Nt5dc1 (5'-nucleotidase domain containing 1) - Rat Genome Database

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Gene: Nt5dc1 (5'-nucleotidase domain containing 1) Rattus norvegicus
Analyze
Symbol: Nt5dc1
Name: 5'-nucleotidase domain containing 1
RGD ID: 1305214
Description: Predicted to have 5'-nucleotidase activity. Predicted to be involved in dephosphorylation. Orthologous to human NT5DC1 (5'-nucleotidase domain containing 1); INTERACTS WITH (S)-nicotine; bisphenol A; endosulfan.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 5'-nucleotidase domain-containing protein 1; 5'-nucleotidase domain-containing protein 1-like; 5'-nucleotidase, cytosolic II-like 1; LOC102554902; LOC294456; Nt5c2l1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22038,105,677 - 38,208,613 (-)NCBI
Rnor_6.0 Ensembl2041,106,991 - 41,209,728 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02041,106,990 - 41,209,765 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02042,836,806 - 42,938,666 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42038,646,201 - 38,750,613 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12038,670,228 - 38,776,528 (-)NCBI
Celera2038,888,068 - 38,989,368 (-)NCBICelera
Cytogenetic Map20q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

References

Additional References at PubMed
PMID:12477932  


Genomics

Comparative Map Data
Nt5dc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22038,105,677 - 38,208,613 (-)NCBI
Rnor_6.0 Ensembl2041,106,991 - 41,209,728 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02041,106,990 - 41,209,765 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02042,836,806 - 42,938,666 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42038,646,201 - 38,750,613 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12038,670,228 - 38,776,528 (-)NCBI
Celera2038,888,068 - 38,989,368 (-)NCBICelera
Cytogenetic Map20q12NCBI
NT5DC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6116,100,851 - 116,249,497 (+)EnsemblGRCh38hg38GRCh38
GRCh386116,100,833 - 116,249,497 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh376116,422,016 - 116,570,660 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366116,528,692 - 116,673,546 (+)NCBINCBI36hg18NCBI36
Build 346116,528,691 - 116,673,545NCBI
Celera6117,165,022 - 117,309,890 (+)NCBI
Cytogenetic Map6q22.1NCBI
HuRef6114,002,198 - 114,147,046 (+)NCBIHuRef
CHM1_16116,685,819 - 116,830,746 (+)NCBICHM1_1
Nt5dc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391034,179,605 - 34,294,585 (-)NCBIGRCm39mm39
GRCm39 Ensembl1034,164,284 - 34,294,548 (-)Ensembl
GRCm381034,303,609 - 34,418,589 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1034,288,288 - 34,418,552 (-)EnsemblGRCm38mm10GRCm38
MGSCv371034,023,418 - 34,138,334 (-)NCBIGRCm37mm9NCBIm37
MGSCv361033,993,225 - 34,107,944 (-)NCBImm8
Celera1035,213,268 - 35,327,093 (-)NCBICelera
Cytogenetic Map10B1NCBI
Nt5dc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955526568,307 - 604,941 (-)NCBIChiLan1.0ChiLan1.0
NT5DC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16118,049,363 - 118,194,017 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v06113,903,473 - 114,051,784 (+)NCBIMhudiblu_PPA_v0panPan3
NT5DC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11271,790,973 - 71,909,109 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1271,791,748 - 71,907,498 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1271,550,833 - 71,670,015 (+)NCBI
ROS_Cfam_1.01272,672,270 - 72,791,171 (+)NCBI
UMICH_Zoey_3.11272,024,246 - 72,143,173 (+)NCBI
UNSW_CanFamBas_1.01271,866,027 - 71,984,731 (+)NCBI
UU_Cfam_GSD_1.01272,254,898 - 72,373,702 (+)NCBI
LOC101970611
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946107,080,662 - 107,116,124 (+)NCBI
SpeTri2.0NW_004936824805,647 - 841,113 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NT5DC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl181,746,022 - 81,881,113 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1181,745,918 - 81,880,691 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2191,861,465 - 91,997,370 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NT5DC1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11357,568,061 - 57,715,702 (-)NCBI
ChlSab1.1 Ensembl1357,569,744 - 57,715,604 (-)Ensembl
Vero_WHO_p1.0NW_02366604029,889,313 - 30,038,021 (-)NCBI
Nt5dc1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248562,246,730 - 2,389,020 (-)NCBI

Position Markers
RH133024  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22038,163,353 - 38,163,570 (+)MAPPER
Rnor_6.02041,164,532 - 41,164,748NCBIRnor6.0
Rnor_5.02042,893,619 - 42,893,835UniSTSRnor5.0
Celera2038,944,144 - 38,944,360UniSTS
RH 3.4 Map20405.55UniSTS
Cytogenetic Map20q12UniSTS
RH94871  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22038,188,033 - 38,188,329 (+)MAPPER
Rnor_6.02041,189,210 - 41,189,505NCBIRnor6.0
Rnor_5.02042,918,112 - 42,918,407UniSTSRnor5.0
RGSC_v3.42038,730,059 - 38,730,354UniSTSRGSC3.4
Celera2038,968,837 - 38,969,132UniSTS
RH 3.4 Map20408.35UniSTS
Cytogenetic Map20q12UniSTS
BE106510  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22038,193,210 - 38,193,402 (+)MAPPER
Rnor_6.02041,194,387 - 41,194,578NCBIRnor6.0
Rnor_5.02042,923,289 - 42,923,480UniSTSRnor5.0
RGSC_v3.42038,735,236 - 38,735,427UniSTSRGSC3.4
Celera2038,974,014 - 38,974,205UniSTS
RH 3.4 Map20408.51UniSTS
Cytogenetic Map20q12UniSTS
BE107833  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22038,107,305 - 38,107,459 (+)MAPPER
Rnor_6.02041,108,619 - 41,108,772NCBIRnor6.0
Rnor_5.02042,838,434 - 42,838,587UniSTSRnor5.0
RGSC_v3.42038,647,829 - 38,647,982UniSTSRGSC3.4
Celera2038,889,696 - 38,889,849UniSTS
RH 3.4 Map20403.23UniSTS
Cytogenetic Map20q12UniSTS
AU046561  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22038,135,358 - 38,135,499 (+)MAPPER
Rnor_6.02041,136,677 - 41,136,817NCBIRnor6.0
RGSC_v3.42038,675,887 - 38,676,027UniSTSRGSC3.4
Cytogenetic Map20q12UniSTS
RH138488  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22038,207,479 - 38,207,659 (+)MAPPER
Rnor_6.02041,208,656 - 41,208,835NCBIRnor6.0
Rnor_5.02042,937,558 - 42,937,737UniSTSRnor5.0
RGSC_v3.42038,749,505 - 38,749,684UniSTSRGSC3.4
Celera2038,988,260 - 38,988,439UniSTS
RH 3.4 Map20408.51UniSTS
Cytogenetic Map20q12UniSTS
RH139629  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22038,189,069 - 38,189,249 (+)MAPPER
Rnor_6.02041,190,246 - 41,190,425NCBIRnor6.0
Rnor_5.02042,919,148 - 42,919,327UniSTSRnor5.0
RGSC_v3.42038,731,095 - 38,731,274UniSTSRGSC3.4
Celera2038,969,873 - 38,970,052UniSTS
RH 3.4 Map20407.04UniSTS
Cytogenetic Map20q12UniSTS
Col10a1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22038,188,024 - 38,188,449 (+)MAPPER
Rnor_6.02041,189,201 - 41,189,625NCBIRnor6.0
Rnor_5.02042,918,103 - 42,918,527UniSTSRnor5.0
RGSC_v3.42038,730,050 - 38,730,474UniSTSRGSC3.4
Celera2038,968,828 - 38,969,252UniSTS
Cytogenetic Map20q12UniSTS
BF391491  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22038,105,746 - 38,105,941 (+)MAPPER
Rnor_6.02041,107,060 - 41,107,254NCBIRnor6.0
Rnor_5.02042,836,875 - 42,837,069UniSTSRnor5.0
RGSC_v3.42038,646,270 - 38,646,464UniSTSRGSC3.4
Celera2038,888,137 - 38,888,331UniSTS
RH 3.4 Map20404.53UniSTS
Cytogenetic Map20q12UniSTS
Col10a1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22038,187,548 - 38,188,135 (+)MAPPER
Rnor_6.02041,188,725 - 41,189,311NCBIRnor6.0
Rnor_5.02042,917,812 - 42,918,213UniSTSRnor5.0
RGSC_v3.42038,729,602 - 38,730,160UniSTSRGSC3.4
Celera2038,968,357 - 38,968,938UniSTS
Cytogenetic Map20q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201383430956205956Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201383430956205956Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201782709656205956Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201887215049108956Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202085847056205956Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202660884356205956Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202660884356205956Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202660884356205956Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202671232356205956Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)203091348156205956Rat
70158Bp60Blood pressure QTL 603arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)203335478345719230Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:568
Count of miRNA genes:256
Interacting mature miRNAs:319
Transcripts:ENSRNOT00000000657
Prediction methods:Microtar, Miranda, 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.


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 39 23 19 23 10 35 35 11
Low 43 18 18 18 8 11 64 6 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000657   ⟹   ENSRNOP00000000657
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2041,106,991 - 41,209,728 (-)Ensembl
RefSeq Acc Id: NM_001106393   ⟹   NP_001099863
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22038,105,678 - 38,208,588 (-)NCBI
Rnor_6.02041,106,991 - 41,209,764 (-)NCBI
Rnor_5.02042,836,806 - 42,938,666 (-)NCBI
RGSC_v3.42038,646,201 - 38,750,613 (-)RGD
Celera2038,888,068 - 38,989,368 (-)RGD
Sequence:
RefSeq Acc Id: XM_008772981   ⟹   XP_008771203
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22038,105,677 - 38,208,612 (-)NCBI
Rnor_6.02041,106,990 - 41,209,761 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601627   ⟹   XP_017457116
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02041,106,990 - 41,209,765 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039098600   ⟹   XP_038954528
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22038,105,677 - 38,192,104 (-)NCBI
RefSeq Acc Id: XM_039098601   ⟹   XP_038954529
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22038,163,269 - 38,208,613 (-)NCBI
RefSeq Acc Id: XM_039098602   ⟹   XP_038954530
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22038,163,269 - 38,208,613 (-)NCBI
RefSeq Acc Id: XM_039098603   ⟹   XP_038954531
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22038,163,269 - 38,208,613 (-)NCBI
RefSeq Acc Id: XM_039098604   ⟹   XP_038954532
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22038,163,269 - 38,208,613 (-)NCBI
RefSeq Acc Id: XM_039098605   ⟹   XP_038954533
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22038,163,269 - 38,208,613 (-)NCBI
RefSeq Acc Id: XM_039098606   ⟹   XP_038954534
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22038,163,269 - 38,208,613 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001099863   ⟸   NM_001106393
- Sequence:
RefSeq Acc Id: XP_008771203   ⟸   XM_008772981
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457116   ⟸   XM_017601627
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000000657   ⟸   ENSRNOT00000000657
RefSeq Acc Id: XP_038954528   ⟸   XM_039098600
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038954530   ⟸   XM_039098602
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038954534   ⟸   XM_039098606
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038954532   ⟸   XM_039098604
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038954529   ⟸   XM_039098601
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038954533   ⟸   XM_039098605
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038954531   ⟸   XM_039098603
- Peptide Label: isoform X5

Transcriptome

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

Promoters
RGD ID:13701642
Promoter ID:EPDNEW_R12165
Type:initiation region
Name:Nt5dc1_1
Description:5'-nucleotidase domain containing 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_6.02041,209,762 - 41,209,822EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305214 AgrOrtholog
Ensembl Genes ENSRNOG00000000546 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000657 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000657 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.1000 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9098589 IMAGE-MGC_LOAD
InterPro HAD-like_dom UniProtKB/TrEMBL
  HAD-like_sf UniProtKB/TrEMBL
  HAD-SF_hydro_IG_5-nucl UniProtKB/TrEMBL
MGC_CLONE MGC:187900 IMAGE-MGC_LOAD
NCBI Gene 294456 ENTREZGENE
PANTHER PTHR12103 UniProtKB/TrEMBL
Pfam 5_nucleotid UniProtKB/TrEMBL
PhenoGen Nt5dc1 PhenoGen
Superfamily-SCOP HAD-like_dom UniProtKB/TrEMBL
UniProt B1WC66_RAT UniProtKB/TrEMBL
UniProt Secondary F7EPM6 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-29 Nt5dc1  5'-nucleotidase domain containing 1  LOC102554902  5'-nucleotidase domain-containing protein 1-like  Data Merged 737654 PROVISIONAL
2013-12-18 LOC102554902  5'-nucleotidase domain-containing protein 1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 Nt5dc1  5'-nucleotidase domain containing 1   Nt5dc1_predicted  5'-nucleotidase domain containing 1 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Nt5dc1_predicted  5'-nucleotidase domain containing 1 (predicted)  Nt5c2l1_predicted  5'-nucleotidase, cytosolic II-like 1 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-12 Nt5c2l1_predicted  5'-nucleotidase, cytosolic II-like 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED