Ajuba (ajuba LIM protein) - Rat Genome Database

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Gene: Ajuba (ajuba LIM protein) Rattus norvegicus
Analyze
Symbol: Ajuba
Name: ajuba LIM protein
RGD ID: 620407
Description: Predicted to have several functions, including actin filament binding activity; alpha-catenin binding activity; and transcription corepressor activity. Predicted to be involved in several processes, including calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules; regulation of gene expression; and regulation of intracellular signal transduction. Localizes to cell-cell junction. Orthologous to human AJUBA (ajuba LIM protein); PARTICIPATES IN E-cadherin signaling pathway; INTERACTS WITH 1,3-dinitrobenzene; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: ajuba homolog; ajuba homolog (Xenopus laevis); Jub; jub, ajuba homolog; jub, ajuba homolog (Xenopus laevis); LIM domain-containing protein ajuba; MGC93830
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
mRatBN7.21528,019,775 - 28,031,537 (-)NCBI
Rnor_6.0 Ensembl1533,208,216 - 33,218,456 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01533,208,210 - 33,218,456 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01537,092,299 - 37,103,304 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41532,627,633 - 32,637,861 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11532,644,597 - 32,652,711 (-)NCBI
Celera1527,595,895 - 27,610,669 (-)NCBICelera
Cytogenetic Map15p13NCBI
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-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
14-Deoxy-11,12-didehydroandrographolide  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
3,4-dichloroaniline  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-phenylbutyric acid  (ISO)
acetamide  (EXP)
aflatoxin B1  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP)
carbamazepine  (ISO)
carbon nanotube  (ISO)
choline  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
CU-O LINKAGE  (ISO)
cyclosporin A  (ISO)
dibutyl phthalate  (EXP,ISO)
diuron  (EXP,ISO)
dorsomorphin  (ISO)
Enterolactone  (ISO)
entinostat  (ISO)
ethyl methanesulfonate  (ISO)
fenamidone  (ISO)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
furan  (EXP)
hydrogen peroxide  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lipopolysaccharide  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
mifepristone  (EXP)
mono(2-ethylhexyl) phthalate  (EXP)
Monobutylphthalate  (EXP)
N-nitrosodiethylamine  (ISO)
orphenadrine  (EXP)
oxaliplatin  (EXP)
paracetamol  (ISO)
phencyclidine  (ISO)
phenobarbital  (ISO)
pioglitazone  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium dichromate  (EXP)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
topotecan  (EXP)
trichostatin A  (ISO)
troglitazone  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10330178   PMID:12477932   PMID:15728191   PMID:15870270   PMID:15870274   PMID:17909014   PMID:18331720   PMID:18347060   PMID:18805794   PMID:19376971   PMID:20303269   PMID:20616046  
PMID:22286099  


Genomics

Comparative Map Data
Ajuba
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21528,019,775 - 28,031,537 (-)NCBI
Rnor_6.0 Ensembl1533,208,216 - 33,218,456 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01533,208,210 - 33,218,456 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01537,092,299 - 37,103,304 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41532,627,633 - 32,637,861 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11532,644,597 - 32,652,711 (-)NCBI
Celera1527,595,895 - 27,610,669 (-)NCBICelera
Cytogenetic Map15p13NCBI
AJUBA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1422,971,177 - 22,982,551 (-)EnsemblGRCh38hg38GRCh38
GRCh381422,971,177 - 22,982,551 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371423,440,386 - 23,451,760 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361422,510,249 - 22,521,691 (-)NCBINCBI36hg18NCBI36
Build 341422,510,248 - 22,516,272NCBI
Celera143,303,299 - 3,314,741 (-)NCBI
Cytogenetic Map14q11.2NCBI
HuRef143,557,642 - 3,569,085 (-)NCBIHuRef
CHM1_11423,439,014 - 23,450,482 (-)NCBICHM1_1
Ajuba
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391454,804,926 - 54,815,118 (-)NCBIGRCm39mm39
GRCm39 Ensembl1454,804,929 - 54,815,015 (-)Ensembl
GRCm381454,567,469 - 54,577,661 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1454,567,472 - 54,577,558 (-)EnsemblGRCm38mm10GRCm38
MGSCv371455,186,309 - 55,196,253 (-)NCBIGRCm37mm9NCBIm37
MGSCv361453,521,677 - 53,531,621 (-)NCBImm8
Celera1452,356,267 - 52,366,350 (-)NCBICelera
Cytogenetic Map14C2NCBI
Ajuba
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540937,318,597 - 37,329,155 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540937,318,597 - 37,329,068 (+)NCBIChiLan1.0ChiLan1.0
AJUBA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11421,889,443 - 21,900,700 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1421,889,443 - 21,900,700 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0143,791,309 - 3,802,763 (-)NCBIMhudiblu_PPA_v0panPan3
AJUBA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.183,272,408 - 3,302,179 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl83,272,405 - 3,301,708 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha83,219,989 - 3,250,272 (-)NCBI
ROS_Cfam_1.083,379,492 - 3,410,108 (-)NCBI
UMICH_Zoey_3.183,070,717 - 3,101,039 (-)NCBI
UNSW_CanFamBas_1.083,132,252 - 3,162,764 (-)NCBI
UU_Cfam_GSD_1.083,394,515 - 3,424,826 (-)NCBI
Ajuba
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864035,047,132 - 35,057,420 (-)NCBI
SpeTri2.0NW_0049367221,331,568 - 1,341,854 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AJUBA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl776,063,034 - 76,076,594 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1776,063,009 - 76,072,884 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
AJUBA
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12923,341,841 - 23,352,630 (-)NCBI
ChlSab1.1 Ensembl2923,341,249 - 23,352,685 (-)Ensembl
Ajuba
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248209,551,664 - 9,562,773 (+)NCBI

Position Markers
D15Rat6  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21528,030,665 - 28,030,847 (+)MAPPER
Rnor_6.01533,219,101 - 33,219,282NCBIRnor6.0
Rnor_5.01537,103,190 - 37,103,371UniSTSRnor5.0
RGSC_v3.41532,638,412 - 32,638,778RGDRGSC3.4
RGSC_v3.41532,638,506 - 32,638,707UniSTSRGSC3.4
RGSC_v3.11532,654,112 - 32,654,478RGD
RH 2.0 Map15174.3RGD
SHRSP x BN Map1525.6198RGD
Cytogenetic Map15p13UniSTS
D15Rat85  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21528,030,612 - 28,030,847 (+)MAPPER
Rnor_6.01533,219,048 - 33,219,282NCBIRnor6.0
Rnor_5.01537,103,137 - 37,103,371UniSTSRnor5.0
RGSC_v3.41532,638,452 - 32,638,707RGDRGSC3.4
RGSC_v3.41532,638,453 - 32,638,707UniSTSRGSC3.4
RGSC_v3.11532,654,153 - 32,654,407RGD
Celera1527,611,261 - 27,611,582UniSTS
RH 3.4 Map15201.0RGD
RH 3.4 Map15201.0UniSTS
RH 2.0 Map15173.8RGD
SHRSP x BN Map1525.6598RGD
Cytogenetic Map15p13UniSTS
RH131975  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21528,019,869 - 28,020,077 (+)MAPPER
mRatBN7.25139,221,340 - 139,221,548 (-)MAPPER
mRatBN7.25139,221,340 - 139,221,548 (+)MAPPER
mRatBN7.21528,019,869 - 28,020,077 (-)MAPPER
Rnor_6.01533,208,305 - 33,208,512NCBIRnor6.0
Rnor_6.05144,953,185 - 144,953,392NCBIRnor6.0
Rnor_5.05148,723,437 - 148,723,644UniSTSRnor5.0
Rnor_5.01537,092,394 - 37,092,601UniSTSRnor5.0
RGSC_v3.45146,342,495 - 146,342,702UniSTSRGSC3.4
RGSC_v3.41532,627,728 - 32,627,935UniSTSRGSC3.4
Celera1527,595,990 - 27,596,197UniSTS
Celera5137,716,397 - 137,716,604UniSTS
Cytogenetic Map15p13UniSTS
Cytogenetic Map5q36UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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
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
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151071919155719191Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151549236072568189Rat
5685002Bss103Bone structure and strength QTL 1032.8tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)151582824233657761Rat
9590272Scort14Serum corticosterone level QTL 142.780.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)151698090761980907Rat
8694427Bw163Body weight QTL 1634.820.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)151698090761980907Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151724964162249641Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151809320881255430Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151851391388036354Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)152102134241082727Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)152102134252831189Rat
10755503Bp391Blood pressure QTL 3912.37arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)152377896946825072Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1526381041106550657Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1526381041106550657Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1526381041106550657Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152870974173709741Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:846
Count of miRNA genes:307
Interacting mature miRNAs:391
Transcripts:ENSRNOT00000017753
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 28 10 10 10 31 34 36 11
Low 3 15 47 31 19 31 8 11 43 1 5 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000017753   ⟹   ENSRNOP00000017753
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1533,208,216 - 33,218,456 (-)Ensembl
RefSeq Acc Id: NM_053503   ⟹   NP_445955
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21528,019,775 - 28,030,021 (-)NCBI
Rnor_6.01533,208,210 - 33,218,456 (-)NCBI
Rnor_5.01537,092,299 - 37,103,304 (-)NCBI
RGSC_v3.41532,627,633 - 32,637,861 (-)RGD
Celera1527,595,895 - 27,610,669 (-)RGD
Sequence:
RefSeq Acc Id: XR_005493808
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21528,023,989 - 28,031,537 (-)NCBI
Protein Sequences
Protein RefSeqs NP_445955 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH85802 (Get FASTA)   NCBI Sequence Viewer  
  CAC28536 (Get FASTA)   NCBI Sequence Viewer  
  EDM14178 (Get FASTA)   NCBI Sequence Viewer  
  Q5U2Z2 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_445955   ⟸   NM_053503
- UniProtKB: Q5U2Z2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000017753   ⟸   ENSRNOT00000017753
Protein Domains
LIM zinc-binding

Transcriptome

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

Promoters
RGD ID:13699654
Promoter ID:EPDNEW_R10177
Type:single initiation site
Name:Ajuba_1
Description:ajuba LIM protein
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_6.01533,218,422 - 33,218,482EPDNEW

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)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
15 37101695 37101696 T G snv LE/OrlBarth (UDEL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620407 AgrOrtholog
Ensembl Genes ENSRNOG00000012791 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000017753 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000017753 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7110970 IMAGE-MGC_LOAD
InterPro Znf_LIM UniProtKB/Swiss-Prot
KEGG Report rno:85265 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93830 IMAGE-MGC_LOAD
NCBI Gene 85265 ENTREZGENE
Pfam LIM UniProtKB/Swiss-Prot
PhenoGen Ajuba PhenoGen
PROSITE LIM_DOMAIN_1 UniProtKB/Swiss-Prot
  LIM_DOMAIN_2 UniProtKB/Swiss-Prot
SMART LIM UniProtKB/Swiss-Prot
UniProt AJUBA_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q99ND4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-12-06 Ajuba  ajuba LIM protein  Jub  jub, ajuba homolog (Xenopus laevis)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-17 Jub  jub, ajuba homolog (Xenopus laevis)  Jub  ajuba  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-25 Jub  ajuba  Jub  ajuba homolog (Xenopus laevis)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Jub  ajuba homolog (Xenopus laevis)    Ajuba protein  Name updated 1299863 APPROVED
2002-08-07 Jub  Ajuba protein      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localizes to the cytoplasm and translocates to the plasma membrane