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    NEIL2 nei endonuclease VIII-like 2 (E. coli) [ Homo sapiens ]

    Gene ID: 252969, updated on 4-Feb-2012
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    Summary

    Official Symbol
    NEIL2provided by HGNC
    Official Full Name
    nei endonuclease VIII-like 2 (E. coli)provided by HGNC
    Primary source
    HGNC:18956
    See related
    Ensembl:ENSG00000154328; HPRD:16406; MIM:608933; Vega:OTTHUMG00000090753
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NEH2; NEI2
    Summary
    NEIL2 belongs to a class of DNA glycosylases homologous to the bacterial Fpg/Nei family. These glycosylases initiate the first step in base excision repair by cleaving bases damaged by reactive oxygen species and introducing a DNA strand break via the associated lyase reaction (Bandaru et al., 2002 [PubMed 12509226])[supplied by OMIM, Mar 2008]
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    Genomic context

    Location :
    8p23.1
    Sequence :
    Chromosome: 8; NC_000008.10 (11627172..11644854)
    See NEIL2 in Epigenomics, MapViewer

    Chromosome 8 - NC_000008.10Genomic Context describing neighboring genes Neighboring gene GATA binding protein 4 Neighboring gene chromosome 8 open reading frame 49 Neighboring gene SUB1 homolog (S. cerevisiae) pseudogene 1 Neighboring gene farnesyl-diphosphate farnesyltransferase 1

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    Genomic regions, transcripts, and products

    Go to nucleotideGraphics FASTA GenBank

    Go to reference sequence details
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    Bibliography

    Related articles in PubMed

    1. Duffy-null-associated low neutrophil counts influence HIV-1 susceptibility in high-risk South African black women. Ramsuran V, et al. Clin Infect Dis, 2011 May. PMID 21507922.
    2. MicroRNA-related genetic variations as predictors for risk of second primary tumor and/or recurrence in patients with early-stage head and neck cancer. Zhang X, et al. Carcinogenesis, 2010 Dec. PMID 20819778.
    3. Variation within DNA repair pathway genes and risk of multiple sclerosis. Briggs FB, et al. Am J Epidemiol, 2010 Jul 15. PMID 20522537.
    4. Comprehensive screen of genetic variation in DNA repair pathway genes and postmenopausal breast cancer risk. Monsees GM, et al. Breast Cancer Res Treat, 2011 Jan. PMID 20496165.
    5. Inactivation of NEIL2 DNA glycosylase by pyridoxal phosphate reveals a loop important for substrate binding. Grin IR, et al. Biochem Biophys Res Commun, 2010 Mar 26. PMID 20175991.

    See all (31) citations in PubMed

    See citations in PubMed for homologs of this gene provided by HomoloGene

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Variation within DNA repair pathway genes and risk of multiple sclerosis.
    2. the beta2/beta3 loop where Lys50 is located in NEIL2 is important for DNA binding, presumably lies next to a phosphate-binding site, and may represent a target for regulation of the enzyme activity.
      Title: Inactivation of NEIL2 DNA glycosylase by pyridoxal phosphate reveals a loop important for substrate binding.
    3. in vivo variability in NEIL2 expression in humans identifies SNPs in the NEIL2 promoter region that have functional effects.
      Title: Single nucleotide polymorphisms 5' upstream the coding region of the NEIL2 gene influence gene transcription levels and alter levels of genetic damage.
    4. NEIL2, but not NEIL1, polymorphisms may have a role in risk and progression of squamous cell carcinomas of the oral cavity and oropharynx
      Title: Functional variants of the NEIL1 and NEIL2 genes and risk and progression of squamous cell carcinoma of the oral cavity and oropharynx.
    5. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Functional variants of the NEIL1 and NEIL2 genes and risk and progression of squamous cell carcinoma of the oral cavity and oropharynx.
    6. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: MicroRNA-related genetic variations as predictors for risk of second primary tumor and/or recurrence in patients with early-stage head and neck cancer.
    7. YB-1 thus appears to have a novel regulatory role in NEIL2-mediated repair under oxidative stress.
      Title: Stimulation of NEIL2-mediated oxidized base excision repair via YB-1 interaction during oxidative stress.
    8. results show that the NEIL2-initiated repair of 5-hydroxyuracil (5-OHU) requires polynucleotide kinase (PNK)
      Title: NEIL2-initiated, APE-independent repair of oxidized bases in DNA: Evidence for a repair complex in human cells.
    9. A novel missense variant C367A and several other mutations were found in familial colorectal cancer DNA suggesting a limited role for this gene in the devlopment of CRC.
      Title: Evaluation of NTHL1, NEIL1, NEIL2, MPG, TDG, UNG and SMUG1 genes in familial colorectal cancer predisposition.
    10. NEIL2 is involved in global genome repair mainly for removing oxidative products of cytosine.
      Title: Identification and characterization of a novel human DNA glycosylase for repair of cytosine-derived lesions.
    Submit: New GeneRIF Correction See all (15)
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    Phenotypes

    Review eQTL and phenotype association data in this region using PheGenI

    Duffy-null-associated low neutrophil counts influence HIV-1 susceptibility in high-risk South African black women.

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    Interactions

    Products Interactant Other Gene Complex Source Pubs Description
    Q969S2 Q09472 EP300    HPRD  PubMed  
    BioGRID:128946 BioGRID:113164 UBC    BioGRID  PubMed Affinity Capture-Western 
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    General gene information

    Markers

    Genotypes

    Homology

    Pathways from BioSystems

    • 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 ...

    Clone Names

    • MGC2832, MGC4505, FLJ31644

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA-(apurinic or apyrimidinic site) lyase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    damaged DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    hydrolase activity, hydrolyzing N-glycosyl compounds IEA
    Inferred from Electronic Annotation
    more info
    		  
    lyase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    base-excision repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    nucleotide-excision repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
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    General protein information

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

    mRNA and Protein(s)

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

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform.
      Source sequence(s)
      AB079070, AC069185, AK056206, DA207321, DB452586
      Consensus CDS
      CCDS5984.1
      UniProtKB/Swiss-Prot
      Q969S2
      Related
      ENSP00000394023, OTTHUMP00000229180, ENST00000436750, OTTHUMT00000383127
      Conserved Domains (3) summary
      pfam06831
      Location:220 – 266
      Blast Score: 152
      H2TH; Formamidopyrimidine-DNA glycosylase H2TH domain
      cd08968
      Location:1 – 185
      Blast Score: 503
      MeNeil2_N; N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2)
      PRK01103
      Location:219 – 321
      Blast Score: 193
      PRK01103; formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated

    2. NM_001135747.1 → NP_001129219.1  endonuclease 8-like 2 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, uses an alternate splice site at the end of an exon, and lacks an alternate exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AB079070, AC069185, AK097389, DB452586
      Consensus CDS
      CCDS47803.1
      UniProtKB/Swiss-Prot
      Q969S2
      Related
      ENSP00000384070, OTTHUMP00000229498, ENST00000403422, OTTHUMT00000383663
      Conserved Domains (3) summary
      pfam06831
      Location:159 – 205
      Blast Score: 153
      H2TH; Formamidopyrimidine-DNA glycosylase H2TH domain
      cd08968
      Location:62 – 124
      Blast Score: 322
      MeNeil2_N; N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2)
      PRK01103
      Location:158 – 260
      Blast Score: 194
      PRK01103; formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated

    3. NM_001135748.1 → NP_001129220.1  endonuclease 8-like 2 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and lacks an alternate exon compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a.
      Source sequence(s)
      AB079070, AC069185, AK294224, DB452586
      Consensus CDS
      CCDS47802.1
      UniProtKB/TrEMBL
      B4DFR7
      UniProtKB/Swiss-Prot
      Q969S2
      Related
      ENSP00000435657, OTTHUMP00000229179, ENST00000528323, OTTHUMT00000383126
      Conserved Domains (3) summary
      pfam06831
      Location:104 – 150
      Blast Score: 154
      H2TH; Formamidopyrimidine-DNA glycosylase H2TH domain
      PRK01103
      Location:103 – 205
      Blast Score: 193
      PRK01103; formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
      cl03119
      Location:1 – 69
      Blast Score: 244
      FpgNei_N; N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases

    4. NM_145043.2 → NP_659480.1  endonuclease 8-like 2 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 2 both encode the same isoform.
      Source sequence(s)
      AB079070, AC069185, AK056206, DA205315, DB452586
      Consensus CDS
      CCDS5984.1
      UniProtKB/Swiss-Prot
      Q969S2
      Related
      ENSP00000284503, OTTHUMP00000116006, ENST00000284503, OTTHUMT00000207583
      Conserved Domains (3) summary
      pfam06831
      Location:220 – 266
      Blast Score: 152
      H2TH; Formamidopyrimidine-DNA glycosylase H2TH domain
      cd08968
      Location:1 – 185
      Blast Score: 503
      MeNeil2_N; N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2)
      PRK01103
      Location:219 – 321
      Blast Score: 193
      PRK01103; formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated

    RefSeqs of Annotated Genomes: Build 37.3

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

    Reference GRCh37.p5 Primary Assembly

    Genomic

    1. NC_000008.10 Reference GRCh37.p5 Primary Assembly

      Range
      11627172..11644854
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000140.1 Alternate HuRef

      Range
      10558132..10575813
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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    Related Sequences

    Nucleotide Protein
    Heading Accession and Version
    genomic AC069185.7 (93663..111261) None
    genomic AY306127.1 AAP45052.1
    genomic CH471157.1 EAW65623.1
      EAW65624.1
      EAW65625.1
      EAW65626.1
    mRNA AB079070.1 BAC06478.1
    mRNA AK056206.1 BAB71120.1
    mRNA AK097389.1 BAC05030.1
    mRNA AK225837.1 None
    mRNA AK294224.1 BAG57528.1
    mRNA BC013952.2 AAH13952.1
    mRNA BC013964.2 AAH13964.1
    mRNA BC045822.1 AAH45822.1
    mRNA BX537529.1 CAD97774.1
    mRNA DA205315.1 None
    mRNA DA207321.1 None
    mRNA DB452586.1 None
    other-genetic AM393587.1 CAL38464.1
    other-genetic EU832351.1 ACE87608.1
    other-genetic EU832436.1 ACE86921.1
    Protein Accession Links
    GenePept Link UniProtKB Link
    Q3ZCR7 GenPept UniProtKB/TrEMBL:Q3ZCR7
    Q969S2.3 GenPept UniProtKB/Swiss-Prot:Q969S2
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    Additional Links

    Additional Links

    Gene LinkOut

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

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