Ndc80 (NDC80 kinetochore complex component) - Rat Genome Database

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Gene: Ndc80 (NDC80 kinetochore complex component) Rattus norvegicus
Analyze
Symbol: Ndc80
Name: NDC80 kinetochore complex component
RGD ID: 1310154
Description: Predicted to have cyclin binding activity and identical protein binding activity. Predicted to be involved in several processes, including G2/MI transition of meiotic cell cycle; microtubule cytoskeleton organization; and nuclear division. Predicted to localize to several cellular components, including centrosome; kinetochore; and nucleoplasm. Orthologous to human NDC80 (NDC80 kinetochore complex component); INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: kinetochore associated 2; kinetochore protein NDC80 homolog; Kntc2; LOC301701; NDC80 homolog, kinetochore complex component; NDC80 homolog, kinetochore complex component (S. cerevisiae)
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
mRatBN7.29111,407,191 - 111,440,921 (-)NCBI
Rnor_6.0 Ensembl9119,839,016 - 119,871,382 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.09119,837,857 - 119,871,435 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.09119,291,271 - 119,324,839 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.49110,702,935 - 110,718,894 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.19110,912,517 - 110,945,708 (-)NCBI
Celera9108,536,354 - 108,552,152 (-)NCBICelera
Cytogenetic Map9q38NCBI
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
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-diaminotoluene  (ISO)
2-methylcholine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (EXP,ISO)
aflatoxin B1  (EXP,ISO)
aflatoxin M1  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
azathioprine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
Benzo[k]fluoranthene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
cadmium atom  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
CU-O LINKAGE  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dibenz[a,h]anthracene  (ISO)
dicrotophos  (ISO)
dieldrin  (EXP)
disodium selenite  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
flutamide  (EXP)
fluvastatin  (ISO)
folic acid  (ISO)
fulvestrant  (ISO)
furan  (EXP)
genistein  (ISO)
glycidol  (EXP)
hydrogen peroxide  (ISO)
Indeno[1,2,3-cd]pyrene  (ISO)
indometacin  (ISO)
leflunomide  (ISO)
lucanthone  (ISO)
menadione  (ISO)
methamphetamine  (EXP)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylparaben  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-Nitrosopyrrolidine  (ISO)
naphthalene  (ISO)
nickel atom  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
palbociclib  (ISO)
paracetamol  (ISO)
perfluorononanoic acid  (ISO)
phenanthrene  (ISO)
phenformin  (EXP)
phytoestrogen  (ISO)
piroxicam  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
propanal  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
senecionine  (EXP)
Senkirkine  (EXP)
silicon dioxide  (ISO)
sirolimus  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP,ISO)
tetrachloromethane  (EXP,ISO)
tetraphene  (ISO)
thioacetamide  (EXP)
titanium dioxide  (EXP)
topotecan  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)
vincaleukoblastine  (ISO)
zaragozic acid A  (EXP,ISO)
zoledronic acid  (ISO)

References

Additional References at PubMed
PMID:12477932   PMID:14699129   PMID:17363900   PMID:18195732   PMID:19468067   PMID:19946888   PMID:20360068   PMID:22581055   PMID:23891108   PMID:24752407   PMID:25416956   PMID:25743205  


Genomics

Comparative Map Data
Ndc80
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.29111,407,191 - 111,440,921 (-)NCBI
Rnor_6.0 Ensembl9119,839,016 - 119,871,382 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.09119,837,857 - 119,871,435 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.09119,291,271 - 119,324,839 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.49110,702,935 - 110,718,894 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.19110,912,517 - 110,945,708 (-)NCBI
Celera9108,536,354 - 108,552,152 (-)NCBICelera
Cytogenetic Map9q38NCBI
NDC80
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl182,571,557 - 2,616,635 (+)EnsemblGRCh38hg38GRCh38
GRCh38182,571,557 - 2,616,635 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37182,571,556 - 2,616,634 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36182,561,605 - 2,606,629 (+)NCBINCBI36hg18NCBI36
Build 34182,561,604 - 2,606,626NCBI
Celera182,446,814 - 2,491,757 (+)NCBI
Cytogenetic Map18p11.32NCBI
HuRef182,532,999 - 2,577,942 (+)NCBIHuRef
CHM1_1182,570,883 - 2,615,800 (+)NCBICHM1_1
Ndc80
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391771,803,095 - 71,833,852 (-)NCBIGRCm39mm39
GRCm39 Ensembl1771,803,095 - 71,833,852 (-)Ensembl
GRCm381771,496,100 - 71,526,857 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1771,496,100 - 71,526,857 (-)EnsemblGRCm38mm10GRCm38
MGSCv371771,845,440 - 71,876,197 (-)NCBIGRCm37mm9NCBIm37
MGSCv361771,400,962 - 71,431,714 (-)NCBImm8
Celera1775,767,449 - 75,800,160 (-)NCBICelera
Cytogenetic Map17E1.3NCBI
Ndc80
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554027,691,937 - 7,729,690 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554027,692,009 - 7,728,876 (-)NCBIChiLan1.0ChiLan1.0
NDC80
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11813,972,637 - 14,018,261 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1813,972,637 - 14,018,261 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01811,666,099 - 11,711,456 (-)NCBIMhudiblu_PPA_v0panPan3
NDC80
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1769,268,218 - 69,317,126 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl769,268,242 - 69,317,072 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha768,723,201 - 68,772,189 (+)NCBI
ROS_Cfam_1.0769,329,940 - 69,378,870 (+)NCBI
UMICH_Zoey_3.1769,012,589 - 69,061,471 (+)NCBI
UNSW_CanFamBas_1.0769,032,710 - 69,081,627 (+)NCBI
UU_Cfam_GSD_1.0769,329,927 - 69,378,829 (+)NCBI
Ndc80
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494465,630,900 - 65,669,747 (+)NCBI
SpeTri2.0NW_0049366721,872,205 - 1,910,956 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NDC80
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6103,998,698 - 104,055,762 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16104,000,794 - 104,055,785 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2697,024,076 - 97,061,162 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NDC80
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11861,835,027 - 61,882,660 (+)NCBI
ChlSab1.1 Ensembl1861,835,064 - 61,881,627 (+)Ensembl
Vero_WHO_p1.0NW_02366605036,694,925 - 36,740,902 (+)NCBI
Ndc80
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477012,937,887 - 12,974,352 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)981411073119983851Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)990024661119983851Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:74
Count of miRNA genes:69
Interacting mature miRNAs:71
Transcripts:ENSRNOT00000018644
Prediction methods:Microtar, 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 26 29 22 14 22 37 20 36
Low 1 15 22 13 5 13 4 5 35 11 5 11 4
Below cutoff 2 6 6 6 4 6 2 4 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000018644   ⟹   ENSRNOP00000018644
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl9119,840,326 - 119,871,382 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000080498   ⟹   ENSRNOP00000072111
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl9119,839,016 - 119,869,639 (-)Ensembl
RefSeq Acc Id: NM_001126270   ⟹   NP_001119742
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29111,409,661 - 111,425,609 (-)NCBI
Rnor_6.09119,840,326 - 119,856,147 (-)NCBI
Rnor_5.09119,291,271 - 119,324,839 (-)NCBI
RGSC_v3.49110,702,935 - 110,718,894 (-)RGD
Celera9108,536,354 - 108,552,152 (-)RGD
Sequence:
RefSeq Acc Id: XM_006245657   ⟹   XP_006245719
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29111,407,191 - 111,440,921 (-)NCBI
Rnor_6.09119,837,857 - 119,871,434 (-)NCBI
Rnor_5.09119,291,271 - 119,324,839 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767423   ⟹   XP_008765645
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29111,407,191 - 111,440,898 (-)NCBI
Rnor_6.09119,837,857 - 119,871,435 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039083429   ⟹   XP_038939357
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29111,407,191 - 111,440,761 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001119742 (Get FASTA)   NCBI Sequence Viewer  
  XP_006245719 (Get FASTA)   NCBI Sequence Viewer  
  XP_008765645 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939357 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI61935 (Get FASTA)   NCBI Sequence Viewer  
  EDL90957 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001119742   ⟸   NM_001126270
- Sequence:
RefSeq Acc Id: XP_006245719   ⟸   XM_006245657
- Peptide Label: isoform X1
- UniProtKB: F7F189 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008765645   ⟸   XM_008767423
- Peptide Label: isoform X1
- UniProtKB: F7F189 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072111   ⟸   ENSRNOT00000080498
RefSeq Acc Id: ENSRNOP00000018644   ⟸   ENSRNOT00000018644
RefSeq Acc Id: XP_038939357   ⟸   XM_039083429
- Peptide Label: isoform X1
Protein Domains
DUF5595

Transcriptome

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

Promoters
RGD ID:13696917
Promoter ID:EPDNEW_R7439
Type:initiation region
Name:Ndc80_1
Description:NDC80 kinetochore complex component
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_6.09119,871,421 - 119,871,481EPDNEW

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310154 AgrOrtholog
Ensembl Genes ENSRNOG00000013727 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000018644 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000072111 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018644 UniProtKB/TrEMBL
  ENSRNOT00000080498 UniProtKB/TrEMBL
Gene3D-CATH 1.10.418.30 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9022458 IMAGE-MGC_LOAD
InterPro DUF5595 UniProtKB/TrEMBL
  Kinetochore_Ndc80 UniProtKB/TrEMBL
  Ndc80_sf UniProtKB/TrEMBL
MGC_CLONE MGC:187716 IMAGE-MGC_LOAD
NCBI Gene 301701 ENTREZGENE
PANTHER PTHR10643 UniProtKB/TrEMBL
Pfam DUF5595 UniProtKB/TrEMBL
  Ndc80_HEC UniProtKB/TrEMBL
PhenoGen Ndc80 PhenoGen
UniProt F7F189 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary B1WBY4 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-02-27 Ndc80  NDC80 kinetochore complex component  Ndc80  NDC80 homolog, kinetochore complex component (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Ndc80  NDC80 homolog, kinetochore complex component (S. cerevisiae)  Kntc2_predicted  kinetochore associated 2 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED