Npas3 (neuronal PAS domain protein 3) - Rat Genome Database
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Gene: Npas3 (neuronal PAS domain protein 3) Rattus norvegicus
Analyze
Symbol: Npas3
Name: neuronal PAS domain protein 3
RGD ID: 1307181
Description: Predicted to have protein heterodimerization activity. Predicted to be involved in several processes, including maternal behavior; positive regulation of transcription, DNA-templated; and startle response. Predicted to localize to nucleoplasm. Orthologous to human NPAS3 (neuronal PAS domain protein 3); INTERACTS WITH 17beta-estradiol; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC299016; LOW QUALITY PROTEIN: neuronal PAS domain-containing protein 3; neuronal PAS domain-containing protein 3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
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
mRatBN7.2670,702,773 - 71,527,928 (+)NCBI
Rnor_6.0674,081,995 - 74,913,025 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0683,635,089 - 84,459,466 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4674,192,110 - 74,209,762 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1674,075,148 - 74,329,176 (+)NCBI
Celera669,567,922 - 70,382,732 (+)NCBICelera
Cytogenetic Map6q23NCBI
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

Cellular Component
nucleoplasm  (ISO)
nucleus  (ISO)

Molecular Function

References

Additional References at PubMed
PMID:7743923   PMID:15347806   PMID:25862168   PMID:27782878  


Genomics

Comparative Map Data
Npas3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2670,702,773 - 71,527,928 (+)NCBI
Rnor_6.0674,081,995 - 74,913,025 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0683,635,089 - 84,459,466 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4674,192,110 - 74,209,762 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1674,075,148 - 74,329,176 (+)NCBI
Celera669,567,922 - 70,382,732 (+)NCBICelera
Cytogenetic Map6q23NCBI
NPAS3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1432,934,396 - 33,804,176 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1432,934,933 - 33,804,176 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1432,934,396 - 33,820,863 (+)EnsemblGRCh38hg38GRCh38
GRCh381432,934,785 - 33,804,176 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371433,408,085 - 34,273,379 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361432,478,200 - 33,340,702 (+)NCBINCBI36hg18NCBI36
Build 341432,478,273 - 33,340,066NCBI
Celera1413,273,962 - 14,138,956 (+)NCBI
Cytogenetic Map14q13.1NCBI
HuRef1413,641,962 - 14,390,327 (+)NCBIHuRef
CHM1_11433,407,064 - 34,271,980 (+)NCBICHM1_1
Npas3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391253,294,874 - 54,118,956 (+)NCBIGRCm39mm39
GRCm39 Ensembl1253,294,940 - 54,118,958 (+)Ensembl
GRCm381253,248,026 - 54,072,173 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1253,248,677 - 54,072,175 (+)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl1253,248,157 - 54,072,175 (+)EnsemblGRCm38mm10GRCm38
MGSCv371254,349,664 - 55,173,162 (+)NCBIGRCm37mm9NCBIm37
MGSCv361254,170,303 - 54,990,700 (+)NCBImm8
Celera1254,549,790 - 55,376,477 (+)NCBICelera
Cytogenetic Map12C1NCBI
Npas3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540927,137,667 - 27,975,282 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540927,134,610 - 27,975,282 (-)NCBIChiLan1.0ChiLan1.0
NPAS3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11431,990,835 - 32,759,347 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1431,893,101 - 32,758,096 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01413,701,786 - 14,568,738 (+)NCBIMhudiblu_PPA_v0panPan3
NPAS3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1811,959,895 - 12,799,448 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Npas3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364947,965,156 - 8,144,244 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NPAS3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl765,928,075 - 66,801,611 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1765,924,986 - 66,800,820 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2770,862,116 - 70,974,873 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Npas3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248383,003,455 - 3,904,964 (-)NCBI

Position Markers
RH131599  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0674,795,759 - 74,795,973NCBIRnor6.0
Rnor_5.0684,341,739 - 84,341,953UniSTSRnor5.0
RGSC_v3.4674,209,600 - 74,209,814UniSTSRGSC3.4
Celera670,265,014 - 70,265,228UniSTS
Cytogenetic Map6q23UniSTS
BE103570  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0674,218,628 - 74,218,784NCBIRnor6.0
Rnor_5.0683,771,059 - 83,771,215UniSTSRnor5.0
RGSC_v3.4673,603,406 - 73,603,562UniSTSRGSC3.4
Celera669,704,588 - 69,704,744UniSTS
Cytogenetic Map6q23UniSTS
RH141323  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0674,913,333 - 74,913,529NCBIRnor6.0
Rnor_5.0684,457,823 - 84,458,019UniSTSRnor5.0
RGSC_v3.4674,326,863 - 74,327,059UniSTSRGSC3.4
Celera670,381,089 - 70,381,285UniSTS
Cytogenetic Map6q23UniSTS
AU049986  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0674,823,549 - 74,823,815NCBIRnor6.0
Rnor_5.0684,369,529 - 84,369,795UniSTSRnor5.0
RGSC_v3.4674,237,110 - 74,237,376UniSTSRGSC3.4
Celera670,292,531 - 70,292,797UniSTS
Cytogenetic Map6q23UniSTS
fc03e11.x1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0674,814,625 - 74,815,541NCBIRnor6.0
Rnor_5.0684,360,605 - 84,361,521UniSTSRnor5.0
RGSC_v3.4674,228,186 - 74,229,102UniSTSRGSC3.4
Celera670,283,607 - 70,284,523UniSTS
Cytogenetic Map6q23UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6175623393Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)6112039375023446Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)6616172276002731Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6616172276002731Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63436743680490628Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63499565675623393Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63626028884763275Rat
1354632Scl29Serum cholesterol level QTL 293.74blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)63760898075023446Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)63810630883106308Rat
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)64167904686679046Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)64167904686679046Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)64167904686679046Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)648432758108268790Rat
4889848Pur25Proteinuria QTL 25140.003total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)65980306594001333Rat
1558641Cm47Cardiac mass QTL 472.90.001heart mass (VT:0007028)heart wet weight (CMO:0000069)660606431108154445Rat
6893332Cm74Cardiac mass QTL 740.40.64heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)660606431108154445Rat
70176Mcsm1Mammary carcinoma susceptibility modifier QTL 1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)662263348107263348Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)666129520111129520Rat
2293088Iddm28Insulin dependent diabetes mellitus QTL 285.21blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)66622261275023308Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)671206251116206251Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:130
Count of miRNA genes:103
Interacting mature miRNAs:113
Transcripts:ENSRNOT00000049945
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.


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_039078152 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078153 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078154 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078155 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078156 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078157 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078158 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078159 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078160 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078161 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078162 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078163 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078164 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078165 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473947 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000164 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: XM_017594552   ⟹   XP_017450041
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0674,081,995 - 74,913,025 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017603159   ⟹   XP_017458648
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera669,567,922 - 70,382,732 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039078152   ⟹   XP_038934080
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2670,702,773 - 71,527,928 (+)NCBI
RefSeq Acc Id: XM_039078153   ⟹   XP_038934081
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2670,702,773 - 71,527,928 (+)NCBI
RefSeq Acc Id: XM_039078154   ⟹   XP_038934082
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2670,702,774 - 71,527,928 (+)NCBI
RefSeq Acc Id: XM_039078155   ⟹   XP_038934083
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2670,702,774 - 71,527,928 (+)NCBI
RefSeq Acc Id: XM_039078156   ⟹   XP_038934084
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2670,702,775 - 71,527,928 (+)NCBI
RefSeq Acc Id: XM_039078157   ⟹   XP_038934085
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2670,702,774 - 71,527,928 (+)NCBI
RefSeq Acc Id: XM_039078158   ⟹   XP_038934086
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2670,702,775 - 71,527,928 (+)NCBI
RefSeq Acc Id: XM_039078159   ⟹   XP_038934087
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2670,702,775 - 71,527,928 (+)NCBI
RefSeq Acc Id: XM_039078160   ⟹   XP_038934088
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2670,702,774 - 71,527,928 (+)NCBI
RefSeq Acc Id: XM_039078161   ⟹   XP_038934089
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2670,706,894 - 71,527,928 (+)NCBI
RefSeq Acc Id: XM_039078162   ⟹   XP_038934090
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2670,702,775 - 71,527,928 (+)NCBI
RefSeq Acc Id: XM_039078163   ⟹   XP_038934091
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2670,702,776 - 71,527,928 (+)NCBI
RefSeq Acc Id: XM_039078164   ⟹   XP_038934092
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2670,930,752 - 71,527,928 (+)NCBI
RefSeq Acc Id: XM_039078165   ⟹   XP_038934093
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2670,706,894 - 71,527,928 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_017458648   ⟸   XM_017603159
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017450041   ⟸   XM_017594552
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_038934080   ⟸   XM_039078152
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934081   ⟸   XM_039078153
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038934082   ⟸   XM_039078154
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038934083   ⟸   XM_039078155
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038934085   ⟸   XM_039078157
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038934088   ⟸   XM_039078160
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038934084   ⟸   XM_039078156
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038934086   ⟸   XM_039078158
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038934087   ⟸   XM_039078159
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038934090   ⟸   XM_039078162
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038934091   ⟸   XM_039078163
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038934089   ⟸   XM_039078161
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038934093   ⟸   XM_039078165
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038934092   ⟸   XM_039078164
- Peptide Label: isoform X13


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:1307181 AgrOrtholog
NCBI Gene 299016 ENTREZGENE
PhenoGen Npas3 PhenoGen


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Npas3  neuronal PAS domain protein 3   Npas3_predicted  neuronal PAS domain protein 3 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Npas3_predicted  neuronal PAS domain protein 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED