Gdf5 (growth differentiation factor 5) - Rat Genome Database

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Gene: Gdf5 (growth differentiation factor 5) Rattus norvegicus
Analyze
Symbol: Gdf5
Name: growth differentiation factor 5
RGD ID: 620102
Description: Exhibits signaling receptor binding activity. Involved in several processes, including negative regulation of neuron apoptotic process; ossification involved in bone remodeling; and positive regulation of neuron differentiation. Predicted to localize to extracellular space. Biomarker of Parkinson's disease. Human ortholog(s) of this gene implicated in Parkinson's disease and bone disease (multiple). Orthologous to human GDF5 (growth differentiation factor 5); PARTICIPATES IN transforming growth factor-beta superfamily mediated signaling pathway; INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; C60 fullerene.
Type: protein-coding
RefSeq Status: MODEL
Also known as: cartilage-derived morphogenetic protein 1; Cdmp1; growth/differentiation factor 5
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
mRatBN7.23144,454,306 - 144,458,757 (-)NCBI
Rnor_6.0 Ensembl3151,483,249 - 151,486,693 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03151,482,672 - 151,487,129 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03157,849,749 - 157,853,231 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera3143,176,803 - 143,181,254 (-)NCBICelera
Cytogenetic Map3q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Basit S, etal., BMC Med Genet. 2008 Nov 27;9:102. doi: 10.1186/1471-2350-9-102.
2. Byrnes AM, etal., Hum Mutat. 2010 Oct;31(10):1155-62. doi: 10.1002/humu.21338.
3. Costello DJ, etal., J Cell Mol Med. 2012 Oct;16(10):2451-60. doi: 10.1111/j.1582-4934.2012.01562.x.
4. Dai J, etal., Arthritis Res Ther. 2008;10(5):R126. doi: 10.1186/ar2540. Epub 2008 Oct 24.
5. Dawson K, etal., Am J Hum Genet. 2006 Apr;78(4):708-12. Epub 2006 Feb 24.
6. Degenkolbe E, etal., Bone. 2015 Apr;73:111-9. doi: 10.1016/j.bone.2014.12.017. Epub 2014 Dec 24.
7. Dines JS, etal., J Shoulder Elbow Surg. 2007 Sep-Oct;16(5 Suppl):S215-21. Epub 2007 May 15.
8. Faiyaz-Ul-Haque M, etal., Clin Genet. 2002 Jun;61(6):454-8.
9. Faiyaz-Ul-Haque M, etal., J Bone Miner Metab. 2008;26(6):648-52. doi: 10.1007/s00774-008-0853-5. Epub 2008 Nov 1.
10. Farooq M, etal., Hum Genet. 2013 Nov;132(11):1253-64. doi: 10.1007/s00439-013-1330-3. Epub 2013 Jun 29.
11. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
12. Gavin AM, etal., Neurosci Lett. 2014 Feb 21;561:176-81. doi: 10.1016/j.neulet.2013.12.046. Epub 2013 Dec 25.
13. Kanauchi Y, etal., J Hand Surg Am. 2008 Nov;33(9):1589-96. doi: 10.1016/j.jhsa.2008.05.015.
14. NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. O'Keeffe GW, etal., J Neurocytol. 2004 Sep;33(5):479-88.
16. OMIM Disease Annotation Pipeline
17. Online Mendelian Inheritance in Man, OMIM (TM).
18. Pipeline to import KEGG annotations from KEGG into RGD
19. RGD automated data pipeline
20. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
21. RGD automated import pipeline for gene-chemical interactions
22. RGD comprehensive gene curation
23. Sato M, etal., J Bone Miner Res. 1999 Jul;14(7):1084-95.
24. Schwabe GC, etal., Am J Med Genet A. 2004 Feb 1;124A(4):356-63.
25. Sena K, etal., J Dent Res 2003 Mar;82(3):166-71.
26. Stange K, etal., J Mol Biol. 2014 Sep 23;426(19):3221-31. doi: 10.1016/j.jmb.2014.07.029. Epub 2014 Aug 1.
27. Tashiro T, etal., J Orthop Res. 2006 Jan;24(1):71-9.
Additional References at PubMed
PMID:8145850   PMID:9885252   PMID:9950587   PMID:15246706   PMID:15542031   PMID:17085896   PMID:17118748   PMID:18363966   PMID:18569021   PMID:21976273   PMID:24098149   PMID:24682653  
PMID:25174448   PMID:26010756  


Genomics

Comparative Map Data
Gdf5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23144,454,306 - 144,458,757 (-)NCBI
Rnor_6.0 Ensembl3151,483,249 - 151,486,693 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03151,482,672 - 151,487,129 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03157,849,749 - 157,853,231 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera3143,176,803 - 143,181,254 (-)NCBICelera
Cytogenetic Map3q42NCBI
GDF5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2035,433,347 - 35,454,746 (-)EnsemblGRCh38hg38GRCh38
GRCh382035,433,347 - 35,454,749 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372034,021,145 - 34,042,571 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362033,484,563 - 33,489,441 (-)NCBINCBI36hg18NCBI36
Build 342033,484,562 - 33,489,441NCBI
Celera2030,769,772 - 30,774,651 (-)NCBI
Cytogenetic Map20q11.22NCBI
HuRef2030,798,624 - 30,803,509 (-)NCBIHuRef
CHM1_12033,922,575 - 33,943,940 (-)NCBICHM1_1
Gdf5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392155,782,943 - 155,787,287 (-)NCBIGRCm39mm39
GRCm39 Ensembl2155,782,943 - 155,787,287 (-)Ensembl
GRCm382155,941,023 - 155,945,367 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2155,941,023 - 155,945,367 (-)EnsemblGRCm38mm10GRCm38
MGSCv372155,766,759 - 155,771,100 (-)NCBIGRCm37mm9NCBIm37
MGSCv362155,632,468 - 155,636,808 (-)NCBImm8
Celera2161,874,286 - 161,878,600 (-)NCBICelera
Cytogenetic Map2H1NCBI
cM Map277.26NCBI
Gdf5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542225,992,081 - 25,997,122 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542225,992,081 - 25,997,122 (+)NCBIChiLan1.0ChiLan1.0
GDF5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12032,882,094 - 32,903,044 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2032,882,094 - 32,886,899 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02031,761,199 - 31,766,229 (-)NCBIMhudiblu_PPA_v0panPan3
GDF5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12424,395,699 - 24,400,302 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2424,395,263 - 24,399,928 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2424,041,515 - 24,046,000 (-)NCBI
ROS_Cfam_1.02425,088,106 - 25,092,591 (-)NCBI
UMICH_Zoey_3.12424,374,851 - 24,379,335 (-)NCBI
UNSW_CanFamBas_1.02424,469,869 - 24,474,354 (-)NCBI
UU_Cfam_GSD_1.02424,908,900 - 24,913,385 (-)NCBI
Gdf5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640173,399,611 - 173,406,429 (-)NCBI
SpeTri2.0NW_0049365615,343,038 - 5,347,721 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GDF5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1738,792,323 - 38,797,446 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11738,792,854 - 38,796,806 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21743,913,724 - 43,917,676 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GDF5
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1256,340,371 - 56,346,378 (-)NCBI
ChlSab1.1 Ensembl256,340,933 - 56,345,053 (-)Ensembl
Gdf5
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248423,958,814 - 3,963,713 (+)NCBI

Position Markers
U08337  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03151,482,879 - 151,483,000NCBIRnor6.0
Rnor_5.03157,849,400 - 157,849,521UniSTSRnor5.0
Celera3143,177,010 - 143,177,131UniSTS
UniSTS:143190  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03151,482,734 - 151,483,275NCBIRnor6.0
Rnor_5.03157,849,255 - 157,849,796UniSTSRnor5.0
Celera3143,176,865 - 143,177,406UniSTS
UniSTS:496658  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03151,486,709 - 151,486,912NCBIRnor6.0
Rnor_5.03157,852,921 - 157,853,124UniSTSRnor5.0
Celera3143,180,834 - 143,181,037UniSTS
REN57716  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03151,483,668 - 151,483,892NCBIRnor6.0
Rnor_5.03157,850,189 - 157,850,413UniSTSRnor5.0
Celera3143,177,799 - 143,178,023UniSTS
REN57733  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03151,486,878 - 151,487,119NCBIRnor6.0
Rnor_5.03157,853,090 - 157,853,331UniSTSRnor5.0
Celera3143,181,003 - 143,181,244UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)330846101172879276Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)343295930163640485Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)343295930163640485Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)345406058177699992Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)348561928155263151Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)358204463170534769Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)361241033165369047Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)381136227154416635Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)399465522168732722Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)3102152812155263151Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)3103141814176418101Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)3103141814176418101Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3103141814176418101Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3103141944170934860Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3114376250159376250Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3119471263164471263Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3125848628170848628Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3126575595153412619Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3126575595165355668Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128986468173986468Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3129787213177699992Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3130006659175006659Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3132875075176418101Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3136876155170935007Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3138374177177699992Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3138374177177699992Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3139578365177699992Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3146232777177699992Rat
5686842Rf59Renal function QTL 59urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)3147072047154807958Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3148034701177699992Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3148348517171467264Rat
61335Bp20Blood pressure QTL 203arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3148348739163640325Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3150368003177699992Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:160
Count of miRNA genes:126
Interacting mature miRNAs:140
Transcripts:ENSRNOT00000071099, ENSRNOT00000073736
Prediction methods:Microtar, Miranda, Rnahybrid
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 1
Low 3 2 6 5 42 16 27
Below cutoff 22 11 3 12 3 6 8 28 18 12 9 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000071099   ⟹   ENSRNOP00000063921
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3151,483,844 - 151,486,693 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000073736   ⟹   ENSRNOP00000066703
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3151,483,249 - 151,486,693 (-)Ensembl
RefSeq Acc Id: XM_001066344   ⟹   XP_001066344
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera3143,176,803 - 143,181,254 (-)NCBI
Sequence:
RefSeq Acc Id: XM_003749600   ⟹   XP_003749648
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23144,454,306 - 144,458,757 (-)NCBI
Rnor_6.03151,482,672 - 151,487,129 (-)NCBI
Rnor_5.03157,849,749 - 157,853,231 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_003749648 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAC02713 (Get FASTA)   NCBI Sequence Viewer  
  BAD83809 (Get FASTA)   NCBI Sequence Viewer  
  EDL85884 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_001066344   ⟸   XM_001066344
- Sequence:
RefSeq Acc Id: XP_003749648   ⟸   XM_003749600
- UniProtKB: M0RAY4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000063921   ⟸   ENSRNOT00000071099
RefSeq Acc Id: ENSRNOP00000066703   ⟸   ENSRNOT00000073736
Protein Domains
TGF_BETA_2   TGFb_propeptide

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)
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)
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)
FHL/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
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:620102 AgrOrtholog
Ensembl Genes ENSRNOG00000050123 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000063921 UniProtKB/TrEMBL
  ENSRNOP00000066703 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071099 UniProtKB/TrEMBL
  ENSRNOT00000073736 UniProtKB/TrEMBL
Gene3D-CATH 2.10.90.10 UniProtKB/TrEMBL
InterPro Cystine-knot_cytokine UniProtKB/TrEMBL
  TGF-b_C UniProtKB/TrEMBL
  TGF-b_N UniProtKB/TrEMBL
  TGF-beta-rel UniProtKB/TrEMBL
  TGFb_CS UniProtKB/TrEMBL
KEGG Report rno:252835 UniProtKB/TrEMBL
NCBI Gene 252835 ENTREZGENE
PANTHER PTHR11848 UniProtKB/TrEMBL
Pfam TGF_beta UniProtKB/TrEMBL
  TGFb_propeptide UniProtKB/TrEMBL
PhenoGen Gdf5 PhenoGen
PROSITE TGF_BETA_1 UniProtKB/TrEMBL
  TGF_BETA_2 UniProtKB/TrEMBL
SMART TGFB UniProtKB/TrEMBL
Superfamily-SCOP SSF57501 UniProtKB/TrEMBL
UniProt M0R3K5_RAT UniProtKB/TrEMBL
  M0RAY4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Gdf5  growth differentiation factor 5      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Gdf5  growth differentiation factor 5      Symbol and Name status set to provisional 70820 PROVISIONAL