Nt5dc3 (5'-nucleotidase domain containing 3) - Rat Genome Database

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Gene: Nt5dc3 (5'-nucleotidase domain containing 3) Rattus norvegicus
Analyze
Symbol: Nt5dc3
Name: 5'-nucleotidase domain containing 3
RGD ID: 1593358
Description: Predicted to enable 5'-nucleotidase activity. Predicted to be located in cytosol. Predicted to be part of receptor complex. Orthologous to human NT5DC3 (5'-nucleotidase domain containing 3); INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: 5'-nucleotidase domain-containing protein 3; LOC691922; similar to CG1814-PA, isoform A
RGD Orthologs
Human
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8723,078,078 - 23,134,899 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl723,078,078 - 23,134,899 (+)EnsemblGRCr8
mRatBN7.2721,190,554 - 21,247,374 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl721,190,554 - 21,247,374 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx723,165,366 - 23,221,904 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0725,328,078 - 25,384,616 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0725,105,145 - 25,161,685 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0727,309,963 - 27,365,687 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl727,309,966 - 27,363,394 (+)Ensemblrn6Rnor6.0
Rnor_5.0727,430,564 - 27,484,279 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4723,409,376 - 23,464,050 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera718,370,488 - 18,423,913 (+)NCBICelera
Cytogenetic Map7q13NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytosol  (IEA)
mitochondrion  (ISO)
receptor complex  (IEA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15827139   PMID:18614015   PMID:23382219   PMID:34800366  


Genomics

Comparative Map Data
Nt5dc3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8723,078,078 - 23,134,899 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl723,078,078 - 23,134,899 (+)EnsemblGRCr8
mRatBN7.2721,190,554 - 21,247,374 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl721,190,554 - 21,247,374 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx723,165,366 - 23,221,904 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0725,328,078 - 25,384,616 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0725,105,145 - 25,161,685 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0727,309,963 - 27,365,687 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl727,309,966 - 27,363,394 (+)Ensemblrn6Rnor6.0
Rnor_5.0727,430,564 - 27,484,279 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4723,409,376 - 23,464,050 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera718,370,488 - 18,423,913 (+)NCBICelera
Cytogenetic Map7q13NCBI
NT5DC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812103,746,315 - 103,841,234 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl12103,770,453 - 103,841,260 (-)Ensemblhg38GRCh38
GRCh3712104,166,088 - 104,235,012 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3612102,690,218 - 102,759,105 (-)NCBIBuild 36Build 36hg18NCBI36
Celera12103,830,372 - 103,899,271 (-)NCBICelera
Cytogenetic Map12q23.3NCBI
HuRef12101,226,196 - 101,295,114 (-)NCBIHuRef
CHM1_112104,132,386 - 104,201,230 (-)NCBICHM1_1
T2T-CHM13v2.012103,707,632 - 103,803,005 (-)NCBIT2T-CHM13v2.0
Nt5dc3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540538,536,748 - 38,577,924 (-)Ensembl
ChiLan1.0NW_00495540538,539,512 - 38,560,450 (-)NCBIChiLan1.0ChiLan1.0
NT5DC3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v210111,835,733 - 111,904,790 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan112111,832,130 - 111,901,181 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v012101,354,773 - 101,418,386 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.112104,748,793 - 104,813,214 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12104,748,793 - 104,813,640 (-)EnsemblpanPan2panpan1.1
NT5DC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11542,333,179 - 42,423,216 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1542,331,664 - 42,414,626 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1542,703,190 - 42,750,924 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01542,990,553 - 43,038,766 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1542,990,553 - 43,078,238 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11542,256,460 - 42,304,974 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01542,354,889 - 42,403,721 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01542,626,345 - 42,674,440 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Nt5dc3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494517,517,819 - 17,659,393 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649210,639,571 - 10,672,056 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493649210,528,865 - 10,611,832 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NT5DC3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl580,644,245 - 80,692,941 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1580,625,669 - 80,692,481 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2584,105,579 - 84,227,628 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NT5DC3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11198,963,956 - 99,029,917 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1198,965,202 - 99,029,845 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666037145,963,355 - 146,027,554 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nt5dc3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247504,813,374 - 4,863,432 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247504,813,553 - 4,864,629 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Nt5dc3
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11165,899,604 - 165,956,876 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Nt5dc3
689 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:44
Count of miRNA genes:39
Interacting mature miRNAs:44
Transcripts:ENSRNOT00000031871
Prediction methods: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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)72154197751639954Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7123748937Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7721609752216097Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)71051708662346019Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7170952746709527Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)71011291660150541Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7946087754460877Rat
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7129716167Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)72154197751639954Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134650782Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)72154197735707405Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7132612984Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7166965846669658Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)71011291699900612Rat
2290372Gluco33Glucose level QTL 332.71blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)7131777942Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)71104117804Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)71509236116977875Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7132612984Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)72154197786817926Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)71049882055498820Rat
61369Mcs2Mammary carcinoma susceptibility QTL 23.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72092049437412865Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71746044762460447Rat
70207Niddm31Non-insulin dependent diabetes mellitus QTL 313.9blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)72005723265057232Rat

Markers in Region
RH137003  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2721,188,998 - 21,189,180 (+)MAPPERmRatBN7.2
Rnor_6.0727,308,411 - 27,308,592NCBIRnor6.0
Rnor_5.0727,429,009 - 27,429,190UniSTSRnor5.0
RGSC_v3.4723,407,821 - 23,408,002UniSTSRGSC3.4
Celera718,368,933 - 18,369,114UniSTS
RH 3.4 Map7120.5UniSTS
Cytogenetic Map7q13UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000031871   ⟹   ENSRNOP00000036388
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl723,078,078 - 23,134,899 (+)Ensembl
mRatBN7.2 Ensembl721,190,554 - 21,247,374 (+)Ensembl
Rnor_6.0 Ensembl727,309,966 - 27,363,394 (+)Ensembl
RefSeq Acc Id: NM_001134887   ⟹   NP_001128359
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8723,078,078 - 23,134,899 (+)NCBI
mRatBN7.2721,190,554 - 21,247,374 (+)NCBI
Rnor_6.0727,309,966 - 27,363,394 (+)NCBI
Rnor_5.0727,430,564 - 27,484,279 (+)NCBI
RGSC_v3.4723,409,376 - 23,464,050 (+)RGD
Celera718,370,488 - 18,423,913 (+)RGD
Sequence:
RefSeq Acc Id: XR_005486729
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8723,078,078 - 23,119,944 (+)NCBI
mRatBN7.2721,190,557 - 21,232,422 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001128359 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM17047 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000036388
  ENSRNOP00000036388.6
RefSeq Acc Id: NP_001128359   ⟸   NM_001134887
- UniProtKB: D3ZAI6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000036388   ⟸   ENSRNOT00000031871

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZAI6-F1-model_v2 AlphaFold D3ZAI6 1-546 view protein structure

Transcriptome

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

Promoters
RGD ID:13695117
Promoter ID:EPDNEW_R5642
Type:multiple initiation site
Name:Nt5dc3_1
Description:5'-nucleotidase domain containing 3
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_6.0727,309,994 - 27,310,054EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1593358 AgrOrtholog
BioCyc Gene G2FUF-34543 BioCyc
BioCyc Pathway PWY-5695 [inosine 5'-phosphate degradation] BioCyc
  PWY-6608 [guanosine nucleotides degradation III] BioCyc
  PWY-7185 [UTP and CTP dephosphorylation I] BioCyc
  SALVADEHYPOX-PWY [adenosine nucleotides degradation II] BioCyc
BioCyc Pathway Image PWY-5695 BioCyc
  PWY-6608 BioCyc
  PWY-7185 BioCyc
  SALVADEHYPOX-PWY BioCyc
Ensembl Genes ENSRNOG00000026793 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000031871 ENTREZGENE
  ENSRNOT00000031871.7 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.1000 UniProtKB/TrEMBL
InterPro HAD-like_dom UniProtKB/TrEMBL
  HAD-like_sf UniProtKB/TrEMBL
  HAD-SF_hydro_IG_5-nucl UniProtKB/TrEMBL
  Pur_nucleotidase UniProtKB/TrEMBL
KEGG Report rno:691922 UniProtKB/TrEMBL
NCBI Gene 691922 ENTREZGENE
PANTHER 5'-NUCLEOTIDASE DOMAIN-CONTAINING PROTEIN 3 UniProtKB/TrEMBL
  HAD-SF_hydro_IG_5-nucl UniProtKB/TrEMBL
Pfam 5_nucleotid UniProtKB/TrEMBL
PhenoGen Nt5dc3 PhenoGen
PIRSF Purine_5'-nucleotidase UniProtKB/TrEMBL
RatGTEx ENSRNOG00000026793 RatGTEx
Superfamily-SCOP HAD-like_dom UniProtKB/TrEMBL
UniProt D3ZAI6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-17 Nt5dc3   5'-nucleotidase domain containing 3  LOC687698  similar to CG1814-PA, isoform A  Data merged from RGD:1583009 1643240 APPROVED
2008-09-08 Nt5dc3   5'-nucleotidase domain containing 3  LOC691922  similar to CG1814-PA, isoform A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC691922  similar to CG1814-PA, isoform A      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC687698  similar to CG1814-PA, isoform A      Symbol and Name status set to provisional 70820 PROVISIONAL