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: Exhibits nucleic acid binding activity and transcription factor binding activity. Involved in several processes, including cellular response to epidermal growth factor stimulus; cellular response to thapsigargin; and cellular response to tunicamycin. Localizes to 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27134,375,318 - 134,381,610 (+)NCBI
Rnor_6.0 Ensembl7144,865,608 - 144,871,585 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07144,865,302 - 144,871,592 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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)
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)
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 (+)NCBI
Rnor_6.0 Ensembl7144,865,608 - 144,871,585 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07144,865,302 - 144,871,592 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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_11254,641,212 - 54,647,610 (+)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
CanFam3.1 Ensembl271,015,868 - 1,019,891 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1271,013,459 - 1,020,083 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Hnrnpa1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11150,397,173 - 50,403,192 (+)NCBI
ChlSab1.1 Ensembl1150,396,888 - 50,400,802 (+)Ensembl
Hnrnpa1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249042,314,197 - 2,320,900 (+)NCBI


QTLs in Region (Rnor_6.0)
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)751251919145729302Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)771448715145729302Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7100028953145729302Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)7100192194145192194Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)7106564316145729302Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7114825174145729302Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7115922628145729302Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7120746024145692398Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7121654760145729302Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7129412003145729302Rat

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
Rnor_6.0 Ensembl7144,865,623 - 144,871,585 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091596   ⟹   ENSRNOP00000074880
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7144,865,608 - 144,869,926 (+)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
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 (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 142648018 142648019 C G snv BUF/MNa (KyushuU), F344/NSlc (KyushuU), BDIX/NemOda (KyushuU), F344/Jcl (KyushuU), RCS/Kyo (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 144866288 144866289 G A snv CDR
7 144866942 144866943 A C snv COP/CrCrl (MCW & UW)
7 144866949 144866950 A C snv COP/CrCrl (MCW & UW)
7 144866990 144866991 A C snv WN/N (MCW), ACI/N (MCW)
7 144866994 144866995 C G snv COP/CrCrl (MCW & UW), SBH/Ygl (MCW), CDR
7 144867001 144867002 G A snv COP/CrCrl (MCW & UW), SBH/Ygl (MCW), CDR


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69234 AgrOrtholog
Ensembl Genes ENSRNOG00000036839 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000052160 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074880 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000055285 ENTREZGENE, 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