Dnph1 (2'-deoxynucleoside 5'-phosphate N-hydrolase 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Dnph1 (2'-deoxynucleoside 5'-phosphate N-hydrolase 1) Rattus norvegicus
Analyze
Symbol: Dnph1
Name: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
RGD ID: 620382
Description: 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); INTERACTS WITH 1,3-dinitrobenzene; 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: c-Myc-responsive protein Rcl; C6orf108; chromosome 6 open reading frame 108; deoxyribonucleoside 5'-monophosphate N-glycosidase; Nucleoside 2-deoxyribosyltransferase domain containing protein RGD620382; putative c-Myc-responsive; Rcl; RGD620382
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2914,481,296 - 14,484,034 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl914,481,066 - 14,484,022 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx923,064,957 - 23,067,689 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0928,127,963 - 28,130,702 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0926,428,337 - 26,431,069 (-)NCBIRnor_WKY
Rnor_6.0916,845,764 - 16,848,514 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl916,845,525 - 16,848,503 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0915,747,108 - 15,749,858 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.499,865,096 - 9,867,833 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.199,862,418 - 9,865,155 (-)NCBI
Celera912,229,311 - 12,232,048 (-)NCBICelera
Cytogenetic Map9q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA)
nucleus  (IBA,IDA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Induction of rcl, a novel growth-related gene by coptidis rhizoma in rat H4IIE cells. Chan CP, etal., Life Sci 2002 Feb 22;70(14):1691-9.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. The c-Myc target gene Rcl (C6orf108) encodes a novel enzyme, deoxynucleoside 5'-monophosphate N-glycosidase. Ghiorghi YK, etal., J Biol Chem. 2007 Mar 16;282(11):8150-6. Epub 2007 Jan 18.
4. Identification of putative c-Myc-responsive genes: characterization of rcl, a novel growth-related gene. Lewis BC, etal., Mol Cell Biol 1997 Sep;17(9):4967-78.
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. GOA pipeline RGD automated data pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16189514   PMID:19056867   PMID:19720067   PMID:19822152   PMID:20962348   PMID:21492153   PMID:23376485   PMID:23385460   PMID:23533145   PMID:25108359   PMID:25416956  


Genomics

Comparative Map Data
Dnph1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2914,481,296 - 14,484,034 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl914,481,066 - 14,484,022 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx923,064,957 - 23,067,689 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0928,127,963 - 28,130,702 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0926,428,337 - 26,431,069 (-)NCBIRnor_WKY
Rnor_6.0916,845,764 - 16,848,514 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl916,845,525 - 16,848,503 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0915,747,108 - 15,749,858 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.499,865,096 - 9,867,833 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.199,862,418 - 9,865,155 (-)NCBI
Celera912,229,311 - 12,232,048 (-)NCBICelera
Cytogenetic Map9q12NCBI
DNPH1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38643,225,629 - 43,229,481 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl643,225,629 - 43,229,481 (-)EnsemblGRCh38hg38GRCh38
GRCh37643,193,367 - 43,197,219 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36643,301,345 - 43,305,189 (-)NCBINCBI36Build 36hg18NCBI36
Celera644,745,576 - 44,749,420 (-)NCBICelera
Cytogenetic Map6p21.1NCBI
HuRef642,910,063 - 42,913,907 (-)NCBIHuRef
CHM1_1643,196,302 - 43,200,146 (-)NCBICHM1_1
T2T-CHM13v2.0643,054,425 - 43,058,274 (-)NCBIT2T-CHM13v2.0
Dnph1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391746,807,715 - 46,810,544 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1746,807,637 - 46,810,550 (+)EnsemblGRCm39 Ensembl
GRCm381746,496,789 - 46,499,618 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1746,496,711 - 46,499,624 (+)EnsemblGRCm38mm10GRCm38
MGSCv371746,633,738 - 46,636,567 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361745,959,989 - 45,962,263 (+)NCBIMGSCv36mm8
Celera1749,932,506 - 49,935,335 (+)NCBICelera
Cytogenetic Map17CNCBI
Dnph1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554379,145,737 - 9,147,387 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554379,145,737 - 9,147,388 (-)NCBIChiLan1.0ChiLan1.0
DNPH1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1644,111,148 - 44,111,975 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0642,817,392 - 42,821,257 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
DNPH1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11211,715,215 - 11,718,622 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1211,715,271 - 11,718,717 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1211,741,713 - 11,745,559 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01212,197,074 - 12,200,947 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1212,197,609 - 12,201,457 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11211,724,395 - 11,728,261 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01211,808,785 - 11,812,597 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01211,903,616 - 11,907,485 (-)NCBIUU_Cfam_GSD_1.0
Dnph1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494647,217,364 - 47,219,582 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647616,740,581 - 16,742,866 (+)EnsemblSpeTri2.0
SpeTri2.0NW_00493647616,740,643 - 16,742,831 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DNPH1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl738,263,822 - 38,266,887 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1738,263,819 - 38,267,361 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2743,764,179 - 43,767,693 (-)NCBISscrofa10.2Sscrofa10.2susScr3
DNPH1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11728,923,202 - 28,927,227 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604443,287,459 - 43,291,712 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Dnph1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475416,333,054 - 16,334,882 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475416,333,021 - 16,334,882 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Dnph1
8 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:112
Count of miRNA genes:93
Interacting mature miRNAs:100
Transcripts:ENSRNOT00000024815
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9510982642921101Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9795472022071169Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)9895256053952560Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9895256053952560Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)91353377042791750Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 24 33 33 5 33 55 20 36 2
Low 19 24 8 14 8 8 11 19 15 5 9 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000024815   ⟹   ENSRNOP00000024815
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl914,481,066 - 14,484,022 (-)Ensembl
Rnor_6.0 Ensembl916,845,525 - 16,848,503 (-)Ensembl
RefSeq Acc Id: NM_133525   ⟹   NP_598209
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2914,481,296 - 14,484,034 (-)NCBI
Rnor_6.0916,845,764 - 16,848,514 (-)NCBI
Rnor_5.0915,747,108 - 15,749,858 (-)NCBI
RGSC_v3.499,865,096 - 9,867,833 (-)RGD
Celera912,229,311 - 12,232,048 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_598209 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB95314 (Get FASTA)   NCBI Sequence Viewer  
  EDM18826 (Get FASTA)   NCBI Sequence Viewer  
  O35820 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_598209   ⟸   NM_133525
- UniProtKB: O35820 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000024815   ⟸   ENSRNOT00000024815

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O35820-F1-model_v2 AlphaFold O35820 1-163 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13696519
Promoter ID:EPDNEW_R7044
Type:multiple initiation site
Name:Dnph1_1
Description:2'-deoxynucleoside 5'-phosphate N-hydrolase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0916,848,518 - 16,848,578EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620382 AgrOrtholog
BioCyc Gene G2FUF-28228 BioCyc
Ensembl Genes ENSRNOG00000018397 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000024815 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000024815 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro DNPH1 UniProtKB/Swiss-Prot
  Nucleoside_deoxyribTrfase UniProtKB/Swiss-Prot
KEGG Report rno:171047 UniProtKB/Swiss-Prot
NCBI Gene 171047 ENTREZGENE
Pfam Nuc_deoxyrib_tr UniProtKB/Swiss-Prot
PhenoGen Dnph1 PhenoGen
UniProt DNPH1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-12-10 Dnph1  2'-deoxynucleoside 5'-phosphate N-hydrolase 1  RGD620382  Nucleoside 2-deoxyribosyltransferase domain containing protein RGD620382  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-11-17 RGD620382  Nucleoside 2-deoxyribosyltransferase domain containing protein RGD620382  C6orf108  chromosome 6 open reading frame 108  Symbol and Name updated 1299863 APPROVED
2004-09-10 C6orf108  chromosome 6 open reading frame 108  Rcl  putative c-Myc-responsive  Symbol and Name updated 1299863 APPROVED
2002-08-07 Rcl  putative c-Myc-responsive      Symbol and Name status set to provisional 70820 PROVISIONAL