LOC680039 (hypothetical protein LOC680039) - Rat Genome Database

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Gene: LOC680039 (hypothetical protein LOC680039) Rattus norvegicus
Analyze
Symbol: LOC680039
Name: hypothetical protein LOC680039
RGD ID: 1596848
Description: Orthologous to human KIAA0232 (KIAA0232); INTERACTS WITH bisphenol A; 1,2-dichloroethane (ortholog); 1,2-dimethylhydrazine (ortholog).
Type: protein-coding
RefSeq Status: PREDICTED
Also known as: uncharacterized protein KIAA0232 homolog; uncharacterized protein LOC680039
RGD Orthologs
Human
Mouse
Chinchilla
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
mRatBN7.21474,094,421 - 74,159,316 (+)NCBI
Rnor_6.0 Ensembl1479,261,092 - 79,325,896 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01479,261,052 - 79,325,916 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01478,899,420 - 78,964,649 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41479,675,324 - 79,740,145 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1473,032,886 - 73,097,680 (+)NCBICelera
Cytogenetic Map14q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:25002582  


Genomics

Comparative Map Data
LOC680039
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21474,094,421 - 74,159,316 (+)NCBI
Rnor_6.0 Ensembl1479,261,092 - 79,325,896 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01479,261,052 - 79,325,916 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01478,899,420 - 78,964,649 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41479,675,324 - 79,740,145 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1473,032,886 - 73,097,680 (+)NCBICelera
Cytogenetic Map14q21NCBI
KIAA0232
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl46,781,375 - 6,884,170 (+)EnsemblGRCh38hg38GRCh38
GRCh3846,782,727 - 6,884,164 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3746,784,454 - 6,885,891 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3646,835,360 - 6,936,800 (+)NCBINCBI36hg18NCBI36
Celera46,708,296 - 6,787,947 (+)NCBI
Cytogenetic Map4p16.1NCBI
HuRef46,715,310 - 6,816,571 (+)NCBIHuRef
CHM1_146,782,716 - 6,884,149 (+)NCBICHM1_1
D5Ertd579e
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39536,757,827 - 36,854,083 (-)NCBIGRCm39mm39
GRCm39 Ensembl536,757,829 - 36,853,368 (-)Ensembl
GRCm38536,600,483 - 36,696,732 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl536,600,485 - 36,696,024 (-)EnsemblGRCm38mm10GRCm38
MGSCv37537,063,986 - 37,087,208 (-)NCBIGRCm37mm9NCBIm37
MGSCv37536,943,134 - 36,962,379 (-)NCBIGRCm37mm9NCBIm37
MGSCv36536,917,579 - 36,938,344 (-)NCBImm8
Celera534,082,811 - 34,124,927 (-)NCBICelera
Cytogenetic Map5B3NCBI
cM Map519.18NCBI
Kiaa0232
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555143,581,652 - 3,667,824 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555143,581,654 - 3,630,754 (-)NCBIChiLan1.0ChiLan1.0
KIAA0232
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.146,866,012 - 6,952,975 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl46,894,495 - 6,950,583 (+)Ensemblpanpan1.1panPan2
KIAA0232
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1358,891,939 - 58,983,763 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl358,926,237 - 59,097,621 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha361,536,664 - 61,630,746 (+)NCBI
ROS_Cfam_1.0359,355,847 - 59,455,308 (+)NCBI
UMICH_Zoey_3.1358,858,574 - 58,952,650 (+)NCBI
UNSW_CanFamBas_1.0359,060,788 - 59,154,618 (+)NCBI
UU_Cfam_GSD_1.0359,409,404 - 59,508,805 (+)NCBI
Kiaa0232
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528564,975,600 - 65,044,356 (+)NCBI
KIAA0232
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.183,943,029 - 4,031,395 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.283,195,025 - 3,265,318 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KIAA0232
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12742,904,723 - 43,001,248 (+)NCBI
ChlSab1.1 Ensembl2742,942,854 - 42,998,993 (+)Ensembl
Vero_WHO_p1.0NW_02366604789,715,210 - 89,809,686 (+)NCBI
Kiaa0232
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475523,061,089 - 23,149,092 (+)NCBI

Position Markers
RH133865  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21474,159,036 - 74,159,227 (+)MAPPER
Rnor_6.01479,325,637 - 79,325,827NCBIRnor6.0
Rnor_5.01478,964,370 - 78,964,560UniSTSRnor5.0
RGSC_v3.41479,739,873 - 79,740,063UniSTSRGSC3.4
Celera1473,097,408 - 73,097,598UniSTS
Cytogenetic Map14q21UniSTS
SHGC-59523  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21474,159,113 - 74,159,226 (+)MAPPER
Rnor_6.01479,325,714 - 79,325,826NCBIRnor6.0
Rnor_5.01478,964,447 - 78,964,559UniSTSRnor5.0
RGSC_v3.41479,739,950 - 79,740,062UniSTSRGSC3.4
Celera1473,097,485 - 73,097,597UniSTS
Cytogenetic Map14q21UniSTS
BE116146  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21474,159,036 - 74,159,191 (+)MAPPER
Rnor_6.01479,325,637 - 79,325,791NCBIRnor6.0
Rnor_5.01478,964,370 - 78,964,524UniSTSRnor5.0
RGSC_v3.41479,739,873 - 79,740,027UniSTSRGSC3.4
Celera1473,097,408 - 73,097,562UniSTS
Cytogenetic Map14q21UniSTS
D21S1952  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21474,131,191 - 74,132,380 (+)MAPPER
mRatBN7.22243,300,928 - 243,301,355 (+)MAPPER
Rnor_6.02260,631,130 - 260,631,556NCBIRnor6.0
Rnor_6.01479,297,793 - 79,298,981NCBIRnor6.0
Rnor_5.01478,936,526 - 78,937,714UniSTSRnor5.0
Rnor_5.02279,292,982 - 279,293,408UniSTSRnor5.0
RGSC_v3.42252,272,500 - 252,272,926UniSTSRGSC3.4
RGSC_v3.41479,712,027 - 79,713,215UniSTSRGSC3.4
Celera1473,069,562 - 73,070,750UniSTS
Celera2235,226,814 - 235,227,240UniSTS
Cytogenetic Map14q21UniSTS
G48108  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21474,127,716 - 74,127,831 (+)MAPPER
mRatBN7.2466,348,687 - 66,348,805 (+)MAPPER
Rnor_6.0465,300,923 - 65,301,040NCBIRnor6.0
Rnor_6.01479,294,318 - 79,294,432NCBIRnor6.0
Rnor_5.01478,933,051 - 78,933,165UniSTSRnor5.0
Rnor_5.0465,121,501 - 65,121,618UniSTSRnor5.0
RGSC_v3.4465,174,423 - 65,174,540UniSTSRGSC3.4
RGSC_v3.41479,708,552 - 79,708,666UniSTSRGSC3.4
Celera1473,066,087 - 73,066,201UniSTS
Celera461,378,933 - 61,379,050UniSTS
Cytogenetic Map14q21UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143259392686191589Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)144031561085315610Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)144031561085315610Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)144031561085315610Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)144031561085315610Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)144163756980841518Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1442442731108833671Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1443910761105074364Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1451818462105074364Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1460980905105980905Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1460980905105980905Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)146187332388870994Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1461993178106993178Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1463548095108548095Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)147339146788870994Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765102549388Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)1478172765102549388Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1478172765102549388Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765102549388Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765106641756Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1478446303110402569Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:231
Count of miRNA genes:170
Interacting mature miRNAs:187
Transcripts:ENSRNOT00000029191
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
Medium 2 42 50 34 19 34 8 10 74 35 38 11 8
Low 1 1 7 7 7 1 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000029191   ⟹   ENSRNOP00000032427
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1479,261,092 - 79,325,896 (+)Ensembl
RefSeq Acc Id: NM_001109388   ⟹   NP_001102858
RefSeq Status: PREDICTED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21474,094,488 - 74,159,309 (+)NCBI
Rnor_6.01479,261,092 - 79,325,909 (+)NCBI
Rnor_5.01478,899,420 - 78,964,649 (+)NCBI
RGSC_v3.41479,675,324 - 79,740,145 (+)RGD
Celera1473,032,886 - 73,097,680 (+)RGD
Sequence:
RefSeq Acc Id: XM_006251140   ⟹   XP_006251202
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21474,094,422 - 74,159,316 (+)NCBI
Rnor_6.01479,261,053 - 79,325,916 (+)NCBI
Rnor_5.01478,899,420 - 78,964,649 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006251141   ⟹   XP_006251203
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21474,094,421 - 74,157,138 (+)NCBI
Rnor_6.01479,261,052 - 79,323,685 (+)NCBI
Rnor_5.01478,899,420 - 78,964,649 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008770360   ⟹   XP_008768582
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01479,305,082 - 79,325,916 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039092426   ⟹   XP_038948354
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21474,094,423 - 74,157,138 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001102858 (Get FASTA)   NCBI Sequence Viewer  
  XP_006251202 (Get FASTA)   NCBI Sequence Viewer  
  XP_006251203 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948354 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM00043 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001102858   ⟸   NM_001109388
- UniProtKB: D3ZYT3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251203   ⟸   XM_006251141
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006251202   ⟸   XM_006251140
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008768582   ⟸   XM_008770360
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000032427   ⟸   ENSRNOT00000029191
RefSeq Acc Id: XP_038948354   ⟸   XM_039092426
- Peptide Label: isoform X3

Transcriptome

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

Promoters
RGD ID:13699379
Promoter ID:EPDNEW_R9904
Type:initiation region
Name:LOC680039_1
Description:hypothetical protein LOC680039
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_6.01479,261,108 - 79,261,168EPDNEW

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)
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)
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/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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1596848 AgrOrtholog
Ensembl Genes ENSRNOG00000027623 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000032427 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000029191 ENTREZGENE, UniProtKB/TrEMBL
InterPro DUF4603 UniProtKB/TrEMBL
KEGG Report rno:680039 UniProtKB/TrEMBL
NCBI Gene 680039 ENTREZGENE
PANTHER PTHR17611 UniProtKB/TrEMBL
Pfam DUF4603 UniProtKB/TrEMBL
PhenoGen LOC680039 PhenoGen
UniProt D3ZYT3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-01-09 LOC680039  hypothetical protein LOC680039  LOC682082  hypothetical protein LOC682082  Data Merged 1643240 APPROVED
2006-11-20 LOC680039  hypothetical protein LOC680039      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC682082  hypothetical protein LOC682082      Symbol and Name status set to provisional 70820 PROVISIONAL