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

Gene ID: 84656, updated on 23-Nov-2023

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
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Genomic context

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See GLYR1 in Genome Data Viewer
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 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 IBA
Inferred from Biological aspect of Ancestor
more info
  
enables methylated histone binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables nucleosome binding IDA
Inferred from Direct Assay
more info
 PubMed 
NOT enables oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
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 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

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