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    GLYR1 glyoxylate reductase 1 homolog [ Homo sapiens (human) ]

    Gene ID: 84656, updated on 11-Apr-2024

    Summary

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    Official Symbol
    GLYR1provided by HGNC
    Official Full Name
    glyoxylate reductase 1 homologprovided by HGNC
    Primary source
    HGNC:HGNC:24434
    See related
    Ensembl:ENSG00000140632 MIM:610660; AllianceGenome:HGNC:24434
    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
    NP60; NPAC; hNDF; BM045; HIBDL; N-PAC
    Summary
    Enables DNA binding activity; methylated histone binding activity; and nucleosome binding activity. Involved in positive regulation of histone acetylation and positive regulation of transcription by RNA polymerase II. Located in cytosol and nucleoplasm. Part of nucleosome. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in kidney (RPKM 24.0), brain (RPKM 23.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    16p13.3
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (4803203..4847288, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (4832757..4876778, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (4853204..4897289, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene septin 12 Neighboring gene small integral membrane protein 22 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:4852142-4852642 Neighboring gene Sharpr-MPRA regulatory region 4562 Neighboring gene rogdi atypical leucine zipper Neighboring gene uncharacterized LOC124903638 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10346 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:4897448-4898290 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:4901871-4903070 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:4908973-4910172 Neighboring gene ubinuclein 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:4920799-4920984 Neighboring gene MPRA-validated peak2474 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4935135-4935635 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4945259-4946104 Neighboring gene uncharacterized LOC124903637 Neighboring gene periplakin

    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. Nuclear protein NP60 regulates p38 MAPK activity. Fu J, et al. J Cell Sci, 2006 Jan 1. PMID 16352664
    2. Downregulation of GLYR1 contributes to microsatellite instability colorectal cancer by targeting p21 via the p38MAPK and PI3K/AKT pathways. Hu Z, et al. J Exp Clin Cancer Res, 2020 May 5. PMID 32370786, Free PMC Article
    3. A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex. Marabelli C, et al. Cell Rep, 2019 Apr 9. PMID 30970244
    4. NDF, a nucleosome-destabilizing factor that facilitates transcription through nucleosomes. Fei J, et al. Genes Dev, 2018 May 1. PMID 29759984, Free PMC Article
    5. LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation. Fang R, et al. Mol Cell, 2013 Feb 7. PMID 23260659, Free PMC Article

    See all (81) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables NAD binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables NADP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables chromatin-protein adaptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables methylated histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables nucleosome binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables nucleosome binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in transcription elongation-coupled chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transcription elongation-coupled chromatin remodeling IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in transcription initiation-coupled chromatin remodeling IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    part_of nucleosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    cytokine-like nuclear factor N-PAC
    Names
    3-hydroxyisobutyrate dehydrogenase-like protein
    cytokine-like nuclear factor n-pac
    nuclear protein 60 kDa
    nuclear protein 60kDa
    nuclear protein NP60
    nuclear protein of 60 kDa
    nucleosome-destabilizing factor
    putative oxidoreductase GLYR1

    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.

    mRNA and Protein(s)

    1. NM_001308096.2 → NP_001295025.1  cytokine-like nuclear factor N-PAC isoform 2

      See identical proteins and their annotated locations for NP_001295025.1

      Status: VALIDATED

      Source sequence(s)
      AC020663, AF217521, AF326966, HY130375
      Consensus CDS
      CCDS81945.1
      UniProtKB/TrEMBL
      K7EMM8
      Related
      ENSP00000468328.1, ENST00000591451.5
      Conserved Domains (3) summary
      cd05836
      Location:6 → 90
      N_Pac_NP60; The PWWP domain is an essential part of the cytokine-like nuclear factor n-pac protein, or NP60, which enhances the activity of MAP2K4 and MAP2K6 kinases to phosphorylate p38-alpha. In a variety of cell lines, NP60 has been shown to localize to the ...
      COG2084
      Location:268 → 545
      MmsB; 3-hydroxyisobutyrate dehydrogenase or related beta-hydroxyacid dehydrogenase [Lipid transport and metabolism]
      pfam15376
      Location:110 → 173
      DUF4603; Domain of unknown function (DUF4603)

    2. NM_001324096.2 → NP_001311025.2  cytokine-like nuclear factor N-PAC isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC020663, KF456151
      UniProtKB/TrEMBL
      K7EMM8
      Conserved Domains (2) summary
      cd05836
      Location:6 → 90
      N_Pac_NP60; The PWWP domain is an essential part of the cytokine-like nuclear factor n-pac protein, or NP60, which enhances the activity of MAP2K4 and MAP2K6 kinases to phosphorylate p38-alpha. In a variety of cell lines, NP60 has been shown to localize to the ...
      COG2084
      Location:187 → 464
      MmsB; 3-hydroxyisobutyrate dehydrogenase or related beta-hydroxyacid dehydrogenase [Lipid transport and metabolism]

    3. NM_001324097.2 → NP_001311026.2  cytokine-like nuclear factor N-PAC isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC020663, AK296842
      Consensus CDS
      CCDS92098.1
      UniProtKB/TrEMBL
      K7EMM8
      Related
      ENSP00000390276.4, ENST00000436648.9
      Conserved Domains (3) summary
      cd05836
      Location:6 → 90
      N_Pac_NP60; The PWWP domain is an essential part of the cytokine-like nuclear factor n-pac protein, or NP60, which enhances the activity of MAP2K4 and MAP2K6 kinases to phosphorylate p38-alpha. In a variety of cell lines, NP60 has been shown to localize to the ...
      COG2084
      Location:187 → 470
      MmsB; 3-hydroxyisobutyrate dehydrogenase or related beta-hydroxyacid dehydrogenase [Lipid transport and metabolism]
      cl21454
      Location:129 → 221
      NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

    4. NM_001324098.2 → NP_001311027.2  cytokine-like nuclear factor N-PAC isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC020663, KF456151
      UniProtKB/TrEMBL
      K7EMM8
      Related
      ENSP00000466570.1, ENST00000589389.5
      Conserved Domains (3) summary
      cd05836
      Location:6 → 90
      N_Pac_NP60; The PWWP domain is an essential part of the cytokine-like nuclear factor n-pac protein, or NP60, which enhances the activity of MAP2K4 and MAP2K6 kinases to phosphorylate p38-alpha. In a variety of cell lines, NP60 has been shown to localize to the ...
      COG2084
      Location:251 → 534
      MmsB; 3-hydroxyisobutyrate dehydrogenase or related beta-hydroxyacid dehydrogenase [Lipid transport and metabolism]
      pfam15376
      Location:110 → 173
      DUF4603; Domain of unknown function (DUF4603)

    5. NM_032569.4 → NP_115958.2  cytokine-like nuclear factor N-PAC isoform 1

      See identical proteins and their annotated locations for NP_115958.2

      Status: VALIDATED

      Source sequence(s)
      AF244907, CB529066, CK430984, CR933687, DB492328
      Consensus CDS
      CCDS10524.1
      UniProtKB/Swiss-Prot
      B4DL47, C9JJ40, C9JJ60, Q49A26, Q5U632, Q6P1Q2, Q6V3W7, Q9BTI1, Q9BXK2
      UniProtKB/TrEMBL
      K7EMM8
      Related
      ENSP00000322716.6, ENST00000321919.14
      Conserved Domains (4) summary
      cd05836
      Location:6 → 90
      N_Pac_NP60; The PWWP domain is an essential part of the cytokine-like nuclear factor n-pac protein, or NP60, which enhances the activity of MAP2K4 and MAP2K6 kinases to phosphorylate p38-alpha. In a variety of cell lines, NP60 has been shown to localize to the ...
      COG2084
      Location:268 → 551
      MmsB; 3-hydroxyisobutyrate dehydrogenase or related beta-hydroxyacid dehydrogenase [Lipid transport and metabolism]
      pfam15376
      Location:110 → 173
      DUF4603; Domain of unknown function (DUF4603)
      cl21454
      Location:210 → 302
      NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

    RNA

    1. NR_136695.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC020663, BC047223, BC064940
      Related
      ENST00000588732.5

    2. NR_136696.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC020663, KF456151

    3. NR_136697.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC020663, KF456151

    4. NR_136698.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC020663, KF456151

    5. NR_136699.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC020663, KF456151

    6. NR_136700.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC020663, KF456151

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      4803203..4847288 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      4832757..4876778 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q49A26.4 GenPept UniProtKB/Swiss-Prot:Q49A26

    Gene LinkOut

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

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