Hnrnpa1 (heterogeneous nuclear ribonucleoprotein A1) - Rat Genome Database

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Gene: Hnrnpa1 (heterogeneous nuclear ribonucleoprotein A1) Rattus norvegicus
Analyze
Symbol: Hnrnpa1
Name: heterogeneous nuclear ribonucleoprotein A1
RGD ID: 69234
Description: Enables nucleic acid binding activity. Involved in several processes, including cellular response to epidermal growth factor stimulus; cellular response to thapsigargin; and cellular response to tunicamycin. Located in cytosol and nucleoplasmic periphery of the nuclear pore complex. Human ortholog(s) of this gene implicated in amyotrophic lateral sclerosis type 20; inclusion body myopathy with early-onset Paget disease of bone with or without frontotemporal dementia 3; and tropical spastic paraparesis. Orthologous to several human genes including HNRNPA1L2 (heterogeneous nuclear ribonucleoprotein A1 like 2); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 2,4-dibromophenyl 2,4,5-tribromophenyl ether.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: HDP; helix-destabilizing protein; hnRNP A1; hnRNP core protein A1; Hnrpa1; single-strand RNA-binding protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Hnrnpa1-ps1  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27134,375,318 - 134,381,610 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7134,375,150 - 134,381,609 (+)Ensembl
Rnor_6.07144,865,302 - 144,871,592 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7144,865,608 - 144,871,585 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07142,647,071 - 142,652,967 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47142,150,229 - 142,154,520 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17142,230,417 - 142,234,709 (+)NCBI
Celera7130,801,278 - 130,805,569 (+)NCBICelera
Cytogenetic Map7q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
14-Deoxy-11,12-didehydroandrographolide  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP)
1H-pyrazole  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (EXP)
2,6-di-tert-butyl-4-methylphenol  (ISO)
2,6-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-methylcholanthrene  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acetylsalicylic acid  (EXP)
acrolein  (ISO)
actinomycin D  (ISO)
aflatoxin B1  (ISO)
alachlor  (EXP)
alpha-pinene  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beryllium sulfate  (ISO)
bisphenol A  (EXP,ISO)
buspirone  (EXP)
butanal  (ISO)
butyric acid  (EXP)
cadmium atom  (ISO)
caffeine  (ISO)
calcitriol  (ISO)
capsaicin  (EXP)
carbon nanotube  (ISO)
carvedilol  (ISO)
cefaloridine  (EXP)
chloroprene  (EXP)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
colforsin daropate hydrochloride  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
corticosterone  (EXP)
crocidolite asbestos  (ISO)
curcumin  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
endosulfan  (EXP)
enzyme inhibitor  (ISO)
ethanol  (EXP)
flutamide  (EXP)
folic acid  (ISO)
furan  (EXP)
gentamycin  (EXP)
glafenine  (EXP)
glycidol  (EXP)
hydrazine  (ISO)
irinotecan  (ISO)
ivermectin  (ISO)
josamycin  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
methylmercury chloride  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
nickel sulfate  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (ISO)
PCB138  (EXP)
pentachlorophenol  (ISO)
perfluorooctanoic acid  (EXP)
phorone  (EXP)
pirinixic acid  (EXP)
propiconazole  (ISO)
quercetin  (EXP,ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
sodium arsenite  (EXP)
sodium dichromate  (EXP)
sunitinib  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thapsigargin  (EXP,ISO)
topotecan  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (ISO)
tunicamycin  (EXP,ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
Yessotoxin  (ISO)
zinc sulfate  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. An P and Grabowski PJ, PLoS Biol. 2007 Feb;5(2):e36.
2. Berson A, etal., EMBO Mol Med. 2012 Aug;4(8):730-42. doi: 10.1002/emmm.201100995. Epub 2012 May 25.
3. Boukakis G, etal., BMC Cancer. 2010 Aug 17;10:434. doi: 10.1186/1471-2407-10-434.
4. Chen YI, etal., Nucleic Acids Res. 2007;35(12):3928-44. Epub 2007 May 30.
5. Chettouh H, etal., Cancer Res. 2013 Jul 1;73(13):3974-86. doi: 10.1158/0008-5472.CAN-12-3824. Epub 2013 Apr 30.
6. Cobianchi F, etal., J Biol Chem 1986 Mar 15;261(8):3536-43.
7. Damiano F, etal., Biochem J. 2013 Jan 15;449(2):543-53. doi: 10.1042/BJ20120906.
8. Di Liegro CM, etal., Neuroscience. 2013 Jan 15;229:71-6. doi: 10.1016/j.neuroscience.2012.10.072. Epub 2012 Nov 14.
9. Faura M, etal., Biochem Biophys Res Commun. 1995 Dec 14;217(2):554-60.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. Hanamura A, etal., RNA. 1998 Apr;4(4):430-44.
12. Hope NR and Murray GI, Hum Pathol. 2011 Mar;42(3):393-402. doi: 10.1016/j.humpath.2010.08.006. Epub 2010 Dec 30.
13. Iborra FJ, etal., J Cell Sci. 2000 Jan;113 Pt 2:291-302.
14. Idriss H, etal., Biochemistry. 1994 Sep 20;33(37):11382-90.
15. Kalume F, etal., J Neurosci Res. 2004 Jul 1;77(1):82-9.
16. Kirigiti P, etal., Mol Pharmacol. 2001 Dec;60(6):1308-24.
17. Kumar A and Wilson SH, Biochemistry. 1990 Dec 4;29(48):10717-22.
18. Levin MC, etal., Nat Med. 2002 May;8(5):509-13.
19. Ma AS, etal., J Biol Chem 2002 May 17;277(20):18010-20.
20. Matsui M, etal., Biochim Biophys Acta. 2000 Sep 7;1493(1-2):33-40.
21. MGD data from the GO Consortium
22. Mikula M, etal., Proteomics. 2006 Apr;6(8):2395-406.
23. NCBI rat LocusLink and RefSeq merged data July 26, 2002
24. OMIM Disease Annotation Pipeline
25. Pipeline to import KEGG annotations from KEGG into RGD
26. Planck SR, etal., Nucleic Acids Res. 1988 Dec 23;16(24):11663-73.
27. Rayani HH, etal., Exp Lung Res. 1998 Jan-Feb;24(1):101-18.
28. RGD automated data pipeline
29. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
30. RGD automated import pipeline for gene-chemical interactions
31. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
32. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
33. Wahl MC, etal., Cell. 2009 Feb 20;136(4):701-18. doi: 10.1016/j.cell.2009.02.009.
Additional References at PubMed
PMID:2447078   PMID:8521471   PMID:9731529   PMID:10332027   PMID:10749975   PMID:11991638   PMID:15615787   PMID:15798186   PMID:16396499   PMID:16641100   PMID:16854843   PMID:17289661  
PMID:18809582   PMID:19946888   PMID:20458337   PMID:21253564   PMID:21984414   PMID:22082260   PMID:22658674   PMID:22681889   PMID:23455423   PMID:23935072   PMID:24529708   PMID:24625528  
PMID:25009770   PMID:25689357   PMID:25931508   PMID:26316108   PMID:27694260   PMID:28431233  


Genomics

Comparative Map Data
Hnrnpa1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27134,375,318 - 134,381,610 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7134,375,150 - 134,381,609 (+)Ensembl
Rnor_6.07144,865,302 - 144,871,592 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7144,865,608 - 144,871,585 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07142,647,071 - 142,652,967 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47142,150,229 - 142,154,520 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17142,230,417 - 142,234,709 (+)NCBI
Celera7130,801,278 - 130,805,569 (+)NCBICelera
Cytogenetic Map7q36NCBI
HNRNPA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1254,280,193 - 54,287,088 (+)EnsemblGRCh38hg38GRCh38
GRCh381254,280,726 - 54,287,087 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371254,674,510 - 54,680,871 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361252,960,755 - 52,965,297 (+)NCBINCBI36hg18NCBI36
Build 341252,960,754 - 52,965,297NCBI
Celera1254,326,467 - 54,331,009 (+)NCBI
Cytogenetic Map12q13.13NCBI
HuRef1251,713,759 - 51,718,301 (+)NCBIHuRef
CHM1_11254,641,226 - 54,645,768 (+)NCBICHM1_1
Hnrnpa1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915103,148,370 - 103,155,125 (+)NCBIGRCm39mm39
GRCm39 Ensembl15103,148,859 - 103,155,119 (+)Ensembl
GRCm3815103,239,943 - 103,246,698 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15103,240,432 - 103,246,692 (+)EnsemblGRCm38mm10GRCm38
MGSCv3715103,070,863 - 103,075,386 (+)NCBIGRCm37mm9NCBIm37
MGSCv3615103,068,466 - 103,072,989 (+)NCBImm8
Celera15105,402,021 - 105,406,544 (+)NCBICelera
Cytogenetic Map15F3NCBI
cM Map1558.58NCBI
Hnrnpa1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554581,530,163 - 1,536,874 (+)NCBIChiLan1.0ChiLan1.0
HNRNPA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11235,182,164 - 35,188,651 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1235,184,943 - 35,188,443 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01234,456,900 - 34,463,317 (-)NCBIMhudiblu_PPA_v0panPan3
HNRNPA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1271,013,459 - 1,020,083 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl271,015,868 - 1,019,891 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2745,235,341 - 45,240,080 (+)NCBI
ROS_Cfam_1.0271,012,273 - 1,017,012 (-)NCBI
UMICH_Zoey_3.1271,031,242 - 1,035,976 (-)NCBI
UNSW_CanFamBas_1.0271,010,967 - 1,017,580 (-)NCBI
UU_Cfam_GSD_1.02745,639,146 - 45,643,882 (+)NCBI
Hnrnpa1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494561,677,106 - 61,683,541 (-)NCBI
SpeTri2.0NW_00493651211,481,017 - 11,487,737 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HNRNPA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl519,485,096 - 19,491,419 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1519,485,033 - 19,491,418 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2520,329,539 - 20,334,145 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HNRNPA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11150,397,173 - 50,403,192 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1150,396,888 - 50,400,802 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037195,638,486 - 195,645,432 (-)NCBIVero_WHO_p1.0
Hnrnpa1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249042,314,197 - 2,320,900 (+)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7119513385135012528Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:181
Count of miRNA genes:130
Interacting mature miRNAs:142
Transcripts:ENSRNOT00000055285
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 2 6 6 6 39 12 17
Medium 3 41 51 35 19 35 8 11 35 23 24 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000055285   ⟹   ENSRNOP00000052160
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7134,375,216 - 134,381,609 (+)Ensembl
Rnor_6.0 Ensembl7144,865,623 - 144,871,585 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091596   ⟹   ENSRNOP00000074880
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7134,375,150 - 134,379,006 (+)Ensembl
Rnor_6.0 Ensembl7144,865,608 - 144,869,926 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000113929   ⟹   ENSRNOP00000094714
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7134,375,150 - 134,379,557 (+)Ensembl
RefSeq Acc Id: NM_017248   ⟹   NP_058944
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27134,375,656 - 134,379,947 (+)NCBI
Rnor_6.07144,865,640 - 144,869,931 (+)NCBI
Rnor_5.07142,647,071 - 142,652,967 (+)NCBI
RGSC_v3.47142,150,229 - 142,154,520 (+)RGD
Celera7130,801,278 - 130,805,569 (+)RGD
Sequence:
RefSeq Acc Id: XM_006242384   ⟹   XP_006242446
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27134,375,318 - 134,379,944 (+)NCBI
Rnor_6.07144,865,302 - 144,869,928 (+)NCBI
Rnor_5.07142,647,071 - 142,652,967 (+)NCBI
Sequence:
RefSeq Acc Id: XR_356017
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27134,375,318 - 134,381,610 (+)NCBI
Rnor_6.07144,865,302 - 144,871,592 (+)NCBI
Rnor_5.07142,647,071 - 142,652,967 (+)NCBI
Sequence:
RefSeq Acc Id: XR_356018
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27134,375,318 - 134,381,610 (+)NCBI
Rnor_6.07144,865,302 - 144,871,592 (+)NCBI
Rnor_5.07142,647,071 - 142,652,967 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_058944   ⟸   NM_017248
- Sequence:
RefSeq Acc Id: XP_006242446   ⟸   XM_006242384
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000052160   ⟸   ENSRNOT00000055285
RefSeq Acc Id: ENSRNOP00000074880   ⟸   ENSRNOT00000091596
RefSeq Acc Id: ENSRNOP00000094714   ⟸   ENSRNOT00000113929
Protein Domains
RRM

Transcriptome

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

Promoters
RGD ID:13695728
Promoter ID:EPDNEW_R6238
Type:multiple initiation site
Name:Hnrnpa1_1
Description:heterogeneous nuclear ribonucleoprotein A1
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_6.07144,865,608 - 144,865,668EPDNEW

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)
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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)
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)
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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)
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)
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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)
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (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)
GK/FarMcwi (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
GK/Ox (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
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)
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
HXB20/IpcvMcwi (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
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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
LE/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
LE/Stm (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
LEW/Crl (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
LEW/Crl (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
LEW/NCrlBR (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
LEXF10A/StmMcwi (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
LEXF11/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/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
LEXF1C/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
LEXF2B/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
LEXF3/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (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
LH/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (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
LL/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (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
LN/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/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
M520/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
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)
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
MNS/Gib (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
MR/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
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)
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
PVG/Seac (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
SBH/Ygl (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: 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)
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: 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)
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/OlalpcvMcwi (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
SHRSP/A3NCrl (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
SHRSP/Gcrc (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
SR/JrHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WAG/RijCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (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/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
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)
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
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:69234 AgrOrtholog
Ensembl Genes ENSRNOG00000036839 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000052160 UniProtKB/TrEMBL
  ENSRNOP00000074880 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000055285 UniProtKB/TrEMBL
  ENSRNOT00000091596 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6920834 IMAGE-MGC_LOAD
  IMAGE:7374689 IMAGE-MGC_LOAD
InterPro HnRNPA1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  hnRNPA1_RRM1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  hnRNPA1_RRM2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucleotide-bd_a/b_plait_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29578 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108719 IMAGE-MGC_LOAD
  MGC:72886 IMAGE-MGC_LOAD
NCBI Gene 29578 ENTREZGENE
Pfam HnRNPA1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Hnrnpa1 PhenoGen
PROSITE RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC228827
UniProt P04256 ENTREZGENE
  Q5I0M7_RAT UniProtKB/TrEMBL
  Q6P6G9_RAT UniProtKB/TrEMBL
  ROA1_RAT UniProtKB/Swiss-Prot
UniProt Secondary F7FEZ6 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-18 Hnrnpa1  heterogeneous nuclear ribonucleoprotein A1  Hnrpa1  heterogeneous nuclear ribonucleoprotein A1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Hnrpa1  heterogeneous nuclear ribonucleoprotein A1      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function protein has two repeats of quasi-RRM domains than bind to mRNA 68800
gene_process protein associated with pre-mRNAs in the nucleus and appear to influence mRNA processing, metabolism and transport 68800