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    NTHL1 nth like DNA glycosylase 1 [ Homo sapiens (human) ]

    Gene ID: 4913, updated on 15-Apr-2019

    Summary

    Official Symbol
    NTHL1provided by HGNC
    Official Full Name
    nth like DNA glycosylase 1provided by HGNC
    Primary source
    HGNC:HGNC:8028
    See related
    Ensembl:ENSG00000065057 MIM:602656
    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
    FAP3; NTH1; OCTS3; hNTH1
    Summary
    The protein encoded by this gene is a DNA N-glycosylase of the endonuclease III family. Like a similar protein in E. coli, the encoded protein has DNA glycosylase activity on DNA substrates containing oxidized pyrimidine residues and has apurinic/apyrimidinic lyase activity. [provided by RefSeq, Oct 2008]
    Expression
    Ubiquitous expression in spleen (RPKM 7.3), ovary (RPKM 6.4) and 25 other tissues See more
    Orthologs

    Genomic context

    See NTHL1 in Genome Data Viewer
    Location:
    16p13.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 16 NC_000016.10 (2039815..2047872, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (2089816..2097931, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene SLC9A3 regulator 2 Neighboring gene neuropeptide W Neighboring gene TSC complex subunit 2 Neighboring gene uncharacterized LOC105371049 Neighboring gene microRNA 1225 Neighboring gene polycystin 1, transient receptor potential channel interacting

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Familial adenomatous polyposis 3
    MedGen: C4225157 OMIM: 616415 GeneReviews: Not available
    Compare labs

    NHGRI GWAS Catalog

    Description
    Joint influence of small-effect genetic variants on human longevity.
    NHGRI GWA Catalog

    Pathways from BioSystems

    • Base Excision Repair, organism-specific biosystem (from REACTOME)
      Base Excision Repair, organism-specific biosystemOf the three major pathways involved in the repair of nucleotide damage in DNA, base excision repair (BER) involves the greatest number of individual enzymatic activities. This is the consequence of ...
    • Base excision repair, organism-specific biosystem (from KEGG)
      Base excision repair, organism-specific biosystemBase excision repair (BER) is the predominant DNA damage repair pathway for the processing of small base lesions, derived from oxidation and alkylation damages. BER is normally defined as DNA repair ...
    • Base excision repair, conserved biosystem (from KEGG)
      Base excision repair, conserved biosystemBase excision repair (BER) is the predominant DNA damage repair pathway for the processing of small base lesions, derived from oxidation and alkylation damages. BER is normally defined as DNA repair ...
    • Base-Excision Repair, AP Site Formation, organism-specific biosystem (from REACTOME)
      Base-Excision Repair, AP Site Formation, organism-specific biosystemBase excision repair is initiated by DNA glycosylases that hydrolytically cleave the base-deoxyribose glycosyl bond of a damaged nucleotide residue, releasing the damaged base (Lindahl and Wood 1999,...
    • Cleavage of the damaged pyrimidine, organism-specific biosystem (from REACTOME)
      Cleavage of the damaged pyrimidine, organism-specific biosystemDamaged pyrimidines are cleaved by pyrimide-specific glycosylases (Lindahl and Wood 1999).
    • DNA Repair, organism-specific biosystem (from REACTOME)
      DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
    • Depyrimidination, organism-specific biosystem (from REACTOME)
      Depyrimidination, organism-specific biosystemDepyrimidination of a damaged nucleotide in DNA is mediated by a pyrimidine-specific DNA glycosylase. The glycosylase cleaves the N-C1' glycosidic bond between the damaged DNA base and the deoxyribos...
    • Displacement of DNA glycosylase by APEX1, organism-specific biosystem (from REACTOME)
      Displacement of DNA glycosylase by APEX1, organism-specific biosystemFollowing cleavage of the damaged base, DNA glycosylase is displaced by APEX1, an AP endonuclease (Parikh et al. 1998).
    • Recognition and association of DNA glycosylase with site containing an affected pyrimidine, organism-specific biosystem (from REACTOME)
      Recognition and association of DNA glycosylase with site containing an affected pyrimidine, organism-specific biosystemBase excision repair is initiated by a DNA glycosylase which first recognizes and removes a damaged or incorrect (e.g. mismatched) base (Sokhansanj et al. 2002).
    • Resolution of Abasic Sites (AP sites), organism-specific biosystem (from REACTOME)
      Resolution of Abasic Sites (AP sites), organism-specific biosystemResolution of AP sites can occur through the single nucleotide replacement pathway or through the multiple nucleotide patch replacement pathway, also known as the long-patch base excision repair (BER...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    base-excision repair, AP site formation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    base-excision repair, AP site formation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    depyrimidination TAS
    Traceable Author Statement
    more info
     
    nucleotide-excision repair, DNA incision, 5'-to lesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nucleotide-excision repair, DNA incision, 5'-to lesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    mitochondrion IEA
    Inferred from Electronic Annotation
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    endonuclease III-like protein 1
    Names
    DNA glycoslyase/AP lyase
    DNA glycosylase/AP lyase
    bifunctional DNA N-glycoslyase/DNA-(apurinic or apyrimidinic site) lyase
    bifunctional DNA N-glycosylase/DNA-(apurinic or apyrimidinic site) lyase
    nth endonuclease III-like 1
    NP_001305123.1
    NP_002519.2
    XP_016878742.1

    NCBI Reference Sequences (RefSeq)

    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_008412.1 RefSeqGene

      Range
      5033..13047
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001318193.2NP_001305122.2  endonuclease III-like protein 1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the 5' coding region, compared to variant 1. It encodes isoform 2, which lacks an internal segment and is shorter, compared to isoform 1.
      Source sequence(s)
      BC003014, BE900738, U79718
      Related
      ENSP00000498821.1, ENST00000651583.1
      Conserved Domains (1) summary
      cl27658
      Location:117245
      HHH; Helix-hairpin-helix motif
    2. NM_001318194.1NP_001305123.1  endonuclease III-like protein 1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and 5' coding region and initiates translation at an alternate start codon, compared to variant 1. It encodes isoform 3, which has a distinct N-terminus, and is shorter, compared to isoform 1.
      Source sequence(s)
      BC003014, BG468617, HY094895
      UniProtKB/Swiss-Prot
      P78549
      Related
      ENSP00000498290.1, ENST00000651522.1
      Conserved Domains (3) summary
      smart00525
      Location:171191
      FES; iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3)
      smart00478
      Location:20169
      ENDO3c; endonuclease III
      COG0177
      Location:11192
      Nth; Endonuclease III [Replication, recombination and repair]
    3. NM_002528.7NP_002519.2  endonuclease III-like protein 1 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      U79718, U81285
      Consensus CDS
      CCDS10457.1
      Related
      ENSP00000219066.1, ENST00000219066.5
      Conserved Domains (1) summary
      COG0177
      Location:121302
      Nth; Endonuclease III [Replication, recombination and repair]

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p12 Primary Assembly

      Range
      2039815..2047872 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017023253.1XP_016878742.1  endonuclease III-like protein 1 isoform X1

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