Tph2 (tryptophan hydroxylase 2) - Rat Genome Database

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Gene: Tph2 (tryptophan hydroxylase 2) Rattus norvegicus
Analyze
Symbol: Tph2
Name: tryptophan hydroxylase 2
RGD ID: 631332
Description: Predicted to have tryptophan 5-monooxygenase activity. Involved in several processes, including cellular response to lithium ion; response to activity; and response to estrogen. Predicted to localize to neuron projection. Human ortholog(s) of this gene implicated in attention deficit hyperactivity disorder; autistic disorder; major depressive disorder; and panic disorder. Orthologous to human TPH2 (tryptophan hydroxylase 2); PARTICIPATES IN tryptophan metabolic pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: neuronal tryptophan hydroxylase; Ntph; tryptophan 5-hydroxylase 2; tryptophan 5-monooxygenase 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Tph2em2Mcwi   Tph2em3Mcwi  
Genetic Models: DA-Tph2em2Mcwi DA-Tph2em3Mcwi DA-Tph2em3Mcwi+/+ DA-Tph2em2Mcwi-/- DA-Tph2em3Mcwi-/- DA-Tph2em2Mcwi+/- DA-Tph2em3Mcwi+/-
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2750,685,694 - 50,789,424 (-)NCBI
Rnor_6.0 Ensembl758,042,281 - 58,149,061 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0758,042,279 - 58,149,220 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0758,053,268 - 58,157,949 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4754,321,033 - 54,430,706 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1754,341,665 - 54,451,339 (-)NCBI
Celera747,478,282 - 47,582,240 (-)NCBICelera
Cytogenetic Map7q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Coon H, etal., Am J Med Genet B Neuropsychiatr Genet. 2005 May 5;135B(1):42-6.
2. De Luca V, etal., Psychopharmacology (Berl). 2005 Dec;183(3):378-82. Epub 2005 Oct 21.
3. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Hiroi R, etal., Biol Psychiatry. 2006 Aug 1;60(3):288-95. Epub 2006 Feb 3.
5. Izikki M, etal., Am J Physiol Lung Cell Mol Physiol. 2007 Oct;293(4):L1045-52. Epub 2007 Aug 3.
6. Lenicov FR, etal., J Neurochem. 2007 Dec;103(5):2047-57. Epub 2007 Sep 14.
7. Liang J, etal., Neuroreport. 2004 Jun 28;15(9):1497-500.
8. Malek ZS, etal., Endocrinology. 2007 Nov;148(11):5165-72. Epub 2007 Jun 26.
9. Maron E, etal., Neurosci Lett. 2007 Jan 16;411(3):180-4. Epub 2006 Nov 22.
10. McNamara RK, etal., J Psychiatr Res. 2009 Mar;43(6):656-63. Epub 2008 Nov 4.
11. MGD data from the GO Consortium
12. OMIM Disease Annotation Pipeline
13. Pipeline to import KEGG annotations from KEGG into RGD
14. Ramoz N, etal., Am J Med Genet B Neuropsychiatr Genet. 2006 Dec 5;141B(8):861-7.
15. RGD automated data pipeline
16. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
17. RGD automated import pipeline for gene-chemical interactions
18. RGD comprehensive gene curation
19. Scheuch K, etal., Brain Res. 2010 Jan 11;1307:14-21. Epub 2009 Oct 17.
20. Shishkina GT, etal., Ann N Y Acad Sci. 2008 Dec;1148:148-53.
21. Walther DJ, etal., Science 2003 Jan 3;299(5603):76.
Additional References at PubMed
PMID:12911638   PMID:16115212   PMID:16917826   PMID:17950541   PMID:18197473   PMID:19559077   PMID:19588223   PMID:19647049   PMID:19906978   PMID:20127812   PMID:21182901   PMID:21272616  
PMID:21924839   PMID:22511363   PMID:31078489   PMID:31415826   PMID:31505169  


Genomics

Comparative Map Data
Tph2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2750,685,694 - 50,789,424 (-)NCBI
Rnor_6.0 Ensembl758,042,281 - 58,149,061 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0758,042,279 - 58,149,220 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0758,053,268 - 58,157,949 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4754,321,033 - 54,430,706 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1754,341,665 - 54,451,339 (-)NCBI
Celera747,478,282 - 47,582,240 (-)NCBICelera
Cytogenetic Map7q22NCBI
TPH2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1271,938,845 - 72,186,618 (+)EnsemblGRCh38hg38GRCh38
GRCh381271,938,845 - 72,032,440 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371272,332,625 - 72,426,220 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361270,618,893 - 70,712,488 (+)NCBINCBI36hg18NCBI36
Build 341270,618,892 - 70,712,488NCBI
Celera1271,995,911 - 72,089,543 (+)NCBI
Cytogenetic Map12q21.1NCBI
HuRef1269,382,235 - 69,474,238 (+)NCBIHuRef
CHM1_11272,299,779 - 72,391,813 (+)NCBICHM1_1
Tph2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910114,914,546 - 115,020,927 (-)NCBIGRCm39mm39
GRCm39 Ensembl10114,914,546 - 115,020,927 (-)Ensembl
GRCm3810115,078,641 - 115,185,022 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10115,078,641 - 115,185,022 (-)EnsemblGRCm38mm10GRCm38
MGSCv3710114,515,697 - 114,622,078 (-)NCBIGRCm37mm9NCBIm37
MGSCv3610114,482,751 - 114,589,132 (-)NCBImm8
Celera10117,006,698 - 117,113,837 (-)NCBICelera
Cytogenetic Map10D2NCBI
Tph2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540511,886,206 - 11,982,550 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540511,877,474 - 11,981,035 (+)NCBIChiLan1.0ChiLan1.0
TPH2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11272,318,908 - 72,412,557 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1272,318,908 - 72,412,557 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01269,460,883 - 69,557,329 (+)NCBIMhudiblu_PPA_v0panPan3
TPH2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11013,442,611 - 13,526,537 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1013,442,611 - 13,527,243 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1013,381,425 - 13,464,836 (+)NCBI
ROS_Cfam_1.01013,578,664 - 13,662,404 (+)NCBI
UMICH_Zoey_3.11013,440,095 - 13,523,686 (+)NCBI
UNSW_CanFamBas_1.01013,688,920 - 13,772,483 (+)NCBI
UU_Cfam_GSD_1.01013,812,858 - 13,896,308 (+)NCBI
Tph2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494544,662,510 - 44,753,680 (-)NCBI
SpeTri2.0NW_004936568974,575 - 1,065,800 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TPH2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl535,918,569 - 36,017,514 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1535,917,159 - 36,016,981 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2538,620,459 - 38,716,640 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TPH2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11167,568,744 - 67,664,911 (+)NCBI
Tph2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475025,702,597 - 25,801,938 (-)NCBI

Position Markers
RH132298  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2750,685,695 - 50,685,852 (+)MAPPER
Rnor_6.0758,042,283 - 58,042,439NCBIRnor6.0
Rnor_5.0758,053,272 - 58,053,428UniSTSRnor5.0
RGSC_v3.4754,321,035 - 54,321,191UniSTSRGSC3.4
Celera747,478,284 - 47,478,440UniSTS
RH 3.4 Map7442.0UniSTS
Cytogenetic Map7q22UniSTS
BI279052  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2750,686,685 - 50,686,866 (+)MAPPER
Rnor_6.0758,043,273 - 58,043,453NCBIRnor6.0
Rnor_5.0758,054,262 - 58,054,442UniSTSRnor5.0
RGSC_v3.4754,322,025 - 54,322,205UniSTSRGSC3.4
Celera747,479,274 - 47,479,454UniSTS
RH 3.4 Map7442.6UniSTS
Cytogenetic Map7q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)71232846767193263Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)712328467106995532Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)71268785067801690Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71395217958952179Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)71444568559445685Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)72216841267168412Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)72473146569731465Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)72536563360317612Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)72536563393155402Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72820465373204653Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)73138152976381529Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)73203505377035053Rat
61439Cia8Collagen induced arthritis QTL 85.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)73257294277572942Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)73304444971352127Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)73586772961047824Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)73586772980867729Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)73586772993155402Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73854770683547706Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)74087268285872682Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)74087268285872682Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)74530157390301573Rat
2303629Vencon3Ventilatory control QTL 37.25respiration trait (VT:0001943)respiration rate (CMO:0000289)74789509963372754Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)748118835128611831Rat
634326Hc3Hypercalciuria QTL 32.1urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)75025210395252103Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)750704769128085642Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)75079381895793818Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)751251919118477612Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)751252005111589099Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)75320034498200344Rat
738030Anxrr8Anxiety related response QTL 84.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)75425951299259512Rat
10059605Kidm47Kidney mass QTL 472.910.05kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)75453499673293934Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)75507286269399731Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)755072862123602998Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)755072862123602998Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)755072862123602998Rat
2300178Bmd54Bone mineral density QTL 545.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)755495689100495689Rat
2293644Bmd29Bone mineral density QTL 295.40.0001femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)755495689100495689Rat
2293667Bss42Bone structure and strength QTL 427.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)755495689100495689Rat
2293678Bss24Bone structure and strength QTL 246.710.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)755495689100495689Rat
2293685Bmd21Bone mineral density QTL 214.20.0003femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)755495689100495689Rat
2293696Bmd32Bone mineral density QTL 325.10.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)755495689100495689Rat
2293707Bss32Bone structure and strength QTL 327.640.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)755495689100495689Rat


Genetic Models
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:308
Count of miRNA genes:199
Interacting mature miRNAs:236
Transcripts:ENSRNOT00000005157
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 appendage
High
Medium 5
Low 8 47 14 21
Below cutoff 3 2 7 3 4 3 1 1 16 13 15 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000005157   ⟹   ENSRNOP00000005157
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl758,042,281 - 58,149,061 (-)Ensembl
RefSeq Acc Id: NM_173839   ⟹   NP_776211
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2750,685,694 - 50,789,424 (-)NCBI
Rnor_6.0758,042,281 - 58,149,061 (-)NCBI
Rnor_5.0758,053,268 - 58,157,949 (-)NCBI
RGSC_v3.4754,321,033 - 54,430,706 (-)RGD
Celera747,478,282 - 47,582,240 (-)RGD
Sequence:
RefSeq Acc Id: XM_008765357   ⟹   XP_008763579
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0758,042,279 - 58,149,218 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017594904   ⟹   XP_017450393
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0758,042,279 - 58,149,220 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_776211 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAM28947 (Get FASTA)   NCBI Sequence Viewer  
  EDM16695 (Get FASTA)   NCBI Sequence Viewer  
  EDM16696 (Get FASTA)   NCBI Sequence Viewer  
  Q8CGU9 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_776211   ⟸   NM_173839
- UniProtKB: Q8CGU9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008763579   ⟸   XM_008765357
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017450393   ⟸   XM_017594904
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000005157   ⟸   ENSRNOT00000005157
Protein Domains
ACT

Transcriptome

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


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)
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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)
FHH/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
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:631332 AgrOrtholog
Ensembl Genes ENSRNOG00000003880 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000005157 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000005157 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.800.10 UniProtKB/Swiss-Prot
InterPro ACT_dom UniProtKB/Swiss-Prot
  ArAA_hydroxylase UniProtKB/Swiss-Prot
  ArAA_hydroxylase_Fe/CU_BS UniProtKB/Swiss-Prot
  ArAA_hydroxylase_sf UniProtKB/Swiss-Prot
  Aro-AA_hydroxylase_C_sf UniProtKB/Swiss-Prot
  Aromatic-AA_hydroxylase_C UniProtKB/Swiss-Prot
  Trp_5_mOase UniProtKB/Swiss-Prot
  TrpOH_cat UniProtKB/Swiss-Prot
  Tyrosine_3-monooxygenase-like UniProtKB/Swiss-Prot
KEGG Report rno:317675 UniProtKB/Swiss-Prot
NCBI Gene 317675 ENTREZGENE
PANTHER PTHR11473 UniProtKB/Swiss-Prot
Pfam Biopterin_H UniProtKB/Swiss-Prot
PharmGKB TPH2 RGD
PhenoGen Tph2 PhenoGen
PIRSF PIRSF000336 UniProtKB/Swiss-Prot
PRINTS FYWHYDRXLASE UniProtKB/Swiss-Prot
PROSITE ACT UniProtKB/Swiss-Prot
  BH4_AAA_HYDROXYL_1 UniProtKB/Swiss-Prot
  BH4_AAA_HYDROXYL_2 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF56534 UniProtKB/Swiss-Prot
TIGRFAMs Trp_5_monoox UniProtKB/Swiss-Prot
UniProt Q8CGU9 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-11 Tph2  tryptophan hydroxylase 2  Ntph  neuronal tryptophan hydroxylase  Symbol and Name updated to reflect Human and Mouse nomenclature 625702 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in brain 633509