Dnph1 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Dnph1provided by RGD
Official Full Name: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1provided by RGD
Primary source: RGD:620382
See related: EnsemblRapid:ENSRNOG00000018397 AllianceGenome:RGD:620382
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Rcl; C6orf108; RGD620382
Summary: Enables deoxyribonucleoside 5'-monophosphate N-glycosidase activity and protein homodimerization activity. Involved in allantoin metabolic process; dGMP catabolic process; and positive regulation of cell growth. Located in nucleus. Orthologous to human DNPH1 (2'-deoxynucleoside 5'-phosphate N-hydrolase 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Liver (RPKM 59.0), Spleen (RPKM 40.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 9q12

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	9	NC_086027.1 (21978894..21981631, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	9	NC_051344.1 (14481296..14484034, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	9	NC_005108.4 (16845764..16848514, complement)

Chromosome 9 - NC_086027.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The crystal structure of oncoprotein Rcl bound to thymidine analogue 6-RADP-1-C6PA confirms and more precisely reveals the organization of its nucleotide-binding site.
Title: Structure of the oncoprotein Rcl bound to three nucleotide analogues.
analysis of human deoxynucleotide N-hydrolase Rcl and rat gene c6orf108
Title: Probing the active site of the deoxynucleotide N-hydrolase Rcl encoded by the rat gene c6orf108.
ligand-induced stabilization of the dimer structure of the enzyme
Title: Structural characterization of the mammalian deoxynucleotide N-hydrolase Rcl and its stabilizing interactions with two inhibitors.
RCL is a symmetric homodimer, with each monomer consisting of a five-stranded parallel beta-sheet sandwiched between five alpha-helices. Three of the helices form the dimer interface, allowing two monomers to pack side by side.
Title: Solution structure of RCL, a novel 2'-deoxyribonucleoside 5'-monophosphate N-glycosidase.
C6orf108 encodes a novel enzyme, deoxynucleoside 5'-monophosphate N-glycosidase
Title: The c-Myc target gene Rcl (C6orf108) encodes a novel enzyme, deoxynucleoside 5'-monophosphate N-glycosidase.
rcl as an important antiapoptotic protein mediating sensitivity to Coptidis Rhizoma induction in cancer cells
Title: Induction of rcl, a novel growth-related gene by coptidis rhizoma in rat H4IIE cells.

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables 5-hydroxymethyl-dUMP N-hydrolase activity	IBA Inferred from Biological aspect of Ancestor more info
enables 5-hydroxymethyl-dUMP N-hydrolase activity	IDA Inferred from Direct Assay more info	PubMed
enables 5-hydroxymethyl-dUMP N-hydrolase activity	ISO Inferred from Sequence Orthology more info
enables 5-hydroxymethyl-dUMP N-hydrolase activity	ISS Inferred from Sequence or Structural Similarity more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in allantoin metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in dGMP catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in deoxyribonucleoside monophosphate catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in deoxyribonucleoside monophosphate catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in deoxyribonucleoside monophosphate catabolic process	ISO Inferred from Sequence Orthology more info
involved_in epithelial cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in nucleoside salvage	ISO Inferred from Sequence Orthology more info
involved_in nucleoside salvage	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell growth	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: 5-hydroxymethyl-dUMP N-hydrolase

Names: Nucleoside 2-deoxyribosyltransferase domain containing protein RGD620382; c-Myc-responsive protein Rcl; deoxyribonucleoside 5'-monophosphate N-glycosidase; putative c-Myc-responsive

NP_598209.1

EC 3.2.2.-

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.