Hmbs (hydroxymethylbilane synthase) - Rat Genome Database

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Gene: Hmbs (hydroxymethylbilane synthase) Rattus norvegicus
Analyze
Symbol: Hmbs
Name: hydroxymethylbilane synthase
RGD ID: 2801
Description: Enables several functions, including amine binding activity; hydroxymethylbilane synthase activity; and uroporphyrinogen-III synthase activity. Involved in several processes, including cellular response to dexamethasone stimulus; cellular response to lead ion; and response to estradiol. Located in several cellular components, including axon; cytosol; and perinuclear region of cytoplasm. Colocalizes with condensed chromosome. Biomarker of bilirubin metabolic disorder and liver carcinoma. Human ortholog(s) of this gene implicated in acute intermittent porphyria and sickle cell anemia. Orthologous to human HMBS (hydroxymethylbilane synthase); PARTICIPATES IN heme biosynthetic pathway; acute intermittent porphyria pathway; erythropoietic porphyria pathway; INTERACTS WITH 1,2,4-trimethylbenzene; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: alternative name: porphobilinogen deaminase; hemC; MGC108753; PBG-D; PBGD; Porphobilinogen deaminase; pre-uroporphyrinogen synthase; URO-S; uroporphyrinogen I synthase
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2844,673,554 - 44,680,950 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl844,673,554 - 44,680,957 (-)Ensembl
Rnor_6.0848,667,278 - 48,674,673 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl848,667,275 - 48,674,748 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0847,286,249 - 47,293,618 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4847,314,235 - 47,321,604 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1847,323,010 - 47,328,455 (-)NCBI
Celera844,259,787 - 44,267,156 (-)NCBICelera
RH 3.4 Map8428.0RGD
Cytogenetic Map8q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2,4-trimethylbenzene  (EXP)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrotoluene  (EXP)
2,4-dinitrotoluene  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
aclacinomycin A  (ISO)
aconitine  (EXP)
acrolein  (ISO)
alpha-pinene  (ISO)
aluminium ion  (EXP)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
arsenous acid  (ISO)
barium ion  (EXP)
benzene-1,2,4-triol  (ISO)
benzo[a]pyrene  (ISO)
butyric acid  (ISO)
calcium ion  (EXP)
carbamazepine  (ISO)
carbon nanotube  (ISO)
catechol  (ISO)
Chebulinic acid  (ISO)
chloroquine  (ISO)
chromium ion  (EXP)
clothianidin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diazinon  (ISO)
dibutyl phthalate  (EXP,ISO)
dihydrofolic acid  (EXP)
elemental selenium  (ISO)
endosulfan  (EXP)
enzyme inhibitor  (ISO)
ethyl methanesulfonate  (ISO)
finasteride  (EXP)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (EXP)
gallic acid  (ISO)
hemin  (ISO)
hexachlorobenzene  (EXP)
hyaluronic acid  (EXP)
hydrogen peroxide  (EXP)
hydroquinone  (ISO)
imipramine  (EXP)
indometacin  (ISO)
ivermectin  (ISO)
lead diacetate  (EXP)
lead ion  (EXP)
lead(II) chloride  (EXP,ISO)
magnesium ion  (EXP)
mercury dichloride  (EXP)
methamphetamine  (EXP)
methapyrilene  (EXP)
methyl methanesulfonate  (ISO)
N-acetyl-L-cysteine  (ISO)
nefazodone  (EXP)
nickel atom  (ISO)
nickel ion  (EXP)
nitrofen  (EXP)
oxaliplatin  (EXP)
ozone  (ISO)
p-chloromercuribenzoic acid  (EXP)
paclitaxel  (EXP)
paracetamol  (ISO)
pentachlorophenol  (ISO)
phenol  (ISO)
pirinixic acid  (EXP)
preuroporphyrinogen  (ISO)
pyrrolidine dithiocarbamate  (ISO)
quercetin  (ISO)
S-adenosyl-L-homocysteine  (ISO)
S-adenosyl-L-methioninate  (ISO)
S-adenosyl-L-methionine  (ISO)
selenium atom  (ISO)
sodium dichromate  (EXP)
sodium fluoride  (ISO)
sulfacetamide  (EXP)
sulfadiazine  (EXP)
sulfamerazine  (EXP)
sulfamoxole  (EXP)
sulfanilamide  (EXP)
sulfapyridine  (EXP)
sulfisomidine  (EXP)
sulfisoxazole  (EXP)
tamoxifen  (ISO)
Tellimagrandin I  (ISO)
thapsigargin  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
urethane  (ISO)
vinclozolin  (EXP)
zinc ion  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. Adjarov DG, etal., Exp Toxicol Pathol. 1994 Aug;46(3):199-202.
2. Aguilar-Gonzalez MG, etal., Toxicol Sci. 1999 Jun;49(2):281-9.
3. Ajioka RS, etal., Biochim Biophys Acta. 2006 Jul;1763(7):723-36. Epub 2006 Jun 3.
4. Anderson KE, etal., Am J Med. 1977 Sep;63(3):359-64.
5. Barupala DP, etal., Arch Biochem Biophys. 2016 Feb 15;592:60-75. doi: 10.1016/j.abb.2016.01.010. Epub 2016 Jan 16.
6. Beru N and Goldwasser E, J Biol Chem. 1985 Aug 5;260(16):9251-7.
7. Bitar M and Weiner M, Biochem Pharmacol. 1983 Jun 15;32(12):1921-8.
8. Cardalda CA, etal., Arch Biochem Biophys. 1997 Nov 1;347(1):69-77.
9. Christenson WR, etal., Life Sci. 1986 May 5;38(18):1679-84.
10. de Rooij FW, etal., Cell Mol Biol (Noisy-le-grand). 2009 Jul 1;55(2):64-9.
11. Dragneva S, etal., JIMD Rep. 2014;16:57-64. doi: 10.1007/8904_2014_320. Epub 2014 Jul 6.
12. Farmer DJ and Hollebone BR, Can J Biochem Cell Biol. 1984 Jan;62(1):49-54. doi: 10.1139/o84-008.
13. Frydman RB, etal., Biochim Biophys Acta. 1986 Apr 22;870(3):520-9.
14. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
15. GenMAPP
16. Gibson SL, etal., Biochem Pharmacol. 1999 Dec 1;58(11):1821-9.
17. GOA data from the GO Consortium
18. Greenbaum L, etal., Br J Cancer. 2002 Mar 18;86(6):1006-11.
19. Greenbaum L, etal., Oncogene. 2003 Aug 14;22(34):5221-8.
20. Greene-Davis ST, etal., Clin Biochem. 1997 Dec;30(8):607-12. doi: 10.1016/s0009-9120(97)00114-8.
21. Grinblat B, etal., J Environ Pathol Toxicol Oncol. 2006;25(1-2):145-58.
22. Guillén-Navarro E, etal., Ann Hum Genet. 2004 Sep;68(Pt 5):509-14. doi: 10.1046/j.1529-8817.2003.00114.x.
23. Homedan C, etal., Hum Mol Genet. 2015 Sep 1;24(17):5015-23. doi: 10.1093/hmg/ddv222. Epub 2015 Jun 12.
24. Jiang L, etal., Nat Med. 2018 Dec;24(12):1899-1909. doi: 10.1038/s41591-018-0199-z. Epub 2018 Oct 8.
25. Johansson A, etal., Mol Med 2003 Sep-Dec;9(9-12):193-9.
26. Jollie DR and Maines MD, Arch Biochem Biophys. 1985 Jul;240(1):51-9.
27. Jorgensen PE, etal., Scand J Clin Lab Invest. 2000 Nov;60(7):635-41.
28. Kang JH, etal., Proteomics. 2009 Oct;9(19):4445-56.
29. King PH, etal., Neurology 2002 Apr 9;58(7):1118-21.
30. Kohashi M, etal., Biochem J. 1984 Jun 15;220(3):755-65.
31. Kohashi M, etal., Life Sci. 1984 Jan 9;34(2):193-6. doi: 10.1016/0024-3205(84)90590-3.
32. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
33. Li N, etal., Bioorg Chem. 2008 Oct;36(5):241-51. Epub 2008 Aug 28.
34. Lindberg RL, etal., Nat Genet. 1996 Feb;12(2):195-9.
35. Loskove Y, etal., Mol Genet Metab. 2019 Nov;128(3):352-357. doi: 10.1016/j.ymgme.2018.10.008. Epub 2018 Oct 26.
36. Lundin G, etal., Hum Genet. 1994 Jan;93(1):59-62. doi: 10.1007/bf00218914.
37. Maeda N, etal., Clin Biochem. 1999 Aug;32(6):411-7. doi: 10.1016/s0009-9120(99)00043-0.
38. Mamet R, etal., Biochem Med Metab Biol. 1994 Jun;52(1):53-7.
39. Mazzetti MB and Tomio JM, Biochim Biophys Acta. 1988 Nov 2;957(1):97-104.
40. Munoz JJ, etal., Pharmacol Toxicol. 1993 Oct;73(4):189-91.
41. Méndez M, etal., Cell Mol Biol (Noisy-le-grand). 2009 Jul 1;55(2):55-63.
42. NCBI rat LocusLink and RefSeq merged data July 26, 2002
43. Neuvians TP, etal., J Biotechnol. 2005 May 4;117(2):163-71.
44. Noriega G, etal., Int J Biochem Cell Biol. 2002 Oct;34(10):1230-40.
45. Ohl F, etal., J Mol Med. 2005 Dec;83(12):1014-24. Epub 2005 Oct 7.
46. Ohl F, etal., J Urol. 2006 May;175(5):1915-20.
47. OMIM Disease Annotation Pipeline
48. Peters PG, etal., Arch Biochem Biophys. 1980 Apr 15;201(1):88-94. doi: 10.1016/0003-9861(80)90490-7.
49. Pipeline to import KEGG annotations from KEGG into RGD
50. Pipeline to import SMPDB annotations from SMPDB into RGD
51. Piper WN and Van Lier BL, Mol Pharmacol. 1977 Nov;13(6):1126-35.
52. Piper WN and Van Lier RB, Life Sci. 1976 Oct 15;19(8):1225-34. doi: 10.1016/0024-3205(76)90258-7.
53. Piper WN, etal., Arch Biochem Biophys. 1986 Apr;246(1):143-8.
54. Princ FG, etal., J Pineal Res. 1998 Jan;24(1):1-8.
55. Puy H, etal., Hum Genet. 1998 Nov;103(5):570-5.
56. RGD automated data pipeline
57. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
58. RGD automated import pipeline for gene-chemical interactions
59. Satija NK and Vij AG, Indian J Physiol Pharmacol. 1995 Oct;39(4):377-82.
60. Schoenfeld N, etal., Eur J Biochem. 1987 Aug 3;166(3):663-6.
61. Serrano-Mendioroz I, etal., Hum Gene Ther. 2018 Apr;29(4):480-491. doi: 10.1089/hum.2017.056. Epub 2018 Jan 2.
62. Shiue JW, etal., Taiwan Yi Xue Hui Za Zhi. 1989 Jul;88(7):729-31.
63. Stubnicer AC, etal., Nucleic Acids Res 1988 Apr 11;16(7):3102.
64. Sul D, etal., Arch Toxicol. 2007 Feb 7;.
65. Sun D, etal., Kidney Int. 2002 Jan;61(1):336-41. doi: 10.1046/j.1523-1755.2002.00105.x.
66. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
67. Tishler PV Life Sci. 1999;65(2):207-14.
68. Tjensvoll K, etal., Dis Markers. 2003-2004;19(1):41-6. doi: 10.1155/2003/384971.
69. Tokola O Br J Pharmacol. 1987 Apr;90(4):661-8.
70. Tomie Y, etal., Res Commun Mol Pathol Pharmacol. 1998 Jan;99(1):5-15.
71. Ulbrichova D, etal., Blood Cells Mol Dis. 2009 Mar-Apr;42(2):167-73. doi: 10.1016/j.bcmd.2008.11.001. Epub 2009 Jan 12.
72. Ulbrichova-Douderova D and Martasek P, Anal Biochem. 2009 Dec 1;395(1):41-8. doi: 10.1016/j.ab.2009.07.050. Epub 2009 Aug 5.
73. Van Hillegersberg R, etal., Gastroenterology. 1992 Aug;103(2):647-51. doi: 10.1016/0016-5085(92)90860-2.
74. Vij AG, etal., Biomed Environ Sci. 1998 Mar;11(1):7-14.
75. Wainstok de Calmanovici R, etal., Biochem J. 1984 Mar 15;218(3):753-63.
76. Wainstok de Calmanovici R, etal., Tumori. 1991 Oct 31;77(5):379-84.
77. Whatley SD, etal., Hum Genet. 1999 Jun;104(6):505-10. doi: 10.1007/s004390050995.
78. Williams DC Biochem J. 1984 Feb 1;217(3):675-83.
79. Woods JS and Fowler BA, Ann N Y Acad Sci. 1987;514:55-64.
80. Woods JS, Biochem Pharmacol. 1976 Oct 1;25(19):2147-52. doi: 10.1016/0006-2952(76)90126-x.
81. Yang J, etal., Gene. 2015 Jul 10;565(2):288-90. doi: 10.1016/j.gene.2015.04.027. Epub 2015 Apr 11.
82. Yasuda M, etal., Hum Mol Genet. 2019 Jun 1;28(11):1755-1767. doi: 10.1093/hmg/ddz003.
Additional References at PubMed
PMID:9712715   PMID:10090993   PMID:12477932   PMID:18004775  


Genomics

Comparative Map Data
Hmbs
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2844,673,554 - 44,680,950 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl844,673,554 - 44,680,957 (-)Ensembl
Rnor_6.0848,667,278 - 48,674,673 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl848,667,275 - 48,674,748 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0847,286,249 - 47,293,618 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4847,314,235 - 47,321,604 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1847,323,010 - 47,328,455 (-)NCBI
Celera844,259,787 - 44,267,156 (-)NCBICelera
RH 3.4 Map8428.0RGD
Cytogenetic Map8q22NCBI
HMBS
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl11119,084,866 - 119,093,549 (+)EnsemblGRCh38hg38GRCh38
GRCh3811119,084,864 - 119,093,549 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3711118,955,591 - 118,964,259 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3611118,460,797 - 118,469,469 (+)NCBINCBI36hg18NCBI36
Build 3411118,460,802 - 118,469,467NCBI
Celera11116,113,008 - 116,121,673 (+)NCBI
Cytogenetic Map11q23.3NCBI
HuRef11114,895,043 - 114,903,707 (+)NCBIHuRef
CHM1_111118,841,878 - 118,850,561 (+)NCBICHM1_1
Hmbs
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39944,247,645 - 44,255,525 (-)NCBIGRCm39mm39
GRCm39 Ensembl944,247,636 - 44,255,525 (-)Ensembl
GRCm38944,336,348 - 44,344,228 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl944,336,339 - 44,344,228 (-)EnsemblGRCm38mm10GRCm38
MGSCv37944,144,431 - 44,152,311 (-)NCBIGRCm37mm9NCBIm37
MGSCv36944,087,343 - 44,095,170 (-)NCBImm8
Celera941,591,069 - 41,599,175 (-)NCBICelera
Cytogenetic Map9A5.2NCBI
cM Map924.84NCBI
Hmbs
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541220,192,522 - 20,202,635 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541220,192,519 - 20,202,635 (+)NCBIChiLan1.0ChiLan1.0
HMBS
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.111117,852,295 - 117,860,757 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11117,852,295 - 117,860,757 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v011113,923,004 - 113,931,732 (+)NCBIMhudiblu_PPA_v0panPan3
HMBS
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1514,767,306 - 14,775,205 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl514,767,666 - 14,775,082 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha514,820,660 - 14,828,175 (-)NCBI
ROS_Cfam_1.0514,710,999 - 14,718,527 (-)NCBI
UMICH_Zoey_3.1514,849,036 - 14,856,511 (-)NCBI
UNSW_CanFamBas_1.0514,753,058 - 14,760,536 (-)NCBI
UU_Cfam_GSD_1.0514,793,431 - 14,800,910 (-)NCBI
Hmbs
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947101,116,546 - 101,124,682 (+)NCBI
SpeTri2.0NW_0049365424,037,888 - 4,046,089 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HMBS
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl946,300,050 - 46,313,936 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1946,300,039 - 46,308,681 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2951,335,231 - 51,343,641 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HMBS
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11110,457,799 - 110,466,361 (+)NCBI
ChlSab1.1 Ensembl1110,457,537 - 110,466,095 (+)Ensembl
Vero_WHO_p1.0NW_02366604315,567,851 - 15,576,221 (-)NCBI
Hmbs
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462478414,467,515 - 14,474,954 (+)NCBI

Position Markers
PMC308923P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2844,676,678 - 44,677,538 (+)MAPPERmRatBN7.2
Rnor_6.0848,670,403 - 48,671,262NCBIRnor6.0
Rnor_5.0847,289,374 - 47,290,233UniSTSRnor5.0
RGSC_v3.4847,317,360 - 47,318,219UniSTSRGSC3.4
Celera844,262,912 - 44,263,771UniSTS
Cytogenetic Map8q22UniSTS
RH128608  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2844,673,678 - 44,673,892 (+)MAPPERmRatBN7.2
Rnor_6.0848,667,403 - 48,667,616NCBIRnor6.0
Rnor_5.0847,286,374 - 47,286,587UniSTSRnor5.0
RGSC_v3.4847,314,360 - 47,314,573UniSTSRGSC3.4
Celera844,259,912 - 44,260,125UniSTS
Cytogenetic Map8q22UniSTS
RH94839  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2844,673,723 - 44,673,827 (+)MAPPERmRatBN7.2
Rnor_6.0848,667,448 - 48,667,551NCBIRnor6.0
Rnor_5.0847,286,419 - 47,286,522UniSTSRnor5.0
RGSC_v3.4847,314,405 - 47,314,508UniSTSRGSC3.4
Celera844,259,957 - 44,260,060UniSTS
Cytogenetic Map8q22UniSTS
RH94840  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map8428.0UniSTS
Cytogenetic Map8q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8767057852670578Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)8768895552688955Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8768895552688955Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)8873663553736635Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)8873663553736635Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)8971222053356647Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81490675159906751Rat
61373Mcs4Mammary carcinoma susceptibility QTL 41.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)81629044461290444Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)81898416884531599Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat
631842Inf1Infertility severity QTL 14.10.001seminal gland mass (VT:0010524)seminal vesicle wet weight (CMO:0001603)82266233067662330Rat
2303564Gluco43Glucose level QTL 433blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)82613018771130187Rat
2303572Insul13Insulin level QTL 132blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)82613018771130187Rat
1359021Bp271Blood pressure QTL 2711.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)82664491246711092Rat
631648Stl5Serum triglyceride level QTL 540.0003blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)82720571554998217Rat
1358892Kidm26Kidney mass QTL 263.69kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)82720571599103503Rat
1358896Bp262Blood pressure QTL 2622.89arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)82720571599103503Rat
1358907Cm40Cardiac mass QTL 401.89heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)82720571599103503Rat
1331804Cm30Cardiac mass QTL 303.77443heart mass (VT:0007028)heart wet weight (CMO:0000069)82824291253961020Rat
1300146Rf17Renal function QTL 172.9renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)82824291273242912Rat
8662823Vetf5Vascular elastic tissue fragility QTL 51.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)82824291299525068Rat
2302278Gluco36Glucose level QTL 364.2blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)82950266550095447Rat
724514Uae15Urinary albumin excretion QTL 152.9urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)82950266570386295Rat
1549908Neudeg1Neurodegradation QTL 15.50nervous system integrity trait (VT:0010566)logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)83018886794457446Rat
1331744Bp217Blood pressure QTL 2173.398arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815458482492Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)83084815461290444Rat
11556286Cm81Cardiac mass QTL 810.01heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)83084815461290444Rat
1359033Bp273Blood pressure QTL 273arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
2313046Bss78Bone structure and strength QTL 783.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)83084815482460899Rat
2313057Bss76Bone structure and strength QTL 7630.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)83084815482460899Rat
2313067Bss77Bone structure and strength QTL 773.10.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)83084815482460899Rat
2313088Bss75Bone structure and strength QTL 753.10.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)83084815482460899Rat
1578755Pur5Proteinuria QTL 53.30.0001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)830848154101699754Rat
1578765Klgr1Kidney lesion grade QTL 13.30.0001kidney morphology trait (VT:0002135)organ lesion measurement (CMO:0000677)830848154101699754Rat
1578769Uae31Urinary albumin excretion QTL 313.30.001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)830848154101699754Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)830848259105647037Rat
1298065Scl16Serum cholesterol level QTL 163.8blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)83085640475856404Rat
1582222Epfw2Epididymal fat weight QTL 23.20.0005epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)83173772976737729Rat
61358Bp39Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83555193880551938Rat
61464Niddm11Non-insulin dependent diabetes mellitus QTL 113.10.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83558203280582032Rat
1331838Niddm61Non-insulin dependent diabetes mellitus QTL 613.530.0004blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83646953599083736Rat
737824Hcar10Hepatocarcinoma resistance QTL 102.9liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)84071306682925667Rat
1358906Bp253Blood pressure QTL 25340.0004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)84071306693965294Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
1331769Rf39Renal function QTL 393.871urine output (VT:0003620)timed urine volume (CMO:0000260)84186687675097878Rat
1298079Activ2Activity QTL 29.50.000001voluntary movement trait (VT:0003491)rearing measurement (CMO:0001515)84186687686866876Rat
631216Stl9Serum triglyceride level QTL 94.710.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)84186701070386132Rat
5684993Bmd84Bone mineral density QTL 844.1tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)84269268450095447Rat
70161Bp62Blood pressure QTL 622.90.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)84269268490165460Rat
12879882Am8Aortic mass QTL 80.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)84329616998968765Rat
12879878Bw183Body weight QTL 1830.001body mass (VT:0001259)body weight (CMO:0000012)84329616998968765Rat
12879879Cm99Cardiac mass QTL 990.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)84329616998968765Rat
12879880Cm100Cardiac mass QTL 1000.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)84329616998968765Rat
12879881Cm101Cardiac mass QTL 1010.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)84329616998968765Rat
12879883Kidm65Kidney mass QTL 650.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)84329616998968765Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:47
Count of miRNA genes:38
Interacting mature miRNAs:46
Transcripts:ENSRNOT00000014127
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 11 68 35 40 11 8
Low 6 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_013168 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242896 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242897 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766148 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766149 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080902 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC105645 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC088162 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473975 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225972 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226062 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230962 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231091 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234793 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234870 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000198 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X06827 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Y12006 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Y17155 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000014127   ⟹   ENSRNOP00000014128
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl844,673,554 - 44,680,957 (-)Ensembl
Rnor_6.0 Ensembl848,667,275 - 48,674,748 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000079275   ⟹   ENSRNOP00000071912
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl844,673,557 - 44,680,938 (-)Ensembl
Rnor_6.0 Ensembl848,667,282 - 48,672,732 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000099584   ⟹   ENSRNOP00000076716
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl844,673,556 - 44,679,341 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000108403   ⟹   ENSRNOP00000082544
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl844,673,653 - 44,680,932 (-)Ensembl
RefSeq Acc Id: NM_013168   ⟹   NP_037300
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2844,673,554 - 44,680,923 (-)NCBI
Rnor_6.0848,667,278 - 48,674,647 (-)NCBI
Rnor_5.0847,286,249 - 47,293,618 (-)NCBI
RGSC_v3.4847,314,235 - 47,321,604 (-)RGD
Celera844,259,787 - 44,267,156 (-)RGD
Sequence:
RefSeq Acc Id: XM_006242896   ⟹   XP_006242958
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2844,673,554 - 44,679,119 (-)NCBI
Rnor_6.0848,667,278 - 48,672,841 (-)NCBI
Rnor_5.0847,286,249 - 47,293,618 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242897   ⟹   XP_006242959
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2844,673,554 - 44,679,120 (-)NCBI
Rnor_6.0848,667,278 - 48,672,842 (-)NCBI
Rnor_5.0847,286,249 - 47,293,618 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008766148   ⟹   XP_008764370
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2844,673,554 - 44,679,121 (-)NCBI
Rnor_6.0848,667,278 - 48,672,845 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008766149   ⟹   XP_008764371
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2844,673,554 - 44,680,948 (-)NCBI
Rnor_6.0848,667,278 - 48,674,673 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039080902   ⟹   XP_038936830
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2844,673,554 - 44,680,950 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_037300   ⟸   NM_013168
- UniProtKB: Q5M893 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242959   ⟸   XM_006242897
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006242958   ⟸   XM_006242896
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008764371   ⟸   XM_008766149
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_008764370   ⟸   XM_008766148
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000071912   ⟸   ENSRNOT00000079275
RefSeq Acc Id: ENSRNOP00000014128   ⟸   ENSRNOT00000014127
RefSeq Acc Id: XP_038936830   ⟸   XM_039080902
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000076716   ⟸   ENSRNOT00000099584
RefSeq Acc Id: ENSRNOP00000082544   ⟸   ENSRNOT00000108403
Protein Domains
Porphobil_deam   Porphobil_deamC

Transcriptome

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

Promoters
RGD ID:13695891
Promoter ID:EPDNEW_R6415
Type:multiple initiation site
Name:Hmbs_1
Description:hydroxymethylbilane synthase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0848,674,666 - 48,674,726EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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
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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2801 AgrOrtholog
Ensembl Genes ENSRNOG00000010390 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000014128 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000071912 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000014127 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000079275 UniProtKB/TrEMBL
Gene3D-CATH 3.30.160.40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7375228 IMAGE-MGC_LOAD
InterPro HemC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Porphobilin_deaminase_cofac_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Porphobilin_deaminase_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Porphobilinogen_deaminase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Porphobilinogen_deaminase_C_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25709 UniProtKB/TrEMBL
MGC_CLONE MGC:108753 IMAGE-MGC_LOAD
NCBI Gene 25709 ENTREZGENE
PANTHER PTHR11557 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Porphobil_deam UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Porphobil_deamC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Hmbs PhenoGen
PIRSF 4pyrrol_synth_OHMeBilane_synth UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS PORPHBDMNASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE PORPHOBILINOGEN_DEAM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54782 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC216644
TIGRFAMs hemC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K1N3_RAT UniProtKB/TrEMBL
  HEM3_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q5M893 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary O08568 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Hmbs  Hydroxymethylbilane synthase      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease in humans, deficiency of this enzyme is associated with acute intermittent porphyria 728563
gene_function deaminase 728563
gene_process enzyme involved in the heme biosynthetic pathway 728563