
    Conserved Domains (6) summary
    smart00408
    Location:156 → 218
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:149 → 230
    IG_like; Immunoglobulin like
    cd00063
    Location:850 → 942
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam07679
    Location:335 → 422
    I-set; Immunoglobulin I-set domain
    pfam00041
    Location:430 → 515
    fn3; Fibronectin type III domain
    cl11960
    Location:350 → 422
    Ig; Immunoglobulin 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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    65381484..65422947 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011521846.4 → XP_011520148.1  immunoglobulin superfamily DCC subclass member 4 isoform X5

    Conserved Domains (6) summary
    smart00408
    Location:156 → 218
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:149 → 230
    IG_like; Immunoglobulin like
    cd00063
    Location:851 → 943
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam07679
    Location:335 → 422
    I-set; Immunoglobulin I-set domain
    pfam00041
    Location:430 → 515
    fn3; Fibronectin type III domain
    cl11960
    Location:350 → 422
    Ig; Immunoglobulin domain

  2. XM_047432908.1 → XP_047288864.1  immunoglobulin superfamily DCC subclass member 4 isoform X2

  3. XM_047432907.1 → XP_047288863.1  immunoglobulin superfamily DCC subclass member 4 isoform X1

  4. XM_017022448.3 → XP_016877937.1  immunoglobulin superfamily DCC subclass member 4 isoform X3

  5. XM_011521845.4 → XP_011520147.1  immunoglobulin superfamily DCC subclass member 4 isoform X4

    Conserved Domains (6) summary
    smart00408
    Location:169 → 231
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:162 → 243
    IG_like; Immunoglobulin like
    cd00063
    Location:863 → 955
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam07679
    Location:348 → 435
    I-set; Immunoglobulin I-set domain
    pfam00041
    Location:443 → 528
    fn3; Fibronectin type III domain
    cl11960
    Location:363 → 435
    Ig; Immunoglobulin domain

  6. XM_017022449.2 → XP_016877938.1  immunoglobulin superfamily DCC subclass member 4 isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    63190848..63232315 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054378546.1 → XP_054234521.1  immunoglobulin superfamily DCC subclass member 4 isoform X5

  2. XM_054378543.1 → XP_054234518.1  immunoglobulin superfamily DCC subclass member 4 isoform X2

  3. XM_054378542.1 → XP_054234517.1  immunoglobulin superfamily DCC subclass member 4 isoform X1

  4. XM_054378544.1 → XP_054234519.1  immunoglobulin superfamily DCC subclass member 4 isoform X3

  5. XM_054378545.1 → XP_054234520.1  immunoglobulin superfamily DCC subclass member 4 isoform X4

  6. XM_054378547.1 → XP_054234522.1  immunoglobulin superfamily DCC subclass member 4 isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TDY8.1 GenPept UniProtKB/Swiss-Prot:Q8TDY8

Gene LinkOut

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