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

Gene ID: 4913, updated on 2-Oct-2018

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; Vega:OTTHUMG00000128744
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 Jun 15 11:32:44 2016

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_001305122.1
NP_001305123.1
NP_002519.1
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
    4998..13052
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001318193.1NP_001305122.1  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, HY094895
    UniProtKB/Swiss-Prot
    P78549
    Related
    ENSP00000455267.1, OTTHUMP00000255475, ENST00000566380.5, OTTHUMT00000434459
    Conserved Domains (2) summary
    smart00525
    Location:232252
    FES; iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3)
    smart00478
    Location:106230
    ENDO3c; endonuclease III
  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
    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_002528.6NP_002519.1  endonuclease III-like protein 1 isoform 1

    See identical proteins and their annotated locations for NP_002519.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    BC003014, HY057336, HY094895, U79718
    Consensus CDS
    CCDS10457.1
    UniProtKB/Swiss-Prot
    P78549
    UniProtKB/TrEMBL
    E5KTI5
    Related
    ENSP00000219066.1, OTTHUMP00000158939, ENST00000219066.5, OTTHUMT00000250656
    Conserved Domains (3) summary
    smart00525
    Location:289309
    FES; iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3)
    smart00478
    Location:138287
    ENDO3c; endonuclease III
    COG0177
    Location:129310
    Nth; Endonuclease III [Replication, recombination and repair]

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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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