Nid2 (nidogen 2) - Rat Genome Database

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Gene: Nid2 (nidogen 2) Rattus norvegicus
Analyze
Symbol: Nid2
Name: nidogen 2
RGD ID: 1311685
Description: Predicted to enable calcium ion binding activity. Predicted to be involved in cell-matrix adhesion. Located in cell surface. Orthologous to human NID2 (nidogen 2); INTERACTS WITH 17alpha-ethynylestradiol; 3,3',4,4',5-pentachlorobiphenyl; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC302248; NID-2; nidogen 2 (osteonidogen); nidogen-2
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
mRatBN7.2154,458,082 - 4,513,808 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl154,894,213 - 4,951,917 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0154,893,999 - 4,951,893 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0158,984,788 - 9,041,180 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4154,801,183 - 4,856,895 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1154,801,182 - 4,806,069 (-)NCBI
Celera1594,572 - 150,317 (+)NCBICelera
Cytogenetic Map15p16NCBI
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
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
6alpha-methylprednisolone  (ISO)
8-Br-cAMP  (ISO)
acetamide  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
aristolochic acid  (ISO)
arsenite(3-)  (ISO)
atrazine  (ISO)
azathioprine  (ISO)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butanal  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
carmustine  (EXP)
choline  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
diethylstilbestrol  (ISO)
dioxygen  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
folic acid  (ISO)
furan  (EXP)
genistein  (ISO)
graphite  (EXP)
L-methionine  (ISO)
Licochalcone B  (ISO)
methotrexate  (EXP,ISO)
mitoxantrone  (ISO)
N-nitrosodiethylamine  (EXP)
paracetamol  (ISO)
pentanal  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenylephrine  (EXP)
pirinixic acid  (ISO)
piroxicam  (ISO)
prednisolone  (ISO)
propanal  (ISO)
resveratrol  (ISO)
Salinomycin  (ISO)
selenium atom  (ISO)
silicon dioxide  (EXP,ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tebuconazole  (ISO)
temozolomide  (ISO)
Tesaglitazar  (EXP)
testosterone  (EXP)
tetrachloromethane  (ISO)
tioguanine  (EXP)
titanium dioxide  (ISO)
trichostatin A  (ISO)
troglitazone  (EXP,ISO)
valproic acid  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cell-matrix adhesion  (IBA,IEA,ISO)

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12243745   PMID:12477932   PMID:15895400   PMID:16607619   PMID:16618944   PMID:18757743   PMID:20551380   PMID:22952693   PMID:23376485   PMID:23533145   PMID:23658023   PMID:24006456  
PMID:27068509   PMID:27559042  


Genomics

Comparative Map Data
Nid2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2154,458,082 - 4,513,808 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl154,894,213 - 4,951,917 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0154,893,999 - 4,951,893 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0158,984,788 - 9,041,180 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4154,801,183 - 4,856,895 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1154,801,182 - 4,806,069 (-)NCBI
Celera1594,572 - 150,317 (+)NCBICelera
Cytogenetic Map15p16NCBI
NID2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1452,004,803 - 52,069,228 (-)EnsemblGRCh38hg38GRCh38
GRCh381452,004,809 - 52,069,059 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371452,471,527 - 52,535,777 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361451,541,270 - 51,605,696 (-)NCBINCBI36hg18NCBI36
Build 341451,541,270 - 51,605,696NCBI
Celera1432,338,519 - 32,403,077 (-)NCBI
Cytogenetic Map14q22.1NCBI
HuRef1432,632,190 - 32,696,681 (-)NCBIHuRef
CHM1_11452,409,979 - 52,475,129 (-)NCBICHM1_1
Nid2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391419,801,325 - 19,861,855 (+)NCBIGRCm39mm39
GRCm39 Ensembl1419,801,333 - 19,861,855 (+)Ensembl
GRCm381419,751,257 - 19,811,787 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1419,751,265 - 19,811,787 (+)EnsemblGRCm38mm10GRCm38
MGSCv371420,570,479 - 20,631,009 (+)NCBIGRCm37mm9NCBIm37
MGSCv361418,541,953 - 18,602,483 (+)NCBImm8
Celera1416,134,631 - 16,194,784 (+)NCBICelera
Cytogenetic Map14A3NCBI
Nid2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540910,977,110 - 11,034,015 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540910,976,114 - 11,034,700 (+)NCBIChiLan1.0ChiLan1.0
NID2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11450,889,602 - 50,953,830 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1450,890,317 - 50,953,830 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01432,604,392 - 32,668,121 (-)NCBIMhudiblu_PPA_v0panPan3
NID2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1828,240,427 - 28,300,729 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl828,102,780 - 28,300,507 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha827,992,186 - 28,052,999 (-)NCBI
ROS_Cfam_1.0828,417,496 - 28,478,303 (-)NCBI
UMICH_Zoey_3.1828,086,734 - 28,147,532 (-)NCBI
UNSW_CanFamBas_1.0828,147,524 - 28,208,416 (-)NCBI
UU_Cfam_GSD_1.0828,494,257 - 28,555,292 (-)NCBI
Nid2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864060,456,233 - 60,515,524 (-)NCBI
SpeTri2.0NW_00493649513,676,224 - 13,735,494 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NID2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1181,699,112 - 181,772,750 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11181,699,098 - 181,773,084 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21201,970,938 - 202,045,321 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NID2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12429,106,450 - 29,186,096 (-)NCBI
ChlSab1.1 Ensembl2429,107,115 - 29,186,059 (-)Ensembl
Vero_WHO_p1.0NW_02366605317,397,183 - 17,460,628 (-)NCBI
Nid2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473116,970,974 - 17,032,515 (+)NCBI

Position Markers
AA945900  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2154,458,226 - 4,458,364 (+)MAPPERmRatBN7.2
Rnor_6.0154,894,144 - 4,894,281NCBIRnor6.0
Rnor_5.0158,984,933 - 8,985,070UniSTSRnor5.0
RGSC_v3.4154,801,328 - 4,801,465UniSTSRGSC3.4
Celera15150,035 - 150,172UniSTS
RH 3.4 Map1568.1UniSTS
Cytogenetic Map15p16UniSTS
BQ204566  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2154,465,925 - 4,466,093 (+)MAPPERmRatBN7.2
Rnor_6.0154,901,841 - 4,902,008NCBIRnor6.0
Rnor_5.0158,992,630 - 8,992,797UniSTSRnor5.0
RGSC_v3.4154,809,027 - 4,809,194UniSTSRGSC3.4
Celera15142,306 - 142,473UniSTS
RH 3.4 Map1568.2UniSTS
Cytogenetic Map15p16UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300142Bp191Blood pressure QTL 1913.14arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)15112800829Rat
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15130597196Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15137708474Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15137708474Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15137708474Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15142844179Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15143521446Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15162301382Rat
5684946Bss98Bone structure and strength QTL 983.90.0026tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)15110589015828368Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)colorectal tumor number (CMO:0001794)15232787726288802Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15232787726288802Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15232787753535766Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)15388113148881131Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:58
Count of miRNA genes:52
Interacting mature miRNAs:53
Transcripts:ENSRNOT00000000383
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 32 22 16 5 16 4 5 53 35 38 5 4
Low 3 11 35 25 14 25 4 6 21 3 6 4
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000383   ⟹   ENSRNOP00000000383
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl154,894,213 - 4,951,917 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000082196   ⟹   ENSRNOP00000072586
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl154,894,539 - 4,951,870 (-)Ensembl
RefSeq Acc Id: NM_001012005   ⟹   NP_001012005
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2154,458,082 - 4,513,808 (-)NCBI
Rnor_6.0154,893,999 - 4,951,893 (-)NCBI
Rnor_5.0158,984,788 - 9,041,180 (-)NCBI
RGSC_v3.4154,801,183 - 4,856,895 (-)RGD
Celera1594,572 - 150,317 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001012005 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH88325 (Get FASTA)   NCBI Sequence Viewer  
  AAI69012 (Get FASTA)   NCBI Sequence Viewer  
  B5DFC9 (Get FASTA)   NCBI Sequence Viewer  
  EDL86201 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001012005   ⟸   NM_001012005
- Peptide Label: precursor
- UniProtKB: B5DFC9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072586   ⟸   ENSRNOT00000082196
RefSeq Acc Id: ENSRNOP00000000383   ⟸   ENSRNOT00000000383
Transcriptome

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

Promoters
RGD ID:13699575
Promoter ID:EPDNEW_R10096
Type:multiple initiation site
Name:Nid2_1
Description:nidogen 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_6.0154,951,924 - 4,951,984EPDNEW

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:1311685 AgrOrtholog
Ensembl Genes ENSRNOG00000000341 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000383 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000072586 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000383 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000082196 UniProtKB/TrEMBL
Gene3D-CATH 2.120.10.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  4.10.800.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro 6-blade_b-propeller_TolB-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-like_Ca-bd_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-type_Asp/Asn_hydroxyl_site UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_Ca-bd_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  G2_nidogen/fibulin_G2F UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GFP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Growth_fac_rcpt_cys_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LDLR_classB_rpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NIDO_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Thyroglobulin_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Thyroglobulin_1_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:302248 UniProtKB/Swiss-Prot
NCBI Gene 302248 ENTREZGENE
Pfam EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  G2F UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ldl_recept_b UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NIDO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Thyroglobulin_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nid2 PhenoGen
PROSITE ASX_HYDROXYL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LDLRB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NIDO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NIDOGEN_G2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  THYROGLOBULIN_1_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  THYROGLOBULIN_1_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART EGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  G2F UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NIDO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00135 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00211 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54511 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF57184 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF57610 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K3C8_RAT UniProtKB/TrEMBL
  B5DFC9 ENTREZGENE, UniProtKB/Swiss-Prot
  W4VSR4_RAT UniProtKB/TrEMBL
UniProt Secondary Q5M812 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-02 Nid2  nidogen 2  Nid2  nidogen 2 (osteonidogen)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-01-22 Nid2  nidogen 2 (osteonidogen)  Nid2  nidogen 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Nid2  nidogen 2  Nid2_predicted  nidogen 2 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Nid2_predicted  nidogen 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED