Maged2 (MAGE family member D2) - Rat Genome Database
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Gene: Maged2 (MAGE family member D2) Rattus norvegicus
Analyze
Symbol: Maged2
Name: MAGE family member D2
RGD ID: 70899
Description: Predicted to be involved in female pregnancy and renal sodium ion absorption. Predicted to localize to cytosol; nucleolus; and nucleoplasm. Human ortholog(s) of this gene implicated in Bartter disease type 5. Orthologous to human MAGED2 (MAGE family member D2); INTERACTS WITH (+)-schisandrin B; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: melanoma antigen family D, 2; melanoma antigen, family D, 2; melanoma-associated antigen D2; MGC124946
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
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
mRatBN7.2X19,733,593 - 19,741,769 (-)NCBI
Rnor_6.0 Ensembl533,174,542 - 33,182,715 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0533,174,539 - 33,182,715 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0537,832,720 - 37,840,896 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X40,056,332 - 40,064,505 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X40,109,805 - 40,116,420 (-)NCBI
CeleraX19,993,517 - 20,001,690 (-)NCBICelera
Cytogenetic Map5q13NCBI
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
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (IEA,ISO)
nucleolus  (IEA,ISO)
nucleoplasm  (IEA,ISO)

Molecular Function

References

References - curated
1. NCBI rat LocusLink and RefSeq merged data July 26, 2002
2. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11856887   PMID:12477932   PMID:17154719   PMID:19946888   PMID:27120771  


Genomics

Comparative Map Data
Maged2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X19,733,593 - 19,741,769 (-)NCBI
Rnor_6.0 Ensembl533,174,542 - 33,182,715 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0533,174,539 - 33,182,715 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0537,832,720 - 37,840,896 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X40,056,332 - 40,064,505 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X40,109,805 - 40,116,420 (-)NCBI
CeleraX19,993,517 - 20,001,690 (-)NCBICelera
Cytogenetic Map5q13NCBI
MAGED2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX54,807,599 - 54,816,015 (+)EnsemblGRCh38hg38GRCh38
GRCh38X54,807,745 - 54,816,015 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X54,834,178 - 54,842,448 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X54,850,896 - 54,859,170 (+)NCBINCBI36hg18NCBI36
Build 34X54,718,513 - 54,725,466NCBI
CeleraX58,666,731 - 58,675,005 (+)NCBI
Cytogenetic MapXp11.21NCBI
HuRefX51,883,893 - 51,892,287 (+)NCBIHuRef
CHM1_1X54,824,597 - 54,833,013 (+)NCBICHM1_1
Maged2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X149,589,417 - 149,597,358 (-)NCBIGRCm39mm39
GRCm39 EnsemblX149,589,366 - 149,597,341 (-)Ensembl
GRCm38X150,806,421 - 150,814,362 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX150,806,370 - 150,814,345 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X147,240,964 - 147,248,825 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X146,147,137 - 146,154,998 (-)NCBImm8
CeleraX133,569,891 - 133,573,893 (-)NCBICelera
Cytogenetic MapXF3NCBI
Maged2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554752,038,189 - 2,046,290 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554752,038,189 - 2,046,240 (-)NCBIChiLan1.0ChiLan1.0
MAGED2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X55,241,161 - 55,249,577 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX55,241,161 - 55,249,256 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X47,010,009 - 47,018,370 (+)NCBIMhudiblu_PPA_v0panPan3
MAGED2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X46,502,459 - 46,510,990 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX46,502,381 - 46,509,436 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX37,893,821 - 37,902,325 (-)NCBI
ROS_Cfam_1.0X50,062,517 - 50,071,011 (-)NCBI
UMICH_Zoey_3.1X46,330,703 - 46,339,207 (+)NCBI
UNSW_CanFamBas_1.0X46,770,546 - 46,779,050 (+)NCBI
Maged2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X39,299,605 - 39,307,769 (+)NCBI
SpeTri2.0NW_0049367511,639,276 - 1,647,494 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MAGED2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X50,898,166 - 50,906,667 (+)NCBI
ChlSab1.1 EnsemblX50,898,324 - 50,906,260 (+)Ensembl
Maged2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462491037,155 - 47,711 (+)NCBI

Position Markers
RH129635  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0533,174,548 - 33,174,715NCBIRnor6.0
Rnor_5.0537,832,729 - 37,832,896UniSTSRnor5.0
RGSC_v3.4X40,056,338 - 40,056,505UniSTSRGSC3.4
CeleraX19,993,523 - 19,993,690UniSTS
RH 3.4 MapX211.23UniSTS
Cytogenetic MapXq21UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5189432042Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5193273395Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51136640934Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)5152509878720537Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5166658771552720Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5325132948722188Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5452573847978104Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5863228553632285Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)59514842103580403Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512651967117554267Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51328888858288888Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51884791363847913Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51884791376608178Rat
8552954Pigfal14Plasma insulin-like growth factor 1 level QTL 149blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)52190436366904363Rat
1549901Neudeg2Neurodegradation QTL 240nervous system integrity trait (VT:0010566)mononuclear cell count (CMO:0002119)52495621244747071Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)52907889974078899Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)52907889974078899Rat
6903292Stl28Serum triglyceride level QTL 282.60.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)52964166174641661Rat
6903306Scl35Serum cholesterol QTL 352.60.0073blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)52964166174641661Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531926122136640934Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:190
Count of miRNA genes:149
Interacting mature miRNAs:162
Transcripts:ENSRNOT00000044483
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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 37 38 27 10 27 4 4 74 35 36 11 4
Low 1 6 19 14 9 14 4 7 5 4
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000044483   ⟹   ENSRNOP00000042515
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl533,174,542 - 33,182,715 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000080358   ⟹   ENSRNOP00000074736
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl533,174,542 - 33,182,147 (-)Ensembl
RefSeq Acc Id: NM_001271109   ⟹   NP_001258038
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X19,733,596 - 19,741,769 (-)NCBI
Rnor_6.0533,174,542 - 33,182,715 (-)NCBI
Rnor_5.0537,832,720 - 37,840,896 (-)NCBI
CeleraX19,993,517 - 20,001,690 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001271110   ⟹   NP_001258039
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X19,733,596 - 19,741,185 (-)NCBI
Rnor_6.0533,174,542 - 33,182,131 (-)NCBI
Rnor_5.0537,832,720 - 37,840,896 (-)NCBI
CeleraX19,993,517 - 20,001,106 (-)NCBI
Sequence:
RefSeq Acc Id: NM_080479   ⟹   NP_536727
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X19,733,596 - 19,741,769 (-)NCBI
Rnor_6.0533,174,542 - 33,182,715 (-)NCBI
Rnor_5.0537,832,720 - 37,840,896 (-)NCBI
RGSC_v3.4X40,056,332 - 40,064,505 (-)RGD
CeleraX19,993,517 - 20,001,690 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237924   ⟹   XP_006237986
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X19,733,593 - 19,740,468 (-)NCBI
Rnor_6.0533,174,539 - 33,181,398 (-)NCBI
Rnor_5.0537,832,720 - 37,840,896 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593115   ⟹   XP_017448604
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X19,733,593 - 19,740,645 (-)NCBI
Rnor_6.0533,174,539 - 33,181,542 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099392   ⟹   XP_038955320
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X19,733,593 - 19,740,483 (-)NCBI
RefSeq Acc Id: XM_039099393   ⟹   XP_038955321
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X19,733,593 - 19,740,053 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_536727   ⟸   NM_080479
- UniProtKB: Q3B7U1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001258038   ⟸   NM_001271109
- UniProtKB: Q3B7U1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001258039   ⟸   NM_001271110
- UniProtKB: Q3B7U1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237986   ⟸   XM_006237924
- Peptide Label: isoform X1
- UniProtKB: Q3B7U1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017448604   ⟸   XM_017593115
- Peptide Label: isoform X1
- UniProtKB: Q3B7U1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074736   ⟸   ENSRNOT00000080358
RefSeq Acc Id: ENSRNOP00000042515   ⟸   ENSRNOT00000044483
RefSeq Acc Id: XP_038955320   ⟸   XM_039099392
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955321   ⟸   XM_039099393
- Peptide Label: isoform X2
Protein Domains
MAGE

Transcriptome

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

Promoters
RGD ID:13693585
Promoter ID:EPDNEW_R4110
Type:initiation region
Name:Maged2_2
Description:MAGE family member D2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R4111  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0533,182,120 - 33,182,180EPDNEW
RGD ID:13693586
Promoter ID:EPDNEW_R4111
Type:multiple initiation site
Name:Maged2_1
Description:MAGE family member D2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R4110  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0533,182,729 - 33,182,789EPDNEW

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)
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/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
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
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
5 37835623 37835624 C T snv DOB/Oda (KyushuU), BUF/MNa (KyushuU), HWY/Slc (KyushuU), BDIX/NemOda (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), LE/Stm (KyushuU)
5 37836412 37836413 G T snv SBH/Ygl (MCW), FHL/EurMcwi (MCW), SR/JrHsd (MCW), FHH/EurMcwi (MCW)
5 37836984 37836985 C T snv SR/JrHsd (MCW), SBN/Ygl (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), ACI/EurMcwi (MCW), GH/OmrMcwi (MCW)
5 37836996 37836997 T G snv FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), SBN/Ygl (MCW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 33178210 33178211 C G snv LE/Stm (RGD), WKY/Gcrc (RGD), SR/JrHsd (RGD), LEW/NCrlBR (RGD), CDS, CDR, BBDP/Wor (RGD), SHR/NHsd (RGD), F344/NCrl (RGD), SBH/Ygl (RGD), MHS/Gib (RGD)
5 33178216 33178217 G A snv LE/Stm (RGD), F344/NCrl (RGD), BBDP/Wor (RGD), CDR, SR/JrHsd (RGD), SHR/NHsd (RGD), SBH/Ygl (RGD), MHS/Gib (RGD), LEW/NCrlBR (RGD)
5 33178221 33178222 A G snv BBDP/Wor (RGD), SR/JrHsd (RGD), SHR/NHsd (RGD), F344/NCrl (RGD), CDR, LEW/NCrlBR (RGD), LE/Stm (RGD)
5 33178231 33178232 G T snv SR/JrHsd (RGD), SHR/NHsd (RGD), F344/NCrl (RGD), CDR, LE/Stm (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 40059232 40059233 C T snv HCR/2Mco (UMich), HCR/1Mco (UMich), LCR/1Mco (UMich), LCR/2Mco (UMich)
X 40060000 40060001 C G snv HCR/2Mco (UMich), LCR/1Mco (UMich), HCR/1Mco (UMich), LCR/2Mco (UMich)
X 40060006 40060007 G A snv HCR/2Mco (UMich), LCR/1Mco (UMich), HCR/1Mco (UMich), LCR/2Mco (UMich)
X 40060011 40060012 A G snv LCR/2Mco (UMich), HCR/2Mco (UMich), HCR/1Mco (UMich), LCR/1Mco (UMich)
X 40060021 40060022 G T snv LCR/2Mco (UMich), HCR/2Mco (UMich), LCR/1Mco (UMich), FHL/EurMcwi (MCW), HCR/1Mco (UMich), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), FHH/EurMcwi (MCW)
X 40060038 40060039 T A snv HCR/1Mco (UMich), LCR/2Mco (UMich), HCR/2Mco (UMich), LCR/1Mco (UMich)
X 40060063 40060064 G T snv LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), HCR/1Mco (UMich)
X 40060066 40060067 T C snv LCR/2Mco (UMich), LCR/1Mco (UMich), HCR/1Mco (UMich), HCR/2Mco (UMich)
X 40060069 40060070 C G snv HCR/2Mco (UMich), HCR/1Mco (UMich), LCR/1Mco (UMich), LCR/2Mco (UMich)
X 40060593 40060594 C T snv FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), ACI/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW)
X 40060605 40060606 T G snv FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), GH/OmrMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:70899 AgrOrtholog
Ensembl Genes ENSRNOG00000002449 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000042515 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074736 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044483 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000080358 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.1200 UniProtKB/TrEMBL
  1.10.10.1210 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7135182 IMAGE-MGC_LOAD
  IMAGE:7459969 IMAGE-MGC_LOAD
InterPro MAGE UniProtKB/TrEMBL
  MAGE UniProtKB/TrEMBL
  MAGE_WH1 UniProtKB/TrEMBL
  MAGE_WH2 UniProtKB/TrEMBL
  MAGED2 UniProtKB/TrEMBL
KEGG Report rno:113947 UniProtKB/TrEMBL
MGC_CLONE MGC:124946 IMAGE-MGC_LOAD
  MGC:93244 IMAGE-MGC_LOAD
NCBI Gene 113947 ENTREZGENE
PANTHER PTHR11736 UniProtKB/TrEMBL
  PTHR11736:SF11 UniProtKB/TrEMBL
Pfam MAGE UniProtKB/TrEMBL
PhenoGen Maged2 PhenoGen
PROSITE MAGE UniProtKB/TrEMBL
SMART MAGE UniProtKB/TrEMBL
UniProt Q3B7U1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-10 Maged2  MAGE family member D2  Maged2  melanoma antigen, family D, 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-07-09 Maged2  melanoma antigen, family D, 2      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference