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

Gene ID: 252969, updated on 5-Mar-2024

Summary

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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; AllianceGenome:HGNC:18956
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
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Genomic context

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See NEIL2 in Genome Data Viewer
Location:
8p23.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (11769710..11787345)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (7952965..7970597, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (11627219..11644854)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene GATA binding protein 4 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:11566565-11567490 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:11567491-11568414 Neighboring gene small nucleolar RNA, H/ACA box 99 Neighboring gene HNF4 motif-containing MPRA enhancer 121 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:11584607-11585590 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:11593264-11593764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27031 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:11594517-11595018 Neighboring gene VISTA enhancer hs2205 Neighboring gene VISTA enhancer hs508 Neighboring gene long intergenic non-protein coding RNA 2905 Neighboring gene uncharacterized LOC124901888 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:11627369-11627869 Neighboring gene uncharacterized LOC105379243 Neighboring gene Sharpr-MPRA regulatory region 11637 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:11657524-11658167 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:11658297-11659039 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:11659040-11659781 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27032 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18941 Neighboring gene SUB1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27033 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18942 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18943 Neighboring gene farnesyl-diphosphate farnesyltransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27035

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. A Low-Activity Polymorphic Variant of Human NEIL2 DNA Glycosylase. Kakhkharova ZI, et al. Int J Mol Sci, 2022 Feb 17. PMID 35216329, Free PMC Article
  2. Dynamics and Conformational Changes in Human NEIL2 DNA Glycosylase Analyzed by Hydrogen/Deuterium Exchange Mass Spectrometry. Zhdanova PV, et al. J Mol Biol, 2022 Jan 30. PMID 34757057
  3. Unique Structural Features of Mammalian NEIL2 DNA Glycosylase Prime Its Activity for Diverse DNA Substrates and Environments. Eckenroth BE, et al. Structure, 2021 Jan 7. PMID 32846144, Free PMC Article
  4. Helicobacter pylori infection downregulates the DNA glycosylase NEIL2, resulting in increased genome damage and inflammation in gastric epithelial cells. Sayed IM, et al. J Biol Chem, 2020 Aug 7. PMID 32518160, Free PMC Article
  5. A variant in a microRNA binding site in NEIL2 3'UTR confers susceptibility to age-related cataracts. Kang L, et al. FASEB J, 2019 Sep. PMID 31253066

See all (66) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Structural and biochemical insights into NEIL2's preference for abasic sites.
    Title: Structural and biochemical insights into NEIL2's preference for abasic sites.
  2. The DNA glycosylase NEIL2 is protective during SARS-CoV-2 infection.
    Title: The DNA glycosylase NEIL2 is protective during SARS-CoV-2 infection.
  3. A Low-Activity Polymorphic Variant of Human NEIL2 DNA Glycosylase.
    Title: A Low-Activity Polymorphic Variant of Human NEIL2 DNA Glycosylase.
  4. Mendelian Randomization Analysis Identified Potential Genes Pleiotropically Associated with Polycystic Ovary Syndrome.
    Title: Mendelian Randomization Analysis Identified Potential Genes Pleiotropically Associated with Polycystic Ovary Syndrome.
  5. Dynamics and Conformational Changes in Human NEIL2 DNA Glycosylase Analyzed by Hydrogen/Deuterium Exchange Mass Spectrometry.
    Title: Dynamics and Conformational Changes in Human NEIL2 DNA Glycosylase Analyzed by Hydrogen/Deuterium Exchange Mass Spectrometry.
  6. Genetic variations in 3'UTRs of SMUG1 and NEIL2 genes modulate breast cancer risk, survival and therapy response.
    Title: Genetic variations in 3'UTRs of SMUG1 and NEIL2 genes modulate breast cancer risk, survival and therapy response.
  7. Unique Structural Features of Mammalian NEIL2 DNA Glycosylase Prime Its Activity for Diverse DNA Substrates and Environments.
    Title: Unique Structural Features of Mammalian NEIL2 DNA Glycosylase Prime Its Activity for Diverse DNA Substrates and Environments.
  8. NEIL1 and NEIL2 Are Recruited as Potential Backup for OGG1 upon OGG1 Depletion or Inhibition by TH5487.
    Title: NEIL1 and NEIL2 Are Recruited as Potential Backup for OGG1 upon OGG1 Depletion or Inhibition by TH5487.
  9. Helicobacter pylori infection downregulates the DNA glycosylase NEIL2, resulting in increased genome damage and inflammation in gastric epithelial cells.
    Title: Helicobacter pylori infection downregulates the DNA glycosylase NEIL2, resulting in increased genome damage and inflammation in gastric epithelial cells.
  10. Requirements for DNA bubble structure for efficient cleavage by helix-two-turn-helix DNA glycosylases.
    Title: Requirements for DNA bubble structure for efficient cleavage by helix-two-turn-helix DNA glycosylases.
Submit: New GeneRIF Correction See all GeneRIFs (40)

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

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC2832, MGC4505, FLJ31644

Gene Ontology Provided by GOA

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

General protein information

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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)

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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_053043.1 RefSeqGene

    Range
    5048..22683
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001135746.3 → NP_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
    B4DFR7, Q7Z3Q7, Q8N842, Q8NG52, Q969S2
    Related
    ENSP00000394023.2, ENST00000436750.7
    Conserved Domains (2) summary
    cd08968
    Location:1 → 185
    MeNeil2_N; N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2)
    cl26942
    Location:155 → 320
    H2TH; Formamidopyrimidine-DNA glycosylase H2TH domain

  2. NM_001135747.3 → NP_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
    Consensus CDS
    CCDS47803.1
    UniProtKB/Swiss-Prot
    Q969S2
    Related
    ENSP00000384070.3, ENST00000403422.7
    Conserved Domains (2) summary
    cl03119
    Location:62 → 124
    FpgNei_N; N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases
    cl26942
    Location:94 → 259
    H2TH; Formamidopyrimidine-DNA glycosylase H2TH domain

  3. NM_001135748.3 → NP_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
    Consensus CDS
    CCDS47802.1
    UniProtKB/Swiss-Prot
    Q969S2
    Related
    ENSP00000435657.1, ENST00000528323.5
    Conserved Domains (2) summary
    pfam06831
    Location:104 → 150
    H2TH; Formamidopyrimidine-DNA glycosylase H2TH domain
    cl03119
    Location:1 → 69
    FpgNei_N; N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases

  4. NM_001349439.2 → NP_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:62 → 124
    FpgNei_N; N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases
    cl26942
    Location:94 → 259
    H2TH; Formamidopyrimidine-DNA glycosylase H2TH domain

  5. NM_001349440.2 → NP_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:62 → 124
    FpgNei_N; N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases
    cl26942
    Location:94 → 259
    H2TH; Formamidopyrimidine-DNA glycosylase H2TH domain

  6. NM_001349441.2 → NP_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:62 → 124
    FpgNei_N; N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases
    cl26942
    Location:94 → 259
    H2TH; Formamidopyrimidine-DNA glycosylase H2TH domain

  7. NM_001349442.2 → NP_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
    UniProtKB/Swiss-Prot
    B4DFR7, Q7Z3Q7, Q8N842, Q8NG52, Q969S2
    Related
    ENSP00000397538.2, ENST00000455213.6
    Conserved Domains (2) summary
    cd08968
    Location:1 → 185
    MeNeil2_N; N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2)
    cl26942
    Location:155 → 320
    H2TH; Formamidopyrimidine-DNA glycosylase H2TH domain

  8. NM_145043.4 → NP_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
    B4DFR7, Q7Z3Q7, Q8N842, Q8NG52, Q969S2
    Related
    ENSP00000284503.6, ENST00000284503.7
    Conserved Domains (2) summary
    cd08968
    Location:1 → 185
    MeNeil2_N; N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2)
    cl26942
    Location:155 → 320
    H2TH; Formamidopyrimidine-DNA glycosylase H2TH domain

RNA

  1. NR_146180.2 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_146181.2 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_146182.2 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: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    11769710..11787345
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654717.1 Reference GRCh38.p14 PATCHES

    Range
    1560751..1578390 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    7952965..7970597 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q969S2.3 GenPept UniProtKB/Swiss-Prot:Q969S2

Gene LinkOut

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