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

Summary

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

Location:: 16p13.3

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (4803203..4847288, complement)
110	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_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Downregulation of GLYR1 contributes to microsatellite instability colorectal cancer by targeting p21 via the p38MAPK and PI3K/AKT pathways.
Title: Downregulation of GLYR1 contributes to microsatellite instability colorectal cancer by targeting p21 via the p38MAPK and PI3K/AKT pathways.
While LSD1/CoREST forms a nucleosome docking platform at silenced gene promoters, LSD2/NPAC is a multifunctional enzyme complex with flexible linkers, tailored for rapid chromatin modification, in conjunction with the advance of the RNA polymerase on actively transcribed genes.
Title: A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex.

Submit: New GeneRIF Correction

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D20S544E (e-PCR)
- UniSTS:43298

SHGC-61126 (e-PCR)
- UniSTS:3120

RH70097 (e-PCR)
- UniSTS:86721

RH44934 (e-PCR)
- UniSTS:87777

SHGC-37555 (e-PCR)
- UniSTS:7144

MARC_17251-17252:1024677488:1 (e-PCR)
- UniSTS:268268

MARC_17251-17252:1032365658:1 (e-PCR)
- UniSTS:268268

Homology

Homologs of the GLYR1 gene: The GLYR1 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, A.thaliana, rice, and frog.
Orthologs from Annotation Pipeline: 465 organisms have orthologs with human gene GLYR1
Orthologs

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 histone binding	IDA Inferred from Direct Assay more info	PubMed
enables methylated histone binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in positive regulation of histone acetylation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
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)

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/Swiss-Prot

Q49A26

UniProtKB/TrEMBL

Q9NZ78

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

Status: VALIDATED

Source sequence(s)

AC020663, KF456151

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]
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

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

Status: VALIDATED

Source sequence(s)

AC020663, KF456151

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)
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

Q49A26, Q9BXK2

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

NR_136695.2 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC020663, BC047223, BC064940

Related

ENST00000588732.5
NR_136696.2 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC020663, KF456151
NR_136697.2 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC020663, KF456151
NR_136698.2 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC020663, KF456151
NR_136699.2 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC020663, KF456151
NR_136700.2 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC020663, KF456151