Hba-a1 (hemoglobin alpha, adult chain 1) - Rat Genome Database

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Gene: Hba-a1 (hemoglobin alpha, adult chain 1) Rattus norvegicus
Analyze
Symbol: Hba-a1
Name: hemoglobin alpha, adult chain 1
RGD ID: 2782
Description: Enables amyloid-beta binding activity. Involved in negative regulation of blood pressure and regulation of sensory perception of pain. Located in synapse. Used to study alpha thalassemia. Biomarker of Alzheimer's disease; PARTICIPATES IN malaria pathway; sleeping sickness pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: alpha-1/2-globin; Hba-a2; Hba1; HBAM; hemoglobin alpha 1 chain; hemoglobin alpha, adult chain 2; hemoglobin alpha-1/2 chain; hemoglobin subunit alpha-1/2; hemoglobin, alpha 1
RGD Orthologs
Mouse
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21015,337,265 - 15,338,121 (-)NCBImRatBN7.2
Rnor_6.01015,602,794 - 15,603,649 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1015,602,794 - 15,603,649 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01015,497,889 - 15,498,744 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41015,584,360 - 15,585,215 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11015,585,407 - 15,586,263 (-)NCBI
Celera1015,004,857 - 15,005,712 (-)NCBICelera
RH 3.4 Map10153.7RGD
Cytogenetic Map10q12NCBI
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
(S)-nicotine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-diaminotoluene  (ISO)
3,3',5-triiodo-L-thyronine  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
Aroclor 1254  (ISO)
benzene  (EXP)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP)
bisphenol F  (ISO)
bromobenzene  (EXP)
buspirone  (EXP)
cadmium atom  (EXP)
cadmium dichloride  (EXP)
caffeine  (ISO)
carbon nanotube  (ISO)
ciguatoxin CTX1B  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
Cuprizon  (EXP)
deoxynivalenol  (ISO)
doxorubicin  (ISO)
flutamide  (EXP)
folic acid  (ISO)
maneb  (ISO)
methotrexate  (EXP,ISO)
N-(6-acetamidohexyl)acetamide  (ISO)
nefazodone  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
nicotine  (ISO)
nimesulide  (EXP)
ozone  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenacetin  (EXP)
phenylhydrazine  (EXP)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
propiconazole  (ISO)
pyrogallol  (ISO)
raloxifene  (EXP)
resveratrol  (ISO)
rotenone  (EXP)
sodium arsenite  (EXP,ISO)
sodium dichromate  (ISO)
sodium fluoride  (ISO)
tamoxifen  (EXP,ISO)
tetrachloromethane  (EXP)
tremolite asbestos  (ISO)
triptonide  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zearalenone  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Alauddin H, etal., Hemoglobin. 2014;38(4):277-81. doi: 10.3109/03630269.2014.916720. Epub 2014 May 14.
2. Ameri A, etal., Blood. 1999 Sep 1;94(5):1825-6.
3. Baklouti F, etal., Eur J Biochem. 1988 Nov 1;177(2):307-12.
4. Chua CG and Carrell RW, Biochim Biophys Acta. 1974 Oct 9;365(2):328-34.
5. Dale CS, etal., Mem Inst Oswaldo Cruz. 2005 Mar;100 Suppl 1:105-6. Epub 2005 Jun 14.
6. Deng L, etal., Hum Reprod. 2009 Jan;24(1):211-8. doi: 10.1093/humrep/den318. Epub 2008 Sep 10.
7. Fucharoen S, etal., Haematologica. 2003 Oct;88(10):1092-8.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. Groff P, etal., Hemoglobin. 1989;13(5):429-36.
10. John ME Eur J Biochem. 1982 May 17;124(2):305-10.
11. Kanduc D J Virol. 2002 Jul;76(14):7040-8.
12. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
13. Liebhaber SA, etal., J Clin Invest. 1985 Sep;76(3):1057-64.
14. Lu M, etal., Chem Res Toxicol. 2004 Dec;17(12):1733-42.
15. MGD data from the GO Consortium
16. Moi P, etal., J Clin Invest. 1987 Nov;80(5):1416-21.
17. Morle F, etal., EMBO J. 1985 May;4(5):1245-50.
18. Mukherjee MB, etal., Indian J Med Res. 1998 Apr;107:178-81.
19. NCBI rat LocusLink and RefSeq merged data July 26, 2002
20. Ohba Y, etal., Hemoglobin. 1987;11(6):539-56.
21. OMIM Disease Annotation Pipeline
22. Oyama R, etal., Biochim Biophys Acta. 2000 Jun 15;1479(1-2):91-102.
23. Pipeline to import KEGG annotations from KEGG into RGD
24. Pirastu M, etal., J Biol Chem. 1984 Oct 25;259(20):12315-7.
25. RGD automated data pipeline
26. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
27. RGD automated import pipeline for gene-chemical interactions
28. Satoh H, etal., Biochem Biophys Res Commun 1987 Jul 31;146(2):618-24.
29. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
30. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
31. Traeger-Synodinos J, etal., Hemoglobin. 1999 Nov;23(4):317-24.
32. Yang H, etal., Indian J Exp Biol. 2011 Feb;49(2):118-24.
Additional References at PubMed
PMID:242324   PMID:1191258   PMID:6098570   PMID:7550311   PMID:8226096   PMID:8334153   PMID:8706699   PMID:10196478   PMID:15489334   PMID:17086191   PMID:17634366   PMID:19479992  
PMID:19740759   PMID:19946888   PMID:20458337   PMID:21805676   PMID:22516433   PMID:22871113   PMID:23012479   PMID:23376485   PMID:23533145   PMID:26316108   PMID:31904090  


Genomics

Comparative Map Data
Hba-a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21015,337,265 - 15,338,121 (-)NCBImRatBN7.2
Rnor_6.01015,602,794 - 15,603,649 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1015,602,794 - 15,603,649 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01015,497,889 - 15,498,744 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41015,584,360 - 15,585,215 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11015,585,407 - 15,586,263 (-)NCBI
Celera1015,004,857 - 15,005,712 (-)NCBICelera
RH 3.4 Map10153.7RGD
Cytogenetic Map10q12NCBI
Hba-a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391132,233,672 - 32,234,486 (+)NCBIGRCm39mm39
GRCm39 Ensembl1132,233,511 - 32,234,465 (+)Ensembl
GRCm381132,283,672 - 32,284,486 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1132,283,511 - 32,284,465 (+)EnsemblGRCm38mm10GRCm38
MGSCv371132,183,672 - 32,184,486 (+)NCBIGRCm37mm9NCBIm37
MGSCv361132,261,880 - 32,262,699 (+)NCBImm8
MGSCv361132,183,674 - 32,184,493 (+)NCBImm8
Celera1134,700,973 - 34,701,816 (+)NCBICelera
Cytogenetic Map11A4NCBI
cM Map1118.86NCBI

Position Markers
BI278462  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21015,323,916 - 15,324,261 (+)MAPPERmRatBN7.2
mRatBN7.21015,337,360 - 15,337,705 (+)MAPPERmRatBN7.2
Rnor_6.01015,602,889 - 15,603,233NCBIRnor6.0
Rnor_6.01015,589,447 - 15,589,791NCBIRnor6.0
Rnor_5.01015,497,984 - 15,498,328UniSTSRnor5.0
Rnor_5.01015,484,542 - 15,484,886UniSTSRnor5.0
RGSC_v3.41015,571,013 - 15,571,357UniSTSRGSC3.4
RGSC_v3.41015,584,455 - 15,584,799UniSTSRGSC3.4
Celera1015,004,952 - 15,005,296UniSTS
Celera1014,991,503 - 14,991,847UniSTS
Cytogenetic Map10q12UniSTS
RH94431  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21015,337,265 - 15,337,360 (+)MAPPERmRatBN7.2
Rnor_6.01015,602,794 - 15,602,888NCBIRnor6.0
Rnor_5.01015,497,889 - 15,497,983UniSTSRnor5.0
RGSC_v3.41015,584,360 - 15,584,454UniSTSRGSC3.4
Celera1015,004,857 - 15,004,951UniSTS
RH 3.4 Map10153.7UniSTS
Cytogenetic Map10q12UniSTS
Cytogenetic Map1q22UniSTS
BI280228  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21015,337,287 - 15,337,451 (+)MAPPERmRatBN7.2
Rnor_6.01015,602,816 - 15,602,979NCBIRnor6.0
Rnor_5.01015,497,911 - 15,498,074UniSTSRnor5.0
RGSC_v3.41015,584,382 - 15,584,545UniSTSRGSC3.4
Celera1015,004,879 - 15,005,042UniSTS
RH 3.4 Map10151.86UniSTS
Cytogenetic Map10q12UniSTS
Cytogenetic Map1q22UniSTS
BI282742  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21015,324,396 - 15,324,668 (+)MAPPERmRatBN7.2
Rnor_6.01015,589,927 - 15,590,198NCBIRnor6.0
Rnor_5.01015,485,022 - 15,485,293UniSTSRnor5.0
RGSC_v3.41015,571,493 - 15,571,764UniSTSRGSC3.4
Celera1014,991,983 - 14,992,254UniSTS
RH 3.4 Map10151.46UniSTS
Cytogenetic Map10q12UniSTS
UniSTS:465391  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21015,324,015 - 15,324,388 (+)MAPPERmRatBN7.2
mRatBN7.21015,337,459 - 15,337,832 (+)MAPPERmRatBN7.2
Rnor_6.01015,602,988 - 15,603,360NCBIRnor6.0
Rnor_6.01015,589,546 - 15,589,918NCBIRnor6.0
Rnor_5.01015,498,083 - 15,498,455UniSTSRnor5.0
Rnor_5.01015,484,641 - 15,485,013UniSTSRnor5.0
RGSC_v3.41015,571,112 - 15,571,484UniSTSRGSC3.4
RGSC_v3.41015,584,554 - 15,584,926UniSTSRGSC3.4
Celera1015,005,051 - 15,005,423UniSTS
Celera1014,991,602 - 14,991,974UniSTS
Cytogenetic Map10q12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402717245662Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10615418215990232Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:33
Count of miRNA genes:32
Interacting mature miRNAs:33
Transcripts:ENSRNOT00000051483
Prediction methods: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 1 46 43 32 13 29 56 25 22 11
Medium 2 3 26 12 6 12 8 11 18 10 19 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_013096 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC096051 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC059150 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC160818 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209733 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209744 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209909 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209912 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210150 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210186 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210349 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210635 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210643 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210690 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210723 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210862 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210866 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211077 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211217 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211220 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211232 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211239 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211351 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211374 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211431 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211513 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211520 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211600 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211755 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211911 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211972 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212025 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212144 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212153 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212186 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212232 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212457 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212854 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213301 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214066 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214223 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216243 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217636 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217723 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217724 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217869 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218117 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218146 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218257 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218612 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219715 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220786 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221656 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221912 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221952 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222431 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222454 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222672 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222750 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224581 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225427 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225429 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225440 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225452 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225777 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225808 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226173 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226175 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226203 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226564 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226615 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227082 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228301 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228436 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230449 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230483 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230901 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231201 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231290 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231308 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232272 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232481 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234683 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M17083 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M32510 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000051483   ⟹   ENSRNOP00000044233
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1015,307,815 - 15,338,130 (-)Ensembl
Rnor_6.0 Ensembl1015,602,794 - 15,603,649 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000052292   ⟹   ENSRNOP00000041451
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1015,307,815 - 15,338,130 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000094747   ⟹   ENSRNOP00000098011
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1015,334,298 - 15,338,328 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118799   ⟹   ENSRNOP00000092961
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1015,334,298 - 15,336,973 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000119140   ⟹   ENSRNOP00000084682
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1015,307,815 - 15,324,872 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000119443   ⟹   ENSRNOP00000097827
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1015,307,815 - 15,338,392 (-)Ensembl
RefSeq Acc Id: NM_013096   ⟹   NP_037228
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21015,337,265 - 15,338,121 (-)NCBI
Rnor_6.01015,602,794 - 15,603,649 (-)NCBI
Rnor_5.01015,497,889 - 15,498,744 (-)NCBI
RGSC_v3.41015,584,360 - 15,585,215 (-)RGD
Celera1015,004,857 - 15,005,712 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_037228   ⟸   NM_013096
- UniProtKB: P01946 (UniProtKB/Swiss-Prot),   B1H216 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000044233   ⟸   ENSRNOT00000051483
RefSeq Acc Id: ENSRNOP00000092961   ⟸   ENSRNOT00000118799
RefSeq Acc Id: ENSRNOP00000097827   ⟸   ENSRNOT00000119443
RefSeq Acc Id: ENSRNOP00000084682   ⟸   ENSRNOT00000119140
RefSeq Acc Id: ENSRNOP00000041451   ⟸   ENSRNOT00000052292
RefSeq Acc Id: ENSRNOP00000098011   ⟸   ENSRNOT00000094747
Protein Domains
GLOBIN

Transcriptome

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

Promoters
RGD ID:13697080
Promoter ID:EPDNEW_R7600
Type:single initiation site
Name:AC096051_1
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_6.01015,600,865 - 15,600,925EPDNEW
RGD ID:13697076
Promoter ID:EPDNEW_R7601
Type:multiple initiation site
Name:Hba-a2_2
Description:hemoglobin alpha, adult chain 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R7599  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01015,603,647 - 15,603,707EPDNEW

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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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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
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:2782 AgrOrtholog
Ensembl Genes ENSRNOG00000029886 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000044233 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000051483 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.490.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6918464 IMAGE-MGC_LOAD
  IMAGE:7375173 IMAGE-MGC_LOAD
  IMAGE:7458326 IMAGE-MGC_LOAD
InterPro Globin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Globin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Globin/Proto UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Haemoglobin_a-typ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Haemoglobin_pi UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25632 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  rno:360504 UniProtKB/Swiss-Prot
MGC_CLONE MGC:114351 IMAGE-MGC_LOAD
  MGC:187279 IMAGE-MGC_LOAD
  MGC:72917 IMAGE-MGC_LOAD
NCBI Gene 25632 ENTREZGENE
Pfam Globin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB HBA1 RGD
PhenoGen Hba-a1 PhenoGen
PRINTS ALPHAHAEM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PIHAEM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE GLOBIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46458 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC228177
UniProt B1H216 ENTREZGENE, UniProtKB/TrEMBL
  HBA_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary P33583 UniProtKB/Swiss-Prot
  Q63243 UniProtKB/Swiss-Prot
  Q80XV2 UniProtKB/Swiss-Prot
  Q91V15 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-31 Hba-a1  hemoglobin alpha, adult chain 1  Hba-a1l  hemoglobin alpha, adult chain 1-like  Name and Symbol changed 629549 APPROVED
2015-12-31 Hba-a1l  hemoglobin alpha, adult chain 1-like  Hba-a2  hemoglobin alpha, adult chain 2  Name and Symbol changed 629549 APPROVED
2015-12-31 Hba-a2  hemoglobin alpha, adult chain 2  Hba-a3  hemoglobin alpha, adult chain 3  Name and Symbol changed 629549 APPROVED
2015-10-06 Hba-a3  hemoglobin alpha, adult chain 3  Hba1  hemoglobin, alpha 1  Name and Symbol changed 629549 APPROVED
2013-01-29 Hba1  hemoglobin, alpha 1  Hba-a2  hemoglobin alpha, adult chain 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-15 Hba-a2  hemoglobin alpha, adult chain 2  Hba-a1  hemoglobin alpha, adult chain 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Hba-a1  hemoglobin alpha, adult chain 1  Hba1  hemoglobin, alpha 1  Symbol and Name updated 1299863 APPROVED
2002-06-10 Hba1  hemoglobin, alpha 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression highly expressed in lung erythroid cells  
gene_transcript transcript is 556 bp 632888