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

    Gene ID: 57722, updated on 27-Nov-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, Nov 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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