Mcmdc2 (minichromosome maintenance domain containing 2) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   
Gene: Mcmdc2 (minichromosome maintenance domain containing 2) Rattus norvegicus
Analyze
Symbol: Mcmdc2
Name: minichromosome maintenance domain containing 2
RGD ID: 1561068
Description: Predicted to have DNA replication origin binding activity and single-stranded DNA binding activity. Predicted to be involved in several processes, including DNA metabolic process; DNA-dependent DNA replication; and gamete generation. Predicted to localize to MCM complex and nucleus. Orthologous to human MCMDC2 (minichromosome maintenance domain containing 2); INTERACTS WITH (S)-nicotine; acetamiprid; amphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC500392; MCM domain-containing protein 2; MCM domain-containing protein C8orf45 homolog; minichromosome maintenance complex component-like; minichromosome maintenance domain-containing protein 2; similar to hypothetical protein FLJ25692; uncharacterized protein C8orf45 homolog
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
mRatBN7.259,291,967 - 9,337,526 (-)NCBI
Rnor_6.0 Ensembl58,978,010 - 9,038,594 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.058,973,861 - 9,039,616 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0513,781,014 - 13,839,762 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.458,842,432 - 8,881,827 (-)NCBIRGSC3.4rn4RGSC3.4
Celera58,810,709 - 8,849,895 (-)NCBICelera
Cytogenetic Map5q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:15489334   PMID:27760146  


Genomics

Comparative Map Data
Mcmdc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.259,291,967 - 9,337,526 (-)NCBI
Rnor_6.0 Ensembl58,978,010 - 9,038,594 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.058,973,861 - 9,039,616 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0513,781,014 - 13,839,762 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.458,842,432 - 8,881,827 (-)NCBIRGSC3.4rn4RGSC3.4
Celera58,810,709 - 8,849,895 (-)NCBICelera
Cytogenetic Map5q11NCBI
MCMDC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl866,870,749 - 66,922,048 (+)EnsemblGRCh38hg38GRCh38
GRCh38866,870,757 - 66,926,436 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37867,783,006 - 67,834,283 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh37867,782,984 - 67,834,283 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36867,948,884 - 67,976,570 (+)NCBINCBI36hg18NCBI36
Celera863,776,478 - 63,827,777 (+)NCBI
Cytogenetic Map8q13.1NCBI
HuRef863,275,571 - 63,326,869 (+)NCBIHuRef
CHM1_1867,837,961 - 67,889,304 (+)NCBICHM1_1
Mcmdc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3919,978,863 - 10,011,179 (+)NCBIGRCm39mm39
GRCm3819,906,157 - 9,943,606 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl19,908,638 - 9,942,085 (+)EnsemblGRCm38mm10GRCm38
MGSCv3719,898,719 - 9,931,035 (+)NCBIGRCm37mm9NCBIm37
MGSCv3619,896,933 - 9,926,168 (+)NCBImm8
Celera19,881,469 - 9,914,977 (+)NCBICelera
Cytogenetic Map1A2NCBI
Mcmdc2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544412,348,543 - 12,382,769 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544412,348,537 - 12,382,769 (-)NCBIChiLan1.0ChiLan1.0
MCMDC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1865,079,264 - 65,128,147 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0863,412,462 - 63,465,258 (+)NCBIMhudiblu_PPA_v0panPan3
MCMDC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2916,426,318 - 16,460,599 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12916,424,088 - 16,462,094 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Mcmdc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364967,149,501 - 7,182,771 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MCMDC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl467,847,817 - 67,895,867 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1467,850,585 - 67,892,438 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2473,908,711 - 73,952,722 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MCMDC2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1862,742,176 - 62,790,994 (+)NCBI
ChlSab1.1 Ensembl862,745,855 - 62,790,143 (+)Ensembl
Mcmdc2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474424,422,656 - 24,483,365 (-)NCBI


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
2312562Pur18Proteinuria QTL 182.60.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5152509833001026Rat
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
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5325132926252076Rat
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
631827Alc4Alcohol consumption QTL 43.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)5787561118592319Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5863228553632285Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:251
Count of miRNA genes:157
Interacting mature miRNAs:192
Transcripts:ENSRNOT00000030053
Prediction methods:Microtar, Miranda, 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 1 7
Low 3 43 53 37 18 37 8 11 74 35 34 11 8
Below cutoff 4 4 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000030053   ⟹   ENSRNOP00000037494
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl58,979,961 - 9,038,594 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000082023   ⟹   ENSRNOP00000070565
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl58,978,010 - 9,035,811 (-)Ensembl
RefSeq Acc Id: NM_001024340   ⟹   NP_001019511
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.259,298,100 - 9,337,485 (-)NCBI
Rnor_6.058,979,960 - 9,038,594 (-)NCBI
Rnor_5.0513,781,014 - 13,839,762 (-)NCBI
RGSC_v3.458,842,432 - 8,881,827 (-)RGD
Celera58,810,709 - 8,849,895 (-)RGD
Sequence:
RefSeq Acc Id: XM_006237781   ⟹   XP_006237843
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.259,299,153 - 9,337,309 (-)NCBI
Rnor_6.058,980,202 - 9,039,612 (-)NCBI
Rnor_5.0513,781,014 - 13,839,762 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237782   ⟹   XP_006237844
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.259,299,153 - 9,337,526 (-)NCBI
Rnor_6.058,980,202 - 9,039,612 (-)NCBI
Rnor_5.0513,781,014 - 13,839,762 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237784   ⟹   XP_006237846
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.259,299,153 - 9,337,309 (-)NCBI
Rnor_6.058,980,202 - 9,039,613 (-)NCBI
Rnor_5.0513,781,014 - 13,839,762 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237785   ⟹   XP_006237847
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.259,299,153 - 9,337,309 (-)NCBI
Rnor_6.058,980,202 - 9,039,616 (-)NCBI
Rnor_5.0513,781,014 - 13,839,762 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237787   ⟹   XP_006237849
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.259,291,967 - 9,337,309 (-)NCBI
Rnor_6.058,973,861 - 9,039,609 (-)NCBI
Rnor_5.0513,781,014 - 13,839,762 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237788   ⟹   XP_006237850
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.259,299,228 - 9,337,309 (-)NCBI
Rnor_6.058,980,202 - 9,039,599 (-)NCBI
Rnor_5.0513,781,014 - 13,839,762 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237789   ⟹   XP_006237851
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.259,301,364 - 9,337,309 (-)NCBI
Rnor_6.058,983,255 - 9,039,598 (-)NCBI
Rnor_5.0513,781,014 - 13,839,762 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039110522   ⟹   XP_038966450
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.259,299,153 - 9,337,526 (-)NCBI
RefSeq Acc Id: XM_039110523   ⟹   XP_038966451
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.259,299,153 - 9,337,309 (-)NCBI
RefSeq Acc Id: XM_039110524   ⟹   XP_038966452
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.259,299,153 - 9,331,473 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001019511   ⟸   NM_001024340
- UniProtKB: Q5XI14 (UniProtKB/Swiss-Prot),   R9PXX4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237849   ⟸   XM_006237787
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006237844   ⟸   XM_006237782
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006237846   ⟸   XM_006237784
- Peptide Label: isoform X2
- UniProtKB: R9PXX4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237847   ⟸   XM_006237785
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006237850   ⟸   XM_006237788
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_006237843   ⟸   XM_006237781
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006237851   ⟸   XM_006237789
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: ENSRNOP00000070565   ⟸   ENSRNOT00000082023
RefSeq Acc Id: ENSRNOP00000037494   ⟸   ENSRNOT00000030053
RefSeq Acc Id: XP_038966450   ⟸   XM_039110522
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038966451   ⟸   XM_039110523
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038966452   ⟸   XM_039110524
- Peptide Label: isoform X8
Protein Domains
MCM   MCM_lid

Transcriptome

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

Promoters
RGD ID:13693535
Promoter ID:EPDNEW_R4060
Type:single initiation site
Name:Mcmdc2_1
Description:minichromosome maintenance domain containing 2
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_6.059,038,600 - 9,038,660EPDNEW

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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (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
SBH/Ygl (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: 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)
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: 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)
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
SHRSP/Gcrc (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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WKY/Gcrc (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
WKY/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
WKY/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
WKY/NHsd (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
WN/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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 8981192 8981193 A C snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), CDS, SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), CDR, FHL/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561068 AgrOrtholog
Ensembl Genes ENSRNOG00000021702 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000037494 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070565 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000030053 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000082023 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7131459 IMAGE-MGC_LOAD
InterPro MCM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MCM_lid UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NA-bd_OB-fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:500392 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:95183 IMAGE-MGC_LOAD
NCBI Gene 500392 ENTREZGENE
PANTHER PTHR11630 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam MCM_lid UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Mcmdc2 PhenoGen
SMART MCM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50249 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt MCMD2_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  R9PXX4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-09-18 Mcmdc2  minichromosome maintenance domain containing 2  LOC500392  similar to hypothetical protein FLJ25692  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC500392  similar to hypothetical protein FLJ25692      Symbol and Name status set to provisional 70820 PROVISIONAL