Gypa (glycophorin A) - Rat Genome Database

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Gene: Gypa (glycophorin A) Rattus norvegicus
Analyze
Symbol: Gypa
Name: glycophorin A
RGD ID: 1582935
Description: Predicted to have identical protein binding activity. Predicted to be involved in regulation of response to osmotic stress. Predicted to localize to several cellular components, including external side of plasma membrane; integral component of plasma membrane; and nucleoplasm; INTERACTS WITH acrylamide; bisphenol A; metformin.
Type: protein-coding
RefSeq Status: MODEL
Also known as: glycophorin-A; glycophorin-A-like; glycophorin-B-like; LOC688972; similar to Glycophorin
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21927,450,311 - 27,465,940 (-)NCBI
Rnor_6.01931,115,545 - 31,131,079 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01942,018,634 - 42,034,309 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41929,301,178 - 29,318,617 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1926,966,530 - 26,982,092 (-)NCBICelera
Cytogenetic Map19q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
malaria  (ISO)
Skin Neoplasms  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
1. OMIM Disease Annotation Pipeline
2. RGD automated data pipeline
3. RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Gypa
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21927,450,311 - 27,465,940 (-)NCBI
Rnor_6.01931,115,545 - 31,131,079 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01942,018,634 - 42,034,309 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41929,301,178 - 29,318,617 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1926,966,530 - 26,982,092 (-)NCBICelera
Cytogenetic Map19q11NCBI
GYPA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl4144,109,303 - 144,140,751 (-)EnsemblGRCh38hg38GRCh38
GRCh384144,109,303 - 144,140,854 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh374145,030,456 - 145,061,871 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364145,249,906 - 145,281,294 (-)NCBINCBI36hg18NCBI36
Build 344145,388,061 - 145,419,449NCBI
Celera4142,359,859 - 142,391,286 (-)NCBI
Cytogenetic Map4q31.21NCBI
HuRef4140,759,973 - 140,791,405 (-)NCBIHuRef
CHM1_14145,007,517 - 145,038,987 (-)NCBICHM1_1
Gypa
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39881,220,674 - 81,237,414 (+)NCBIGRCm39mm39
GRCm39 Ensembl881,220,410 - 81,237,171 (+)Ensembl
GRCm38880,494,045 - 80,510,785 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl880,493,781 - 80,510,542 (+)EnsemblGRCm38mm10GRCm38
MGSCv37883,017,944 - 83,034,684 (+)NCBIGRCm37mm9NCBIm37
MGSCv36883,389,289 - 83,406,230 (+)NCBImm8
Celera884,765,672 - 84,782,460 (+)NCBICelera
Cytogenetic Map8C2NCBI
cM Map838.27NCBI
GYPA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.14147,987,563 - 148,148,082 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4147,987,750 - 148,019,005 (-)Ensemblpanpan1.1panPan2
PanPan1.1 Ensembl4148,117,479 - 148,148,315 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v04136,455,397 - 136,486,858 (-)NCBIMhudiblu_PPA_v0panPan3
GYPA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11543,018,705 - 43,049,726 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1543,018,708 - 43,049,665 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1543,410,710 - 43,441,658 (-)NCBI
ROS_Cfam_1.01543,679,013 - 43,710,005 (-)NCBI
UMICH_Zoey_3.11542,955,325 - 42,986,264 (-)NCBI
UNSW_CanFamBas_1.01543,039,457 - 43,070,052 (-)NCBI
UU_Cfam_GSD_1.01543,310,881 - 43,341,844 (-)NCBI
Gypa
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530147,241,679 - 47,270,744 (+)NCBI
GYPA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1884,037,574 - 84,067,096 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2889,194,118 - 89,222,888 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GYPA
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1790,702,645 - 90,739,106 (-)NCBI
Vero_WHO_p1.0NW_02366603770,291,762 - 70,332,426 (-)NCBI
Gypa
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248533,132,961 - 3,158,461 (-)NCBI

Position Markers
RH141193  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21927,450,558 - 27,450,740 (+)MAPPER
Rnor_6.01931,115,787 - 31,115,968NCBIRnor6.0
Rnor_5.01942,018,876 - 42,019,057UniSTSRnor5.0
RGSC_v3.41929,300,956 - 29,301,137UniSTSRGSC3.4
Celera1926,966,772 - 26,966,953UniSTS
Cytogenetic Map19q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19132379055Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19138221845Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19138221845Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19138221845Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19138221845Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19104464846044648Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19195770746957707Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19243296347217667Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)19370183548701835Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)19370183548701835Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19500757143907843Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19807254547318201Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191130392747879277Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)191529452433991703Rat
1558656Prcs1Prostate cancer susceptibility QTL 15prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)191593952838798459Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191702800352538299Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)192140778762275575Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)192445572643907843Rat
61328Eae8Experimental allergic encephalomyelitis QTL 84nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)192445762737140233Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192481825762275575Rat


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_001069014 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006255409 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006255410 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008774220 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098117 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide FQ225003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225301 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225342 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225559 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225587 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225853 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225938 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226528 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226680 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226806 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227270 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227316 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227754 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227787 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227796 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227815 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227840 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227848 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227911 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228099 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228142 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228197 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230593 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230940 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231131 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231342 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231370 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231585 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231667 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232019 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232094 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232135 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232882 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232994 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233073 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233126 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233305 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233639 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233690 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233854 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233924 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234025 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234117 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234209 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234366 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234440 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234531 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234729 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235107 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000313 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: XM_001069014   ⟹   XP_001069014
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21927,450,311 - 27,465,935 (-)NCBI
Rnor_6.01931,115,545 - 31,131,079 (-)NCBI
Rnor_5.01942,018,634 - 42,034,309 (-)NCBI
RGSC_v3.41929,301,178 - 29,318,617 (-)RGD
Sequence:
RefSeq Acc Id: XM_006255409   ⟹   XP_006255471
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21927,452,402 - 27,465,940 (-)NCBI
Rnor_6.01931,117,630 - 31,131,058 (-)NCBI
Rnor_5.01942,018,634 - 42,034,309 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006255410   ⟹   XP_006255472
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01931,115,545 - 31,131,055 (-)NCBI
Rnor_5.01942,018,634 - 42,034,309 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008774220   ⟹   XP_008772442
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1926,966,530 - 26,982,092 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039098117   ⟹   XP_038954045
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21927,450,311 - 27,465,940 (-)NCBI
Protein Sequences
Protein RefSeqs XP_001069014 (Get FASTA)   NCBI Sequence Viewer  
  XP_006255471 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954045 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_001069014   ⟸   XM_001069014
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006255472   ⟸   XM_006255410
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006255471   ⟸   XM_006255409
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008772442   ⟸   XM_008774220
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_038954045   ⟸   XM_039098117
- Peptide Label: isoform X1


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)
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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)
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)
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
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/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
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 (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
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
19 42034179 42034180 A G snv ACI/EurMcwi (MCW), Crl:SD (UDEL), GH/OmrMcwi (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), LN/MavRrrc (KNAW), MHS/Gib (KNAW), SR/JrHsd (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), WAG/Rij (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), BBDP/WorN (KNAW), SBH/Ygl (KNAW), SBN/Ygl (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), DA/BklArbNsi (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), MNS/Gib (KNAW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), COP/CrCrl (MCW & UW)
19 42034201 42034202 G A snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), LN/MavRrrc (KNAW), MHS/Gib (KNAW), SR/JrHsd (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), WAG/Rij (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), BBDP/WorN (KNAW), SBH/Ygl (KNAW), SBN/Ygl (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), DA/BklArbNsi (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), MNS/Gib (KNAW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
19 31130949 31130950 A G snv ACI/EurMcwi (MCW), WAG/Rij (RGD), SS/JrHsdMcwi (RGD), SS/Jr (RGD), SR/JrHsd (RGD), SHRSP/Gcrc (RGD), SHR/NHsd (RGD), SBN/Ygl (RGD), SBH/Ygl (RGD), MNS/Gib (RGD), MHS/Gib (RGD), LL/MavRrrc (RGD), LN/MavRrrc (RGD), LH/MavRrrc (RGD), LE/Stm (RGD), FHH/EurMcwi (RGD), BBDP/Wor (RGD), ACI/EurMcwi (RGD), FHL/EurMcwi (RGD), ACI/N (MCW), CDS, CDR, SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), SBN/Ygl (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), SBH/Ygl (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW)
19 31130971 31130972 G A snv BBDP/Wor (RGD), ACI/EurMcwi (MCW), MNS/Gib (RGD), ACI/EurMcwi (RGD), FHL/EurMcwi (RGD), SHR/NHsd (RGD), ACI/N (MCW), MHS/Gib (RGD), LL/MavRrrc (RGD), CDS, CDR, SR/JrHsd (RGD), SS/JrHsdMcwi (RGD), SS/JrHsdMcwi (MCW), LN/MavRrrc (RGD), SR/JrHsd (MCW), LH/MavRrrc (RGD), SBN/Ygl (MCW), SBN/Ygl (RGD), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), LE/Stm (RGD), SBH/Ygl (RGD), SBH/Ygl (MCW), GH/OmrMcwi (MCW), FHH/EurMcwi (RGD), COP/CrCrl (MCW & UW), SHRSP/Gcrc (RGD), WAG/Rij (RGD), SS/Jr (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
19 29318523 29318524 A G snv SHR/OlaIpcv (ICL), FHH/EurMcwi (MDC), SHRSP/Gcrc (MDC), SS/JrHsdMcwi (MDC), ACI/N (KNAW), LE/Stm (KNAW), SHR/OlaIpcv (KNAW), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), ACI/EurMcwi (ICL), BBDP/WorN (ICL), LE/Stm (ICL), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), LH/MavRrrc (ICL), LL/MavRrrc (ICL), LN/MavRrrc (ICL), MHS/Gib (ICL), MNS/Gib (ICL), SBH/Ygl (ICL), SBN/Ygl (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), SR/JrHsd (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), WAG/Rij (ICL), DA/BklArbNsi (ICAHN)
19 29318545 29318546 G A snv SHR/OlaIpcv (ICL), DA/BklArbNsi (ICAHN), SHRSP/Gcrc (MDC), SS/JrHsdMcwi (MDC), ACI/N (KNAW), LE/Stm (KNAW), SHR/OlaIpcv (KNAW), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), ACI/EurMcwi (ICL), BBDP/WorN (ICL), LE/Stm (ICL), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), LH/MavRrrc (ICL), LL/MavRrrc (ICL), LN/MavRrrc (ICL), MHS/Gib (ICL), MNS/Gib (ICL), SBH/Ygl (ICL), SBN/Ygl (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), SR/JrHsd (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), WAG/Rij (ICL), FHH/EurMcwi (MDC)


Additional Information

Database Acc Id Source(s)
NCBI Gene 688972 ENTREZGENE
PhenoGen Gypa PhenoGen


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-09-16 Gypa  glycophorin A  LOC688972  similar to Glycophorin  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC688972  similar to Glycophorin      Symbol and Name status set to provisional 70820 PROVISIONAL