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NEIL2 nei like DNA glycosylase 2 [ Homo sapiens (human) ]

Gene ID: 252969, updated on 15-Apr-2019

Summary

Official Symbol
NEIL2provided by HGNC
Official Full Name
nei like DNA glycosylase 2provided by HGNC
Primary source
HGNC:HGNC:18956
See related
Ensembl:ENSG00000154328 MIM:608933
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
NEH2; NEI2
Summary
This gene encodes a member of the Fpg/Nei family of DNA glycosylases. These glycosylases initiate the first step in base excision repair by cleaving oxidatively damaged bases and introducing a DNA strand break via their abasic site lyase activity. This enzyme is primarily associated with DNA repair during transcription and acts prefentially on cytosine-derived lesions, particularly 5-hydroxyuracil and 5-hydroxycytosine. It contains an N-terminal catalytic domain, a hinge region, and a C-terminal DNA-binding domain with helix-two-turn-helix and zinc finger motifs. This enzyme interacts with the X-ray cross complementing factor 1 scaffold protein as part of a multi-protein DNA repair complex. A pseudogene of this gene has been identified. [provided by RefSeq, Mar 2017]
Expression
Ubiquitous expression in testis (RPKM 14.3), brain (RPKM 9.4) and 24 other tissues See more
Orthologs

Genomic context

See NEIL2 in Genome Data Viewer
Location:
8p23.1
Exon count:
5
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 8 NC_000008.11 (11769625..11787355)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (11627172..11644854)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene GATA binding protein 4 Neighboring gene VISTA enhancer hs508 Neighboring gene chromosome 8 open reading frame 49 Neighboring gene uncharacterized LOC105379243 Neighboring gene SUB1 homolog, transcriptional regulator pseudogene 1 Neighboring gene farnesyl-diphosphate farnesyltransferase 1

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

NHGRI GWAS Catalog

Description
A genome-wide association study of behavioral disinhibition.
NHGRI GWA Catalog
Duffy-null-associated low neutrophil counts influence HIV-1 susceptibility in high-risk South African black women.
NHGRI GWA Catalog

Pathways from BioSystems

  • APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway, organism-specific biosystem (from REACTOME)
    APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway, organism-specific biosystemNEIL1 and NEIL2 have a dual DNA glycosylase and beta/delta lyase activity. The AP (apurinic/apyrimidinic) site-directed lyase activity of NEIL1 and NEIL2 is their major physiological role, as they ca...
  • 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...
  • 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

Clone Names

  • MGC2832, MGC4505, FLJ31644

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA N-glycosylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA N-glycosylase activity TAS
Traceable Author Statement
more info
 
DNA-(apurinic or apyrimidinic site) endonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
class I DNA-(apurinic or apyrimidinic site) endonuclease activity IEA
Inferred from Electronic Annotation
more info
 
damaged DNA binding IEA
Inferred from Electronic Annotation
more info
 
microtubule binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
base-excision repair IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
depyrimidination TAS
Traceable Author Statement
more info
 
nucleotide-excision repair IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
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
 
spindle microtubule IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
endonuclease 8-like 2
Names
DNA glycosylase/AP lyase Neil2
DNA-(apurinic or apyrimidinic site) lyase Neil2
nei endonuclease VIII-like 2
nei homolog 2
nei-like protein 2
NP_001129218.1
NP_001129219.1
NP_001129220.1
NP_001336368.1
NP_001336369.1
NP_001336370.1
NP_001336371.1
NP_659480.1

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_053043.1 RefSeqGene

    Range
    4963..22693
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001135746.2NP_001129218.1  endonuclease 8-like 2 isoform a

    See identical proteins and their annotated locations for NP_001129218.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 8 encode the same isoform (a).
    Source sequence(s)
    AB079070, AC069185, AK056206, DA207321, DB452586
    Consensus CDS
    CCDS5984.1
    UniProtKB/Swiss-Prot
    Q969S2
    UniProtKB/TrEMBL
    A0A024R361
    Related
    ENSP00000394023.2, ENST00000436750.7
    Conserved Domains (2) summary
    cd08968
    Location:1185
    MeNeil2_N; N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2)
    cl26942
    Location:155320
    H2TH; Formamidopyrimidine-DNA glycosylase H2TH domain
  2. NM_001135747.2NP_001129219.1  endonuclease 8-like 2 isoform b

    See identical proteins and their annotated locations for NP_001129219.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks an alternate exon in the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus compared to isoform a. Variants 3 and 5-7 encode the same isoform (b).
    Source sequence(s)
    AB079070, AC069185, AK097389, DB452586
    Consensus CDS
    CCDS47803.1
    UniProtKB/Swiss-Prot
    Q969S2
    Related
    ENSP00000384070.3, ENST00000403422.7
    Conserved Domains (2) summary
    cl03119
    Location:62124
    FpgNei_N; N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases
    cl26942
    Location:94259
    H2TH; Formamidopyrimidine-DNA glycosylase H2TH domain
  3. NM_001135748.2NP_001129220.1  endonuclease 8-like 2 isoform c

    See identical proteins and their annotated locations for NP_001129220.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and lacks an alternate exon compared to variant 1. The encoded isoform (c) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AB079070, AC069185, AK294224, DB452586
    Consensus CDS
    CCDS47802.1
    UniProtKB/Swiss-Prot
    Q969S2
    Related
    ENSP00000435657.1, ENST00000528323.5
    Conserved Domains (2) summary
    pfam06831
    Location:104150
    H2TH; Formamidopyrimidine-DNA glycosylase H2TH domain
    cl03119
    Location:169
    FpgNei_N; N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases
  4. NM_001349439.1NP_001336368.1  endonuclease 8-like 2 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus compared to isoform a. Variants 3 and 5-7 encode the same isoform (b).
    Source sequence(s)
    AC069185
    Consensus CDS
    CCDS47803.1
    Conserved Domains (2) summary
    cl03119
    Location:62124
    FpgNei_N; N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases
    cl26942
    Location:94259
    H2TH; Formamidopyrimidine-DNA glycosylase H2TH domain
  5. NM_001349440.1NP_001336369.1  endonuclease 8-like 2 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus compared to isoform a. Variants 3 and 5-7 encode the same isoform (b).
    Source sequence(s)
    AC069185
    Consensus CDS
    CCDS47803.1
    Conserved Domains (2) summary
    cl03119
    Location:62124
    FpgNei_N; N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases
    cl26942
    Location:94259
    H2TH; Formamidopyrimidine-DNA glycosylase H2TH domain
  6. NM_001349441.1NP_001336370.1  endonuclease 8-like 2 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks an alternate exon in the 5' UTR and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus compared to isoform a. Variants 3 and 5-7 encode the same isoform (b).
    Source sequence(s)
    AC069185
    Consensus CDS
    CCDS47803.1
    Conserved Domains (2) summary
    cl03119
    Location:62124
    FpgNei_N; N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases
    cl26942
    Location:94259
    H2TH; Formamidopyrimidine-DNA glycosylase H2TH domain
  7. NM_001349442.1NP_001336371.1  endonuclease 8-like 2 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 8 encode the same isoform (a).
    Source sequence(s)
    AC069185
    Consensus CDS
    CCDS5984.1
    Related
    ENSP00000397538.2, ENST00000455213.6
    Conserved Domains (2) summary
    cd08968
    Location:1185
    MeNeil2_N; N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2)
    cl26942
    Location:155320
    H2TH; Formamidopyrimidine-DNA glycosylase H2TH domain
  8. NM_145043.4NP_659480.1  endonuclease 8-like 2 isoform a

    See identical proteins and their annotated locations for NP_659480.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1, 2, and 8 encode the same isoform (a).
    Source sequence(s)
    AB079070, AC069185, AK056206, DA205315, DB452586
    Consensus CDS
    CCDS5984.1
    UniProtKB/Swiss-Prot
    Q969S2
    UniProtKB/TrEMBL
    A0A024R361
    Related
    ENSP00000284503.6, ENST00000284503.7
    Conserved Domains (2) summary
    cd08968
    Location:1185
    MeNeil2_N; N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2)
    cl26942
    Location:155320
    H2TH; Formamidopyrimidine-DNA glycosylase H2TH domain

RNA

  1. NR_146180.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) uses two alternate splice sites compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC069185
  2. NR_146181.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) uses an alternate 5' and 3' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC069185
  3. NR_146182.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (11) uses an alternate splice site and lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC069185, DA037395

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_000008.11 Reference GRCh38.p12 Primary Assembly

    Range
    11769625..11787355
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 PATCHES

Genomic

  1. NW_018654717.1 Reference GRCh38.p12 PATCHES

    Range
    1560741..1578475 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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