Cald1 (caldesmon 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Cald1 (caldesmon 1) Rattus norvegicus
Analyze
Symbol: Cald1
Name: caldesmon 1
RGD ID: 2256
Description: Enables actin binding activity. Involved in actin filament bundle assembly and positive regulation of protein binding activity. Located in several cellular components, including actin filament; dendritic spine; and postsynaptic density. Orthologous to human CALD1 (caldesmon 1); INTERACTS WITH 1,3,5-trinitro-1,3,5-triazinane; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: CDM; h-caldesmon; l-Cad; L-caldesmon; non-muscle caldesmon
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2463,265,781 - 63,446,936 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl463,265,942 - 63,446,932 (+)Ensembl
Rnor_6.0462,103,948 - 62,291,375 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl462,220,736 - 62,291,489 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0461,835,972 - 62,022,970 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4462,087,364 - 62,156,855 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1462,363,493 - 62,432,985 (+)NCBI
Celera458,427,441 - 58,496,854 (+)NCBICelera
RH 3.4 Map4396.8RGD
Cytogenetic Map4q22NCBI
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
(-)-demecolcine  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3,5-trinitro-1,3,5-triazinane  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2-amino-14,16-dimethyloctadecan-3-ol  (ISO)
2-butoxyethanol  (ISO)
2-methylcholine  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-azacytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrolein  (ISO)
acrylamide  (EXP,ISO)
aflatoxin B1  (ISO)
aflatoxin M1  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
benzatropine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (EXP)
buspirone  (EXP)
cadmium dichloride  (EXP,ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chloroprene  (EXP)
cisplatin  (EXP)
cobalt dichloride  (ISO)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
Cuprizon  (ISO)
DDT  (EXP)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
dioxygen  (ISO)
disulfiram  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
enzyme inhibitor  (ISO)
fenamidone  (ISO)
flutamide  (EXP)
formaldehyde  (ISO)
geldanamycin  (ISO)
genistein  (EXP)
hydrogen cyanide  (ISO)
iron(III) nitrilotriacetate  (EXP)
isotretinoin  (ISO)
ivermectin  (ISO)
lead diacetate  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
lead(II) chloride  (ISO)
manganese(II) chloride  (EXP)
methapyrilene  (EXP)
methylmercury chloride  (ISO)
methylphenidate  (ISO)
N-acetyl-1,4-benzoquinone imine  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nefazodone  (EXP)
oxaliplatin  (EXP)
ozone  (EXP,ISO)
paracetamol  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
potassium cyanide  (ISO)
potassium dichromate  (ISO)
propiconazole  (ISO)
raloxifene  (ISO)
Salinomycin  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (ISO)
sirolimus  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
sunitinib  (ISO)
temozolomide  (ISO)
tetrachloromethane  (ISO)
tetrahydropalmatine  (ISO)
thioacetamide  (EXP)
toluene  (EXP)
topotecan  (EXP)
torcetrapib  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
Triptolide  (EXP)
valproic acid  (ISO)
vancomycin  (ISO)
vincristine  (ISO)
vitamin E  (ISO)
zinc atom  (ISO)
zinc dichloride  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function
actin binding  (IBA,IDA,IEA,TAS)
calmodulin binding  (IEA)
myosin binding  (IBA,IEA)
protein binding  (ISO)

References

References - curated
# Reference Title Reference Citation
1. Subcellular distribution of calponin and caldesmon in rat hippocampus. Agassandian C, etal., Brain Res. 2000 Dec 29;887(2):444-9.
2. Co-localization of caldesmon and calponin with cortical afferents, metabotropic glutamate and neurotrophic receptors in the lateral and central nuclei of the amygdala. Agassandian K and Cassell MD, Brain Res. 2008 Aug 21;1226:39-55. Epub 2008 Jun 11.
3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
6. ERK1/2-mediated phosphorylation of myometrial caldesmon during pregnancy and labor. Li Y, etal., Am J Physiol Regul Integr Comp Physiol 2003 Jan;284(1):R192-9.
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. Caldesmon isoform associated with phenotypic modulation of mesangial cells. Okamoto K, etal., Exp Nephrol. 2000 Jan-Feb;8(1):20-7.
10. Distribution of caldesmon and of the acidic isoform of calponin in cultured cerebellar neurons and in different regions of the rat brain: an immunofluorescence and confocal microscopy study. Represa A, etal., Exp Cell Res. 1995 Dec;221(2):333-43.
11. GOA pipeline RGD automated data pipeline
12. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
13. Characterization of the COOH terminus of non-muscle caldesmon mutants lacking mitosis-specific phosphorylation sites. Yamashiro S, etal., J Biol Chem 1995 Feb 24;270(8):4023-30.
14. Characterization of 83-kilodalton nonmuscle caldesmon from cultured rat cells: stimulation of actin binding of nonmuscle tropomyosin and periodic localization along microfilaments like tropomyosin. Yamashiro-Matsumura S and Matsumura F, J Cell Biol. 1988 Jun;106(6):1973-83.
Additional References at PubMed
PMID:1986309   PMID:2909534   PMID:12757606   PMID:16428310   PMID:16595550   PMID:16888241   PMID:17224451   PMID:17631293   PMID:19349302   PMID:19834610   PMID:19875849   PMID:21350330  
PMID:22158623   PMID:23077044   PMID:24036928   PMID:25468996   PMID:33450132  


Genomics

Candidate Gene Status
Cald1 is a candidate Gene for QTL Bp116
Comparative Map Data
Cald1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2463,265,781 - 63,446,936 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl463,265,942 - 63,446,932 (+)Ensembl
Rnor_6.0462,103,948 - 62,291,375 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl462,220,736 - 62,291,489 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0461,835,972 - 62,022,970 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4462,087,364 - 62,156,855 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1462,363,493 - 62,432,985 (+)NCBI
Celera458,427,441 - 58,496,854 (+)NCBICelera
RH 3.4 Map4396.8RGD
Cytogenetic Map4q22NCBI
CALD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh387134,745,467 - 134,970,729 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl7134,744,252 - 134,970,729 (+)EnsemblGRCh38hg38GRCh38
GRCh377134,464,385 - 134,655,480 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 367134,114,711 - 134,306,014 (+)NCBINCBI36hg18NCBI36
Build 347133,921,425 - 134,112,725NCBI
Celera7129,201,597 - 129,392,887 (+)NCBI
Cytogenetic Map7q33NCBI
HuRef7128,766,283 - 128,958,067 (+)NCBIHuRef
CHM1_17134,398,049 - 134,589,415 (+)NCBICHM1_1
T2T-CHM13v2.07136,087,297 - 136,278,520 (+)NCBI
CRA_TCAGchr7v27133,808,491 - 133,999,799 (+)NCBI
Cald1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39634,575,433 - 34,752,404 (+)NCBIGRCm39mm39
GRCm39 Ensembl634,575,435 - 34,752,408 (+)Ensembl
GRCm38634,598,495 - 34,775,469 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl634,598,500 - 34,775,473 (+)EnsemblGRCm38mm10GRCm38
MGSCv37634,659,444 - 34,725,469 (+)NCBIGRCm37mm9NCBIm37
MGSCv36634,639,637 - 34,704,252 (+)NCBImm8
Celera634,709,193 - 34,775,837 (+)NCBICelera
Cytogenetic Map6B1NCBI
cM Map615.07NCBI
Cald1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554947,578,162 - 7,675,558 (-)NCBIChiLan1.0ChiLan1.0
CALD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17139,249,003 - 139,440,643 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7139,337,692 - 139,440,643 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v07126,743,466 - 126,935,412 (+)NCBIMhudiblu_PPA_v0panPan3
CALD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11613,087,419 - 13,279,648 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1613,084,109 - 13,279,384 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1614,099,621 - 14,291,557 (-)NCBI
ROS_Cfam_1.01613,068,418 - 13,257,206 (-)NCBI
ROS_Cfam_1.0 Ensembl1613,068,504 - 13,256,992 (-)Ensembl
UMICH_Zoey_3.11613,510,057 - 13,701,885 (-)NCBI
UNSW_CanFamBas_1.01612,609,385 - 12,797,864 (-)NCBI
UU_Cfam_GSD_1.01612,748,692 - 12,937,241 (-)NCBI
Cald1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511820,736,003 - 20,913,613 (-)NCBI
SpeTri2.0NW_004936579868,681 - 1,046,198 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CALD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1814,267,959 - 14,486,726 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11814,267,955 - 14,486,641 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21815,075,913 - 15,194,572 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CALD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.121103,435,238 - 103,671,901 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl21103,469,975 - 103,672,699 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666072301,159 - 589,710 (+)NCBIVero_WHO_p1.0
Cald1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476515,357,775 - 15,449,952 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462476515,262,032 - 15,452,201 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D4Rat256  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2463,435,262 - 63,435,482 (+)MAPPERmRatBN7.2
Rnor_6.0462,279,706 - 62,279,923NCBIRnor6.0
Rnor_5.0462,011,299 - 62,011,516UniSTSRnor5.0
RGSC_v3.4462,146,331 - 62,146,549RGDRGSC3.4
RGSC_v3.4462,146,332 - 62,146,549UniSTSRGSC3.4
RGSC_v3.1462,422,462 - 62,422,679RGD
Celera458,486,331 - 58,486,548UniSTS
RH 3.4 Map4393.4RGD
RH 3.4 Map4393.4UniSTS
RH 2.0 Map4424.7RGD
SHRSP x BN Map432.92RGD
Cytogenetic Map4q22UniSTS
RH94611  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2463,444,998 - 63,445,167 (+)MAPPERmRatBN7.2
Rnor_6.0462,289,440 - 62,289,608NCBIRnor6.0
Rnor_5.0462,021,033 - 62,021,201UniSTSRnor5.0
RGSC_v3.4462,156,066 - 62,156,234UniSTSRGSC3.4
Celera458,496,065 - 58,496,233UniSTS
RH 3.4 Map4396.8UniSTS
Cytogenetic Map4q22UniSTS
AI763841  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2463,413,621 - 63,413,750 (+)MAPPERmRatBN7.2
Rnor_6.0462,258,066 - 62,258,194NCBIRnor6.0
Rnor_5.0461,989,671 - 61,989,799UniSTSRnor5.0
RGSC_v3.4462,124,419 - 62,124,547UniSTSRGSC3.4
Celera458,464,723 - 58,464,851UniSTS
RH 3.4 Map4399.22UniSTS
Cytogenetic Map4q22UniSTS
RH138325  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2463,391,117 - 63,391,302 (+)MAPPERmRatBN7.2
Rnor_6.0462,235,564 - 62,235,748NCBIRnor6.0
Rnor_5.0461,967,177 - 61,967,361UniSTSRnor5.0
RGSC_v3.4462,101,917 - 62,102,101UniSTSRGSC3.4
Celera458,442,000 - 58,442,184UniSTS
RH 3.4 Map4393.4UniSTS
Cytogenetic Map4q22UniSTS
RH141748  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2463,437,603 - 63,437,783 (+)MAPPERmRatBN7.2
Rnor_6.0462,282,045 - 62,282,224NCBIRnor6.0
Rnor_5.0462,013,638 - 62,013,817UniSTSRnor5.0
RGSC_v3.4462,148,671 - 62,148,850UniSTSRGSC3.4
Celera458,488,670 - 58,488,849UniSTS
RH 3.4 Map4375.2UniSTS
Cytogenetic Map4q22UniSTS
AI763841  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2463,413,519 - 63,413,643 (+)MAPPERmRatBN7.2
Rnor_6.0462,257,964 - 62,258,087NCBIRnor6.0
Rnor_5.0461,989,569 - 61,989,692UniSTSRnor5.0
RGSC_v3.4462,124,317 - 62,124,440UniSTSRGSC3.4
Celera458,464,621 - 58,464,744UniSTS
RH 3.4 Map4399.22UniSTS
Cytogenetic Map4q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42690728575585128Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)42690728575585128Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42949419581006281Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)432583980114627242Rat
8552782Vie1Viral induced encephalitis QTL 126.4brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8552801Bw143Body weight QTL 1437.3body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)43443048482490359Rat
8552809Vie5Viral induced encephalitis QTL 525.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)436303261103194984Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
61475Aia2Adjuvant induced arthritis QTL 25.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)43950527573892441Rat
1331807Rf31Renal function QTL 312.988urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)43952426474726312Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)439524264116179656Rat
61445Strs3Sensitivity to stroke QTL 33cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)44043338885433388Rat
8694439Bw168Body weight QTL 1689.570.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)44043341485433414Rat
6893678Bw108Body weight QTL 1082.60.006body mass (VT:0001259)body weight (CMO:0000012)44345797688457976Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)444463908148090542Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)444463908148090542Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)445456990146803430Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)450119848146803430Rat
4889969Bss96Bone structure and strength QTL 964.9tibia size trait (VT:0100001)tibia cortical bone volume (CMO:0001725)45664777678882945Rat
4889972Bss97Bone structure and strength QTL 975.6tibia size trait (VT:0100001)tibia total bone volume (CMO:0001724)45664777678882945Rat
5685009Bmd86Bone mineral density QTL 863.7tibia mineral mass (VT:1000283)bone mineral density (CMO:0001226)45664777678882945Rat
5685012Bmd87Bone mineral density QTL 875.1tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)45664777678882945Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)456647873149491524Rat
1641833Alc21Alcohol consumption QTL 218.60.0001drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)456698790126192555Rat
631546Bp86Blood pressure QTL 863.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45711443291360801Rat
634311Sach7Saccharin preference QTL 7taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)457114432102114432Rat
61336Bp21Blood pressure QTL 214.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45711470578881294Rat
1358363Sradr3Stress Responsive Adrenal Weight QTL 36.19adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)457486946102486946Rat
1558651Swd3Spike wave discharge measurement QTL 34.620.000024brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)45843213392991462Rat
631671Iddm11Insulin dependent diabetes mellitus QTL 113.60.0012blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)45863587778886137Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)459948935154902892Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
1578657Bss12Bone structure and strength QTL 128.9femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)460220938105220938Rat
1578658Bss13Bone structure and strength QTL 138femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)460220938105220938Rat
2300179Bmd50Bone mineral density QTL 505.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)460928534105928534Rat
1549843Bw53Body weight QTL 530.0001body mass (VT:0001259)body weight gain (CMO:0000420)461697658103194791Rat
1549839Bw52Body weight QTL 520.0001body mass (VT:0001259)body weight gain (CMO:0000420)461697658115089733Rat
61418Pia5Pristane induced arthritis QTL 54.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)462277855128289560Rat
6478743Anxrr40Anxiety related response QTL 400.83076defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
6478772Anxrr49Anxiety related response QTL 490.15488defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
6478684Anxrr30Anxiety related response QTL 300.00087defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
631651Bp124Blood pressure QTL 1243arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)462879517107879517Rat
7394826Bw126Body weight QTL 1260.002body mass (VT:0001259)body weight gain (CMO:0000420)46293326987483707Rat
8552807Vie4Viral induced encephalitis QTL 47.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)46293350882490359Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in mean arterial blood pressure (CMO:0002035)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in systolic blood pressure (CMO:0000747)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in pulse pressure (CMO:0001882)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)462933508114921294Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:317
Count of miRNA genes:203
Interacting mature miRNAs:247
Transcripts:ENSRNOT00000041264
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 10 74 35 40 11 8
Low 1 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000041264   ⟹   ENSRNOP00000043767
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl463,376,482 - 63,445,793 (+)Ensembl
Rnor_6.0 Ensembl462,221,011 - 62,290,229 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000086377   ⟹   ENSRNOP00000068857
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl463,266,098 - 63,446,908 (+)Ensembl
Rnor_6.0 Ensembl462,220,736 - 62,291,489 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000102454   ⟹   ENSRNOP00000087934
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl463,265,942 - 63,442,260 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000112793   ⟹   ENSRNOP00000086440
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl463,409,514 - 63,442,455 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000115054   ⟹   ENSRNOP00000093810
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl463,376,563 - 63,445,793 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000115634   ⟹   ENSRNOP00000085217
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl463,266,114 - 63,446,932 (+)Ensembl
RefSeq Acc Id: NM_013146   ⟹   NP_037278
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2463,376,563 - 63,445,788 (+)NCBI
Rnor_6.0462,221,011 - 62,290,229 (+)NCBI
Rnor_5.0461,835,972 - 62,022,970 (+)NCBI
RGSC_v3.4462,087,364 - 62,156,855 (+)RGD
Celera458,427,441 - 58,496,854 (+)RGD
Sequence:
RefSeq Acc Id: XM_006236260   ⟹   XP_006236322
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2463,376,530 - 63,446,936 (+)NCBI
Rnor_6.0462,220,944 - 62,291,375 (+)NCBI
Rnor_5.0461,835,972 - 62,022,970 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006236261   ⟹   XP_006236323
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2463,265,781 - 63,446,936 (+)NCBI
Rnor_6.0462,104,120 - 62,291,375 (+)NCBI
Rnor_5.0461,835,972 - 62,022,970 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006236262   ⟹   XP_006236324
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2463,351,157 - 63,446,936 (+)NCBI
Rnor_6.0462,195,488 - 62,291,375 (+)NCBI
Rnor_5.0461,835,972 - 62,022,970 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017592487   ⟹   XP_017447976
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2463,265,895 - 63,446,936 (+)NCBI
Rnor_6.0462,103,948 - 62,291,375 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039107132   ⟹   XP_038963060
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2463,277,212 - 63,446,936 (+)NCBI
RefSeq Acc Id: XM_039107133   ⟹   XP_038963061
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2463,265,781 - 63,446,936 (+)NCBI
RefSeq Acc Id: XM_039107134   ⟹   XP_038963062
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2463,392,718 - 63,446,936 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_037278   ⟸   NM_013146
- Sequence:
RefSeq Acc Id: XP_006236323   ⟸   XM_006236261
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006236324   ⟸   XM_006236262
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006236322   ⟸   XM_006236260
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017447976   ⟸   XM_017592487
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000043767   ⟸   ENSRNOT00000041264
RefSeq Acc Id: ENSRNOP00000068857   ⟸   ENSRNOT00000086377
RefSeq Acc Id: XP_038963061   ⟸   XM_039107133
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038963060   ⟸   XM_039107132
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038963062   ⟸   XM_039107134
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000093810   ⟸   ENSRNOT00000115054
RefSeq Acc Id: ENSRNOP00000086440   ⟸   ENSRNOT00000112793
RefSeq Acc Id: ENSRNOP00000085217   ⟸   ENSRNOT00000115634
RefSeq Acc Id: ENSRNOP00000087934   ⟸   ENSRNOT00000102454

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q62736-F1-model_v2 AlphaFold Q62736 1-531 view protein structure

Transcriptome

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

Promoters
RGD ID:13692955
Promoter ID:EPDNEW_R3479
Type:initiation region
Name:Cald1_1
Description:caldesmon 1
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_6.0462,221,011 - 62,221,071EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2256 AgrOrtholog
BioCyc Gene G2FUF-45269 BioCyc
Ensembl Genes ENSRNOG00000010233 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000043767 ENTREZGENE
  ENSRNOP00000043767.3 UniProtKB/TrEMBL
  ENSRNOP00000068857 ENTREZGENE
  ENSRNOP00000068857.2 UniProtKB/TrEMBL
  ENSRNOP00000085217.1 UniProtKB/TrEMBL
  ENSRNOP00000086440.1 UniProtKB/TrEMBL
  ENSRNOP00000087934 ENTREZGENE
  ENSRNOP00000087934.1 UniProtKB/TrEMBL
  ENSRNOP00000093810.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041264 ENTREZGENE
  ENSRNOT00000041264.4 UniProtKB/TrEMBL
  ENSRNOT00000086377 ENTREZGENE
  ENSRNOT00000086377.2 UniProtKB/TrEMBL
  ENSRNOT00000102454 ENTREZGENE
  ENSRNOT00000102454.1 UniProtKB/TrEMBL
  ENSRNOT00000112793.1 UniProtKB/TrEMBL
  ENSRNOT00000115054.1 UniProtKB/TrEMBL
  ENSRNOT00000115634.1 UniProtKB/TrEMBL
InterPro Caldesmon UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Caldesmon_LSP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25687 UniProtKB/Swiss-Prot
NCBI Gene 25687 ENTREZGENE
PANTHER PTHR18949 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR18949:SF0 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Caldesmon UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cald1 PhenoGen
PRINTS CALDESMON UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JTV2_RAT UniProtKB/TrEMBL
  A0A8I6A6T4_RAT UniProtKB/TrEMBL
  A0A8I6AMH6_RAT UniProtKB/TrEMBL
  A0A8I6GCL3_RAT UniProtKB/TrEMBL
  A0A8I6GEY4_RAT UniProtKB/TrEMBL
  CALD1_RAT UniProtKB/Swiss-Prot
  G3V9E3_RAT UniProtKB/TrEMBL
  Q62736 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Cald1  Caldesmon 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression increased levels of h isoform during pregnancy 628554
gene_function actin binding protein 628554
gene_process increased levels suppress contractility of pregnant myometrium 628554
gene_process may play an active role in the regulation of myometrial contraction during pregnancy 628554
gene_process may contribute to a suppression of the contractility of pregnant myometrium 628554
gene_protein exists in two isoforms, high molecular weight (h) and low molecular weight (l) forms 628554
gene_regulation isoform specific phosphorylation by Erk1/2-mediated pathway may promote uterine contraction during labor 628554
gene_regulation phosphorylation is regulated by Mapk1 and 3 during pregnancy 628554