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    NT5DC1 5'-nucleotidase domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 221294, updated on 27-Nov-2024

    Summary

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    Official Symbol
    NT5DC1provided by HGNC
    Official Full Name
    5'-nucleotidase domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:21556
    See related
    Ensembl:ENSG00000178425 AllianceGenome:HGNC:21556
    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
    LP2642; NT5C2L1; C6orf200
    Summary
    While the exact function of the protein encoded by this gene is not known, it belongs to the 5'(3')-deoxyribonucleotidase family. [provided by RefSeq, May 2010]
    Expression
    Ubiquitous expression in thyroid (RPKM 16.7), prostate (RPKM 14.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NT5DC1 in Genome Data Viewer
    Location:
    6q22.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (116100853..116249497)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (117284838..117433477)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (116422016..116570660)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901385 Neighboring gene NANOG hESC enhancer GRCh37_chr6:116235207-116235708 Neighboring gene fyn related Src family tyrosine kinase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24976 Neighboring gene triosephosphate isomerase 1 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24977 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24978 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_88040 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24979 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:116412309-116412554 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:116421676-116422198 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:116422199-116422719 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24980 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_88050 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_88070 Neighboring gene Sharpr-MPRA regulatory region 2872 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_88113 Neighboring gene MPRA-validated peak6050 silencer Neighboring gene collagen type X alpha 1 chain Neighboring gene NIP7 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24981 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24982 Neighboring gene ribosomal protein S5 pseudogene Neighboring gene TSPY like 4 Neighboring gene RPS5 pseudogene 1 Neighboring gene dermatan sulfate epimerase

    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. Single-nucleotide polymorphisms in the TSPYL-4 and NT5DC1 genes are associated with susceptibility to chronic obstructive pulmonary disease. Guo Y, et al. Mol Med Rep, 2012 Sep. PMID 22736055
    2. Weighted gene co-expression network analysis identifies specific modules and hub genes related to subsyndromal symptomatic depression. Geng R, et al. World J Biol Psychiatry, 2020 Feb. PMID 30489189
    3. Seven new loci associated with age-related macular degeneration. Fritsche LG, et al. Nat Genet, 2013 Apr. PMID 23455636, Free PMC Article
    4. GWAS of dental caries patterns in the permanent dentition. Shaffer JR, et al. J Dent Res, 2013 Jan. PMID 23064961, Free PMC Article
    5. Candidate gene/loci studies in cleft lip/palate and dental anomalies finds novel susceptibility genes for clefts. Vieira AR, et al. Genet Med, 2008 Sep. PMID 18978678, Free PMC Article

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Weighted gene co-expression network analysis identifies specific modules and hub genes related to subsyndromal symptomatic depression.
      Title: Weighted gene co-expression network analysis identifies specific modules and hub genes related to subsyndromal symptomatic depression.
    2. The rs1052443 C allele of NT5DC1 was associated with a protective effect against the deterioration of pulmonary function.
      Title: Single-nucleotide polymorphisms in the TSPYL-4 and NT5DC1 genes are associated with susceptibility to chronic obstructive pulmonary disease.
    3. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    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
    GWAS of dental caries patterns in the permanent dentition.
    EBI GWAS Catalog
    Seven new loci associated with age-related macular degeneration.
    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

    • MGC24302, MGC131837

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 5'-nucleotidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    5'-nucleotidase domain-containing protein 1
    Names
    5'-nucleotidase, cytosolic II-like 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.

    Genomic

    1. NG_021351.2 RefSeqGene

      Range
      5002..153646
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_152729.3 → NP_689942.2  5'-nucleotidase domain-containing protein 1

      See identical proteins and their annotated locations for NP_689942.2

      Status: REVIEWED

      Source sequence(s)
      AL050331, AL121963, KF458258
      Consensus CDS
      CCDS5104.1
      UniProtKB/Swiss-Prot
      B2RND9, B3KR35, Q5TFE4, Q6XYD5
      UniProtKB/TrEMBL
      A8K2Z3
      Related
      ENSP00000326858.3, ENST00000319550.9
      Conserved Domains (1) summary
      cl17687
      Location:11 → 337
      5_nucleotid; 5' nucleotidase family

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      116100853..116249497
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006715378.4 → XP_006715441.1  5'-nucleotidase domain-containing protein 1 isoform X1

      Conserved Domains (1) summary
      cl17687
      Location:11 → 299
      5_nucleotid; 5' nucleotidase family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      117284838..117433477
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354520.1 → XP_054210495.1  5'-nucleotidase domain-containing protein 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5TFE4.1 GenPept UniProtKB/Swiss-Prot:Q5TFE4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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