Mcph1 (microcephalin 1) - Rat Genome Database

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Gene: Mcph1 (microcephalin 1) Rattus norvegicus
Analyze
Symbol: Mcph1
Name: microcephalin 1
RGD ID: 1560642
Description: Predicted to have identical protein binding activity. Predicted to be involved in several processes, including establishment of mitotic spindle orientation; neuronal stem cell population maintenance; and protein localization to centrosome. Predicted to localize to microtubule organizing center. Human ortholog(s) of this gene implicated in breast cancer; endometrial cancer; microcephaly; primary autosomal recessive microcephaly; and primary autosomal recessive microcephaly 1. Orthologous to human MCPH1 (microcephalin 1); PARTICIPATES IN histone modification pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; amphetamine; atrazine.
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC306594; microcephalin; microcephaly, primary autosomal recessive 1; RGD1560642; similar to microcephalin
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
mRatBN7.21671,021,855 - 71,224,067 (-)NCBI
Rnor_6.0 Ensembl1675,904,006 - 76,110,553 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01675,904,087 - 76,110,624 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01675,508,903 - 75,716,058 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41675,839,877 - 76,026,968 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1668,871,372 - 69,069,330 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Alsiary R, etal., PLoS One. 2014 May 15;9(5):e97059. doi: 10.1371/journal.pone.0097059. eCollection 2014.
2. Bilbao C, etal., Eur J Cancer. 2010 Oct;46(15):2821-7. doi: 10.1016/j.ejca.2010.06.116. Epub 2010 Jul 16.
3. Darvish H, etal., J Med Genet. 2010 Dec;47(12):823-8. doi: 10.1136/jmg.2009.076398. Epub 2010 Oct 26.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Jackson AP, etal., Am J Hum Genet. 2002 Jul;71(1):136-42. Epub 2002 Jun 3.
6. Jo YH, etal., Gene. 2013 Apr 1;517(2):184-90. doi: 10.1016/j.gene.2012.12.088. Epub 2013 Jan 4.
7. Maghirang-Rodriguez R, etal., Am J Med Genet A. 2009 Feb 15;149A(4):622-5. doi: 10.1002/ajmg.a.32721.
8. OMIM Disease Annotation Pipeline
9. Patel DJ and Wang Z, Annu Rev Biochem. 2013;82:81-118. doi: 10.1146/annurev-biochem-072711-165700.
10. Rai R, etal., Cancer Cell. 2006 Aug;10(2):145-57. Epub 2006 Jul 27.
11. RGD automated data pipeline
12. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13. RGD automated import pipeline for gene-chemical interactions
14. RGD comprehensive gene curation
15. Richardson J, etal., Breast Cancer Res Treat. 2011 Jun;127(3):639-48. doi: 10.1007/s10549-010-1019-4. Epub 2010 Jul 15.
16. Sajid Hussain M, etal., Clin Genet. 2013 May;83(5):446-51. doi: 10.1111/j.1399-0004.2012.01932.x. Epub 2012 Aug 7.
17. Trimborn M, etal., Am J Hum Genet. 2004 Aug;75(2):261-6. Epub 2004 Jun 15.
18. Venkatesh T, etal., PLoS One. 2013;8(3):e54643. doi: 10.1371/journal.pone.0054643. Epub 2013 Mar 5.
19. Wang N, etal., Int J Clin Exp Pathol. 2014 Jul 15;7(8):4895-903. eCollection 2014.
20. Zhou ZW, etal., DNA Repair (Amst). 2013 Aug;12(8):645-55. doi: 10.1016/j.dnarep.2013.04.017. Epub 2013 May 15.
Additional References at PubMed
PMID:12837246   PMID:18660752   PMID:20169082   PMID:21737879   PMID:21947081   PMID:23516444   PMID:24633962  


Genomics

Comparative Map Data
Mcph1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21671,021,855 - 71,224,067 (-)NCBI
Rnor_6.0 Ensembl1675,904,006 - 76,110,553 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01675,904,087 - 76,110,624 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01675,508,903 - 75,716,058 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41675,839,877 - 76,026,968 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1668,871,372 - 69,069,330 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
MCPH1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl86,406,592 - 6,648,508 (+)EnsemblGRCh38hg38GRCh38
GRCh3886,406,615 - 6,648,508 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3786,264,148 - 6,506,029 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3686,251,529 - 6,493,434 (+)NCBINCBI36hg18NCBI36
Build 3486,276,479 - 6,489,214NCBI
Celera86,241,660 - 6,478,643 (+)NCBI
Cytogenetic Map8p23.1NCBI
HuRef86,046,225 - 6,282,052 (+)NCBIHuRef
CHM1_186,352,911 - 6,595,171 (+)NCBICHM1_1
Mcph1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39818,645,132 - 18,858,105 (+)NCBIGRCm39mm39
GRCm39 Ensembl818,645,147 - 18,853,205 (+)Ensembl
GRCm38818,595,116 - 18,808,089 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl818,595,131 - 18,803,189 (+)EnsemblGRCm38mm10GRCm38
MGSCv37818,595,173 - 18,803,189 (+)NCBIGRCm37mm9NCBIm37
MGSCv36818,595,150 - 18,803,166 (+)NCBImm8
Celera818,728,614 - 18,936,696 (+)NCBICelera
Cytogenetic Map8A1.3NCBI
Mcph1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540354,143,454 - 54,273,201 (-)NCBIChiLan1.0ChiLan1.0
MCPH1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.186,409,072 - 6,651,846 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl86,409,072 - 6,646,394 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v08624,877 - 877,839 (-)NCBIMhudiblu_PPA_v0panPan3
MCPH1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11658,306,761 - 58,529,090 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1658,295,280 - 58,529,433 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1653,827,270 - 54,059,123 (+)NCBI
ROS_Cfam_1.01657,520,814 - 57,753,393 (-)NCBI
UMICH_Zoey_3.11658,441,000 - 58,688,068 (+)NCBI
UNSW_CanFamBas_1.01655,530,366 - 55,762,093 (-)NCBI
UU_Cfam_GSD_1.01655,905,580 - 56,138,767 (-)NCBI
Mcph1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049434,386,615 - 4,580,738 (+)NCBI
SpeTri2.0NW_0049366154,386,667 - 4,580,720 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MCPH1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1537,455,526 - 37,673,663 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11537,455,186 - 37,674,971 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21542,711,671 - 42,747,818 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MCPH1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.186,190,272 - 6,425,683 (+)NCBI
ChlSab1.1 Ensembl86,190,047 - 6,425,131 (+)Ensembl
Vero_WHO_p1.0NW_02366605448,304,204 - 48,541,439 (+)NCBI
Mcph1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248614,373,743 - 4,556,933 (+)NCBI

Position Markers
D16Rat16  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21671,225,672 - 71,225,844 (+)MAPPER
Rnor_6.01676,111,887 - 76,112,058NCBIRnor6.0
Rnor_5.01675,717,429 - 75,717,600UniSTSRnor5.0
RGSC_v3.41676,030,795 - 76,030,967RGDRGSC3.4
RGSC_v3.41676,030,796 - 76,030,967UniSTSRGSC3.4
RGSC_v3.11676,031,061 - 76,031,232RGD
Celera1669,070,598 - 69,070,753UniSTS
RH 3.4 Map16697.1RGD
RH 3.4 Map16697.1UniSTS
RH 2.0 Map16805.2RGD
FHH x ACI Map1640.2499RGD
Cytogenetic Map16q12.5UniSTS
BF399189  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21671,141,121 - 71,141,252 (+)MAPPER
Rnor_6.01676,018,464 - 76,018,594NCBIRnor6.0
Rnor_5.01675,624,285 - 75,624,415UniSTSRnor5.0
RGSC_v3.41675,944,572 - 75,944,702UniSTSRGSC3.4
Celera1668,986,631 - 68,986,761UniSTS
RH 3.4 Map16695.7UniSTS
Cytogenetic Map16q12.5UniSTS
AU048376  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01676,106,388 - 76,106,635NCBIRnor6.0
Rnor_5.01675,711,930 - 75,712,177UniSTSRnor5.0
RGSC_v3.41676,023,455 - 76,023,702UniSTSRGSC3.4
Cytogenetic Map16q12.5UniSTS
RH129137  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21671,138,572 - 71,138,771 (+)MAPPER
Rnor_6.01676,015,918 - 76,016,113NCBIRnor6.0
Rnor_5.01675,621,739 - 75,621,934UniSTSRnor5.0
RGSC_v3.41675,942,023 - 75,942,221UniSTSRGSC3.4
Celera1668,984,082 - 68,984,280UniSTS
RH 3.4 Map16694.1UniSTS
Cytogenetic Map16q12.5UniSTS
RH129360  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21671,138,553 - 71,138,738 (+)MAPPER
Rnor_6.01676,015,899 - 76,016,080NCBIRnor6.0
Rnor_5.01675,621,720 - 75,621,901UniSTSRnor5.0
RGSC_v3.41675,942,004 - 75,942,188UniSTSRGSC3.4
Celera1668,984,063 - 68,984,247UniSTS
RH 3.4 Map16697.0UniSTS
Cytogenetic Map16q12.5UniSTS
RH142622  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21671,223,997 - 71,224,188 (+)MAPPER
Rnor_6.01676,110,212 - 76,110,402NCBIRnor6.0
Rnor_5.01675,715,754 - 75,715,944UniSTSRnor5.0
RGSC_v3.41676,027,279 - 76,027,469UniSTSRGSC3.4
Celera1669,068,919 - 69,069,109UniSTS
RH 3.4 Map16693.0UniSTS
Cytogenetic Map16q12.5UniSTS
BF405139  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21671,078,310 - 71,078,560 (+)MAPPER
Rnor_6.01675,956,427 - 75,956,676NCBIRnor6.0
Rnor_5.01675,562,248 - 75,562,497UniSTSRnor5.0
RGSC_v3.41675,881,704 - 75,881,953UniSTSRGSC3.4
Celera1668,923,800 - 68,924,049UniSTS
RH 3.4 Map16702.6UniSTS
Cytogenetic Map16q12.5UniSTS
RH141778  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21671,089,708 - 71,089,894 (+)MAPPER
Rnor_6.01675,967,825 - 75,968,010NCBIRnor6.0
Rnor_5.01675,573,646 - 75,573,831UniSTSRnor5.0
RGSC_v3.41675,893,102 - 75,893,287UniSTSRGSC3.4
Celera1668,935,192 - 68,935,377UniSTS
RH 3.4 Map16704.71UniSTS
Cytogenetic Map16q12.5UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)16109005486162972Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)162075555680316424Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163900002184000021Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)164151271086512710Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)164151271086512710Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164655818890668790Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165781635790668790Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165781635790668790Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165781635790668790Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165928577589248943Rat
1298527Arunc2Aerobic running capacity QTL 22.9exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)167321963880115794Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:82
Count of miRNA genes:74
Interacting mature miRNAs:77
Transcripts:ENSRNOT00000043384
Prediction methods:Microtar, 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 6 12 6 8 6 51 12 30
Low 3 36 45 35 11 35 8 10 23 23 11 11 8
Below cutoff 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000043384   ⟹   ENSRNOP00000046380
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1675,904,006 - 76,110,553 (-)Ensembl
RefSeq Acc Id: XM_001074501   ⟹   XP_001074501
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1668,871,372 - 69,069,330 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006222284   ⟹   XP_006222346
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1668,871,372 - 69,069,330 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006222286   ⟹   XP_006222348
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1668,871,372 - 69,068,311 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006222289   ⟹   XP_006222351
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1668,889,671 - 69,069,275 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253383   ⟹   XP_006253445
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21671,021,855 - 71,224,067 (-)NCBI
Rnor_6.01675,904,087 - 76,110,624 (-)NCBI
Rnor_5.01675,508,903 - 75,716,058 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253385   ⟹   XP_006253447
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21671,021,855 - 71,223,581 (-)NCBI
Rnor_6.01675,904,087 - 76,109,604 (-)NCBI
Rnor_5.01675,508,903 - 75,716,058 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253388   ⟹   XP_006253450
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01675,922,213 - 76,110,618 (-)NCBI
Rnor_5.01675,508,903 - 75,716,058 (-)NCBI
Sequence:
RefSeq Acc Id: XM_225006   ⟹   XP_225006
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21671,021,855 - 71,224,067 (-)NCBI
Rnor_6.01675,904,087 - 76,110,624 (-)NCBI
Rnor_5.01675,508,903 - 75,716,058 (-)NCBI
RGSC_v3.41675,839,877 - 76,026,968 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs XP_006253445 (Get FASTA)   NCBI Sequence Viewer  
  XP_006253447 (Get FASTA)   NCBI Sequence Viewer  
  XP_225006 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM08954 (Get FASTA)   NCBI Sequence Viewer  
  EDM08955 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_001074501   ⟸   XM_001074501
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_225006   ⟸   XM_225006
- Peptide Label: isoform X1
- UniProtKB: D3ZJM7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006222346   ⟸   XM_006222284
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006222348   ⟸   XM_006222286
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006222351   ⟸   XM_006222289
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006253445   ⟸   XM_006253383
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006253447   ⟸   XM_006253385
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006253450   ⟸   XM_006253388
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000046380   ⟸   ENSRNOT00000043384
Protein Domains
BRCT

Transcriptome

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


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)
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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
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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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
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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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
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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)
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:1560642 AgrOrtholog
Ensembl Genes ENSRNOG00000028586 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000046380 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000043384 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.10190 UniProtKB/TrEMBL
InterPro BRCT UniProtKB/TrEMBL
  BRCT_dom_sf UniProtKB/TrEMBL
  Microcephalin UniProtKB/TrEMBL
  Microcephalin_mammal UniProtKB/TrEMBL
NCBI Gene 306594 ENTREZGENE
PANTHER PTHR14625 UniProtKB/TrEMBL
Pfam BRCT_2 UniProtKB/TrEMBL
  Microcephalin UniProtKB/TrEMBL
  PTCB-BRCT UniProtKB/TrEMBL
PhenoGen Mcph1 PhenoGen
PROSITE BRCT UniProtKB/TrEMBL
SMART BRCT UniProtKB/TrEMBL
Superfamily-SCOP BRCT UniProtKB/TrEMBL
UniProt D3ZJM7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-24 Mcph1  microcephalin 1  Mcph1  microcephaly, primary autosomal recessive 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-28 Mcph1  microcephaly, primary autosomal recessive 1  RGD1560642_predicted  similar to microcephalin (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1560642_predicted  similar to microcephalin (predicted)  LOC306594  similar to microcephalin  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC306594  similar to microcephalin      Symbol and Name status set to provisional 70820 PROVISIONAL