Hnrnpd (heterogeneous nuclear ribonucleoprotein D) - Rat Genome Database

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Gene: Hnrnpd (heterogeneous nuclear ribonucleoprotein D) Rattus norvegicus
Analyze
Symbol: Hnrnpd
Name: heterogeneous nuclear ribonucleoprotein D
RGD ID: 620365
Description: Enables chromatin binding activity; histone deacetylase binding activity; and nucleic acid binding activity. Involved in several processes, including cellular response to estradiol stimulus; cellular response to organonitrogen compound; and regulation of mRNA stability. Located in cytosol and nucleus. Used to study uremia. Biomarker of hepatocellular carcinoma. Orthologous to human HNRNPD (heterogeneous nuclear ribonucleoprotein D); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 1,1-bis(2-aminoethyl)-2-hydroxy-3-oxotriazane; 1,2,4-trimethylbenzene; adenine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: AU-rich element RNA-binding factor 1; AU-rich element RNA-binding protein 1; Auf1; heterogeneous nuclear ribonucleoprotein D0; hnRNP D0; Hnrpd; RNA binding protein p45AUF1
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
mRatBN7.2149,615,375 - 9,638,975 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl149,615,479 - 9,633,786 (+)Ensembl
Rnor_6.01411,256,163 - 11,274,684 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1411,256,268 - 11,274,578 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01411,200,186 - 11,218,696 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41410,917,674 - 10,935,989 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11410,917,909 - 10,935,760 (+)NCBI
Celera149,716,133 - 9,734,433 (+)NCBICelera
Cytogenetic Map14p22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
(Z)-3-butylidenephthalide  (ISO)
1,1-bis(2-aminoethyl)-2-hydroxy-3-oxotriazane  (EXP)
1,2,4-trimethylbenzene  (EXP)
1,2-dimethylhydrazine  (ISO)
14-Deoxy-11,12-didehydroandrographolide  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,6-di-tert-butyl-4-methylphenol  (ISO)
2-amino-14,16-dimethyloctadecan-3-ol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
adenine  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
butanal  (ISO)
cadmium sulfate  (ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chlorpyrifos  (EXP)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
daunorubicin  (ISO)
dexamethasone  (EXP)
dibutyl phthalate  (ISO)
diclofenac  (ISO)
dihydroartemisinin  (ISO)
disodium selenite  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
enzyme inhibitor  (ISO)
ethyl methanesulfonate  (ISO)
fenvalerate  (EXP)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
gentamycin  (EXP)
hydrogen peroxide  (ISO)
hydrogen sulfide  (ISO)
irinotecan  (ISO)
ivermectin  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lead(II) chloride  (ISO)
lipopolysaccharide  (EXP,ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
methylparaben  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
oxaliplatin  (EXP)
paracetamol  (ISO)
paraquat  (ISO)
pentachlorophenol  (ISO)
perfluorooctanoic acid  (EXP)
phenylmercury acetate  (ISO)
phosphorus atom  (EXP)
phosphorus(.)  (EXP)
piroxicam  (ISO)
putrescine  (EXP)
quercetin  (ISO)
quinoline  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
sevoflurane  (EXP)
silver atom  (ISO)
silver(0)  (ISO)
sirolimus  (EXP,ISO)
sodium arsenite  (ISO)
Soman  (EXP)
tetrachloromethane  (EXP)
topotecan  (EXP)
Tributyltin oxide  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vincristine  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytosol  (IDA)
nucleoplasm  (IBA,ISO)
nucleus  (IDA)
ribonucleoprotein complex  (ISO,ISS)
synapse  (ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Arao Y, etal., Biochem J 2002 Jan 1;361(Pt 1):125-32.
2. Arao Y, etal., Mol Endocrinol 2004 Sep;18(9):2255-67. Epub 2004 Jun 10.
3. Blum JL, etal., Am J Physiol Heart Circ Physiol. 2005 Dec;289(6):H2543-50. Epub 2005 Aug 19.
4. Cabilla JP, etal., PLoS One. 2011;6(12):e29402. doi: 10.1371/journal.pone.0029402. Epub 2011 Dec 28.
5. Chen YI, etal., Nucleic Acids Res. 2007;35(12):3928-44. Epub 2007 May 30.
6. Ehrenman K, etal., Gene 1994 Nov 18;149(2):315-9.
7. Faura M, etal., Biochem Biophys Res Commun. 1995 Dec 14;217(2):554-60.
8. Frau M, etal., Hepatology. 2012 Jul;56(1):165-75. doi: 10.1002/hep.25643. Epub 2012 Jun 5.
9. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
10. GOA data from the GO Consortium
11. Hambardzumyan D, etal., J Neurosci Res. 2009 May 1;87(6):1296-309. doi: 10.1002/jnr.21957.
12. Jurado S, etal., J Cell Sci. 2006 Apr 15;119(Pt 8):1622-31. Epub 2006 Mar 28.
13. Kakegawa T, etal., Arch Biochem Biophys. 2007 Sep 1;465(1):274-81. Epub 2007 Jun 9.
14. Lai RY, etal., Am J Physiol Cell Physiol. 2010 Jul;299(1):C155-63. doi: 10.1152/ajpcell.00523.2009. Epub 2010 Apr 7.
15. Lee C, etal., Cereb Cortex. 2008 Dec;18(12):2909-19. doi: 10.1093/cercor/bhn051. Epub 2008 Apr 15.
16. Levi R, etal., J Am Soc Nephrol. 2006 Jan;17(1):107-12. Epub 2005 Nov 16.
17. Liu W, etal., J Neurosci Res. 2006 Aug 1;84(2):360-9.
18. MGD data from the GO Consortium
19. Mikula M, etal., Proteomics. 2006 Apr;6(8):2395-406.
20. NCBI rat LocusLink and RefSeq merged data July 26, 2002
21. Nechama M, etal., FASEB J. 2008 Oct;22(10):3458-68. doi: 10.1096/fj.08-107250. Epub 2008 Jun 26.
22. Rao JS, etal., Pharmacogenomics J. 2006 Nov-Dec;6(6):413-20. Epub 2006 Apr 25.
23. RGD automated import pipeline for gene-chemical interactions
24. Vazquez-Chantada M, etal., Gastroenterology. 2010 May;138(5):1943-53. doi: 10.1053/j.gastro.2010.01.032. Epub 2010 Jan 25.
25. Zou T, etal., Mol Cell Biol. 2010 Nov;30(21):5021-32. doi: 10.1128/MCB.00807-10. Epub 2010 Aug 30.
Additional References at PubMed
PMID:8321232   PMID:14976220   PMID:15514034   PMID:16219914   PMID:16452087   PMID:16603688   PMID:16769718   PMID:17289661   PMID:18789946   PMID:22633954   PMID:22658674   PMID:22681889  
PMID:23106098   PMID:23376485   PMID:24423872   PMID:24625528   PMID:26316108   PMID:27034373   PMID:28986222   PMID:29476059  


Genomics

Comparative Map Data
Hnrnpd
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2149,615,375 - 9,638,975 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl149,615,479 - 9,633,786 (+)Ensembl
Rnor_6.01411,256,163 - 11,274,684 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1411,256,268 - 11,274,578 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01411,200,186 - 11,218,696 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41410,917,674 - 10,935,989 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11410,917,909 - 10,935,760 (+)NCBI
Celera149,716,133 - 9,734,433 (+)NCBICelera
Cytogenetic Map14p22NCBI
HNRNPD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl482,352,498 - 82,374,503 (-)EnsemblGRCh38hg38GRCh38
GRCh38482,352,498 - 82,373,991 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37483,273,651 - 83,295,144 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36483,493,491 - 83,514,173 (-)NCBINCBI36hg18NCBI36
Build 34483,631,645 - 83,652,328NCBI
Celera480,565,274 - 80,585,965 (-)NCBI
Cytogenetic Map4q21.22NCBI
HuRef479,014,546 - 79,035,236 (-)NCBIHuRef
CHM1_1483,250,972 - 83,271,667 (-)NCBICHM1_1
Hnrnpd
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395100,103,794 - 100,126,926 (-)NCBIGRCm39mm39
GRCm39 Ensembl5100,103,794 - 100,126,797 (-)Ensembl
GRCm38599,955,935 - 99,979,130 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl599,955,935 - 99,978,938 (-)EnsemblGRCm38mm10GRCm38
MGSCv375100,384,955 - 100,407,957 (-)NCBIGRCm37mm9NCBIm37
MGSCv365100,201,309 - 100,218,851 (-)NCBImm8
Celera597,269,494 - 97,292,491 (-)NCBICelera
Cytogenetic Map5E4NCBI
Hnrnpd
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554336,454,454 - 6,469,904 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554336,452,931 - 6,470,209 (-)NCBIChiLan1.0ChiLan1.0
HNRNPD
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1447,675,382 - 47,696,894 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl447,676,599 - 47,696,894 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0441,825,518 - 41,846,166 (+)NCBIMhudiblu_PPA_v0panPan3
HNRNPD
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1326,323,444 - 6,341,238 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl326,323,469 - 6,341,166 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3235,539,639 - 35,557,456 (+)NCBI
ROS_Cfam_1.0326,346,646 - 6,364,470 (-)NCBI
UMICH_Zoey_3.1326,376,955 - 6,394,761 (-)NCBI
UNSW_CanFamBas_1.0326,283,881 - 6,301,733 (-)NCBI
UU_Cfam_GSD_1.03233,661,515 - 33,679,335 (+)NCBI
Hnrnpd
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244052855,934,255 - 5,953,306 (+)NCBI
SpeTri2.0NW_0049367382,096,370 - 2,115,135 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HNRNPD
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8135,844,487 - 135,862,633 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18135,844,492 - 135,862,633 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28145,204,594 - 145,218,439 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HNRNPD
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1730,729,697 - 30,749,793 (-)NCBI
ChlSab1.1 Ensembl730,731,175 - 30,749,876 (-)Ensembl
Vero_WHO_p1.0NW_0236660379,284,119 - 9,304,361 (-)NCBI
Hnrnpd
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247578,532,373 - 8,549,840 (+)NCBI

Position Markers
RH136938  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2149,633,559 - 9,633,742 (+)MAPPERmRatBN7.2
Rnor_6.01411,274,350 - 11,274,532NCBIRnor6.0
Rnor_5.01411,218,373 - 11,218,555UniSTSRnor5.0
RGSC_v3.41410,935,756 - 10,935,938UniSTSRGSC3.4
Celera149,734,200 - 9,734,382UniSTS
RH 3.4 Map14130.09UniSTS
Cytogenetic Map14p22UniSTS
MARC_23646-23647:1029444341:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2149,627,896 - 9,628,952 (+)MAPPERmRatBN7.2
Rnor_6.01411,268,685 - 11,269,742NCBIRnor6.0
Rnor_5.01411,212,708 - 11,213,765UniSTSRnor5.0
RGSC_v3.41410,930,091 - 10,931,148UniSTSRGSC3.4
Celera149,728,550 - 9,729,607UniSTS
Cytogenetic Map14p22UniSTS
MARC_23650-23651:1029445581:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2149,632,621 - 9,633,574 (+)MAPPERmRatBN7.2
Rnor_6.01411,273,412 - 11,274,364NCBIRnor6.0
Rnor_5.01411,217,435 - 11,218,387UniSTSRnor5.0
RGSC_v3.41410,934,818 - 10,935,770UniSTSRGSC3.4
Celera149,733,262 - 9,734,214UniSTS
Cytogenetic Map14p22UniSTS
Hnrnpd  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X31,845,062 - 31,845,321 (+)MAPPERmRatBN7.2
Rnor_6.0X33,580,661 - 33,580,919NCBIRnor6.0
Rnor_5.0X33,927,890 - 33,928,148UniSTSRnor5.0
RGSC_v3.4X52,600,676 - 52,600,934UniSTSRGSC3.4
CeleraX32,149,434 - 32,149,692UniSTS
Cytogenetic Map14p22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
71115Niddm15Non-insulin dependent diabetes mellitus QTL 154.8blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14121760611030812Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14121760616960180Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)14381307418274691Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)14381307418274691Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14381307421217635Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14381307424531477Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14381307430767156Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:969
Count of miRNA genes:188
Interacting mature miRNAs:219
Transcripts:ENSRNOT00000003158, ENSRNOT00000003173, ENSRNOT00000047840
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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 37 52 36 19 36 3 6 74 35 41 11 3
Low 6 5 5 5 5 5 5
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001082539 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001082540 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001082541 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_024404 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005493015 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_359351 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB046615 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB046616 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB046617 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB046618 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC131411 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB798484 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474022 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CO560068 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CO567918 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212501 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000248 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000003158   ⟹   ENSRNOP00000003158
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl149,615,479 - 9,633,786 (+)Ensembl
Rnor_6.0 Ensembl1411,256,268 - 11,274,578 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000003173   ⟹   ENSRNOP00000003173
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl149,615,479 - 9,633,786 (+)Ensembl
Rnor_6.0 Ensembl1411,256,268 - 11,274,578 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000047840   ⟹   ENSRNOP00000046491
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl149,615,479 - 9,633,786 (+)Ensembl
Rnor_6.0 Ensembl1411,256,268 - 11,274,578 (+)Ensembl
RefSeq Acc Id: NM_001082539   ⟹   NP_001076008
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2149,615,479 - 9,633,793 (+)NCBI
Rnor_6.01411,256,268 - 11,274,583 (+)NCBI
Rnor_5.01411,200,186 - 11,218,696 (+)NCBI
RGSC_v3.41410,917,674 - 10,935,989 (+)RGD
Celera149,716,133 - 9,734,433 (+)RGD
Sequence:
RefSeq Acc Id: NM_001082540   ⟹   NP_001076009
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2149,615,479 - 9,633,793 (+)NCBI
Rnor_6.01411,256,268 - 11,274,583 (+)NCBI
Rnor_5.01411,200,186 - 11,218,696 (+)NCBI
RGSC_v3.41410,917,674 - 10,935,989 (+)RGD
Celera149,716,133 - 9,734,433 (+)RGD
Sequence:
RefSeq Acc Id: NM_001082541   ⟹   NP_001076010
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2149,615,479 - 9,633,793 (+)NCBI
Rnor_6.01411,256,268 - 11,274,583 (+)NCBI
Rnor_5.01411,200,186 - 11,218,696 (+)NCBI
RGSC_v3.41410,917,674 - 10,935,989 (+)RGD
Celera149,716,133 - 9,734,433 (+)RGD
Sequence:
RefSeq Acc Id: NM_024404   ⟹   NP_077380
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2149,615,479 - 9,633,793 (+)NCBI
Rnor_6.01411,256,268 - 11,274,583 (+)NCBI
Rnor_5.01411,200,186 - 11,218,696 (+)NCBI
RGSC_v3.41410,917,674 - 10,935,989 (+)RGD
Celera149,716,133 - 9,734,433 (+)RGD
Sequence:
RefSeq Acc Id: XR_005493015
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2149,615,375 - 9,638,975 (+)NCBI
RefSeq Acc Id: XR_359351
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2149,615,375 - 9,638,975 (+)NCBI
Rnor_6.01411,256,163 - 11,274,684 (+)NCBI
Rnor_5.01411,200,186 - 11,218,696 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_077380   ⟸   NM_024404
- Peptide Label: isoform a
- UniProtKB: Q9JJ54 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001076010   ⟸   NM_001082541
- Peptide Label: isoform d
- UniProtKB: Q9JJ54 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001076008   ⟸   NM_001082539
- Peptide Label: isoform b
- UniProtKB: Q9JJ54 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001076009   ⟸   NM_001082540
- Peptide Label: isoform c
- UniProtKB: Q9JJ54 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000046491   ⟸   ENSRNOT00000047840
RefSeq Acc Id: ENSRNOP00000003173   ⟸   ENSRNOT00000003173
RefSeq Acc Id: ENSRNOP00000003158   ⟸   ENSRNOT00000003158
Protein Domains
RRM

Transcriptome

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

Promoters
RGD ID:13699199
Promoter ID:EPDNEW_R9723
Type:initiation region
Name:Hnrnpd_1
Description:heterogeneous nuclear ribonucleoprotein D
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_6.01411,256,247 - 11,256,307EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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
ACI/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)
ACI/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
ACI/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
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (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
BN/SsN (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
BN/SsN (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
BUF/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
BXH2/CubMcwi (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
BXH3/CubMcwi (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
Buf/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
COP/CrCrl (MCW & UW)
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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)
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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
F344/DuCrl (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
F344/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
F344/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
F344/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
F344/NRrrc (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
F344/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
FHH/EurMcwi (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
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
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)
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
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)
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
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)
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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 (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)
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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 (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
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:620365 AgrOrtholog
Ensembl Genes ENSRNOG00000002292 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000003158 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000003173 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000046491 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000003158 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000003173 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000047840 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.70.330 UniProtKB/Swiss-Prot
InterPro CARG-binding_factor_N UniProtKB/Swiss-Prot
  Nucleotide-bd_a/b_plait_sf UniProtKB/Swiss-Prot
  RBD_domain_sf UniProtKB/Swiss-Prot
  RRM_dom UniProtKB/Swiss-Prot
KEGG Report rno:79256 UniProtKB/Swiss-Prot
NCBI Gene 79256 ENTREZGENE
Pfam CBFNT UniProtKB/Swiss-Prot
  RRM_1 UniProtKB/Swiss-Prot
PhenoGen Hnrnpd PhenoGen
PROSITE RRM UniProtKB/Swiss-Prot
SMART RRM UniProtKB/Swiss-Prot
Superfamily-SCOP SSF54928 UniProtKB/Swiss-Prot
UniProt HNRPD_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary G3V9G2 UniProtKB/Swiss-Prot
  P17132 UniProtKB/Swiss-Prot
  Q9JJ51 UniProtKB/Swiss-Prot
  Q9JJ52 UniProtKB/Swiss-Prot
  Q9JJ53 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-05-04 Hnrnpd  heterogeneous nuclear ribonucleoprotein D  Hnrpd  heterogeneous nuclear ribonucleoprotein D  Symbol changed 629549 APPROVED
2005-01-20 Hnrpd  heterogeneous nuclear ribonucleoprotein D    RNA binding protein p45AUF1  Name updated 1299863 APPROVED
2002-08-07 Hnrpd  RNA binding protein p45AUF1      Symbol and Name status set to provisional 70820 PROVISIONAL