Smoc2 (SPARC related modular calcium binding 2) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Smoc2 (SPARC related modular calcium binding 2) Rattus norvegicus
Analyze
Symbol: Smoc2
Name: SPARC related modular calcium binding 2
RGD ID: 1306681
Description: Predicted to enable calcium ion binding activity; extracellular matrix binding activity; and heparin binding activity. Predicted to be involved in several processes, including positive regulation of endothelial cell chemotaxis; positive regulation of signal transduction; and positive regulation of vascular wound healing. Predicted to act upstream of or within positive regulation of cell-substrate adhesion. Predicted to be located in interstitial matrix. Predicted to be active in basement membrane and extracellular space. Orthologous to human SMOC2 (SPARC related modular calcium binding 2); INTERACTS WITH 1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane; 1,2-dimethylhydrazine; 1-naphthyl isothiocyanate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC292401; SPARC-related modular calcium-binding protein 2
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
mRatBN7.2155,262,472 - 55,391,804 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl155,262,530 - 55,391,693 (+)Ensembl
Rnor_6.0156,242,289 - 56,374,106 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl156,242,346 - 56,374,120 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0157,434,118 - 57,565,436 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4153,165,792 - 53,295,145 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1153,168,675 - 53,298,175 (+)NCBI
Celera151,480,576 - 51,609,313 (+)NCBICelera
Cytogenetic Map1q12NCBI
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
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3',5'-cyclic AMP  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3,7-dihydropurine-6-thione  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
antirheumatic drug  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
choline  (ISO)
chrysene  (ISO)
cisplatin  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
dexamethasone  (EXP,ISO)
dibutyl phthalate  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
ethanol  (ISO)
flurbiprofen  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
furan  (EXP,ISO)
glafenine  (EXP)
glycidol  (EXP)
hydrogen peroxide  (ISO)
indometacin  (ISO)
isoprenaline  (ISO)
ketamine  (EXP)
L-methionine  (ISO)
menadione  (ISO)
mercaptopurine  (EXP)
mercury dibromide  (ISO)
methapyrilene  (ISO)
microcystin-LR  (EXP,ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
oxaliplatin  (EXP)
panobinostat  (ISO)
paraquat  (EXP)
phenylephrine  (EXP)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (ISO)
purine-6-thiol  (EXP)
pyridaben  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sodium fluoride  (EXP)
testosterone  (EXP)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
topotecan  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)
zoledronic acid  (ISO)

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:12741954   PMID:16774925   PMID:18757743  


Genomics

Comparative Map Data
Smoc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2155,262,472 - 55,391,804 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl155,262,530 - 55,391,693 (+)Ensembl
Rnor_6.0156,242,289 - 56,374,106 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl156,242,346 - 56,374,120 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0157,434,118 - 57,565,436 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4153,165,792 - 53,295,145 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1153,168,675 - 53,298,175 (+)NCBI
Celera151,480,576 - 51,609,313 (+)NCBICelera
Cytogenetic Map1q12NCBI
SMOC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386168,441,184 - 168,667,992 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl6168,441,151 - 168,673,445 (+)EnsemblGRCh38hg38GRCh38
GRCh376168,841,864 - 169,068,672 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366168,584,880 - 168,810,596 (+)NCBINCBI36hg18NCBI36
Build 346168,660,586 - 168,886,303NCBI
Celera6169,559,437 - 169,782,279 (+)NCBI
Cytogenetic Map6q27NCBI
HuRef6166,267,021 - 166,491,991 (+)NCBIHuRef
CHM1_16169,103,759 - 169,328,184 (+)NCBICHM1_1
T2T-CHM13v2.06169,784,308 - 170,014,051 (+)NCBI
Smoc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391714,499,768 - 14,625,052 (+)NCBIGRCm39mm39
GRCm39 Ensembl1714,499,768 - 14,625,052 (+)Ensembl
GRCm381714,279,490 - 14,404,790 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1714,279,506 - 14,404,790 (+)EnsemblGRCm38mm10GRCm38
MGSCv371714,416,513 - 14,541,797 (+)NCBIGRCm37mm9NCBIm37
MGSCv361714,016,132 - 14,141,361 (+)NCBImm8
Celera1715,080,624 - 15,205,897 (+)NCBICelera
Cytogenetic Map17A2NCBI
cM Map178.95NCBI
Smoc2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554114,729,706 - 4,822,140 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554114,729,753 - 4,822,140 (-)NCBIChiLan1.0ChiLan1.0
SMOC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16171,366,929 - 171,588,320 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6171,366,929 - 171,589,084 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06166,430,178 - 166,664,577 (+)NCBIMhudiblu_PPA_v0panPan3
SMOC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1155,826,354 - 55,986,053 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl155,825,666 - 55,986,052 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha156,617,795 - 56,777,591 (+)NCBI
ROS_Cfam_1.0156,009,740 - 56,168,234 (+)NCBI
ROS_Cfam_1.0 Ensembl156,009,366 - 56,168,233 (+)Ensembl
UMICH_Zoey_3.1155,906,584 - 56,065,183 (+)NCBI
UNSW_CanFamBas_1.0155,753,833 - 55,912,398 (+)NCBI
UU_Cfam_GSD_1.0156,380,993 - 56,539,474 (+)NCBI
Smoc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946150,202,183 - 150,342,912 (+)NCBI
SpeTri2.0NW_00493648917,454,274 - 17,594,894 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMOC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl11,193,167 - 1,332,694 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.111,193,163 - 1,332,739 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.212,133,877 - 2,217,364 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMOC2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11396,264,170 - 96,477,393 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1396,264,181 - 96,477,491 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604068,107,603 - 68,398,081 (+)NCBIVero_WHO_p1.0
Smoc2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248504,510,598 - 4,661,056 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046248504,510,700 - 4,658,579 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D1Rat207  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2155,300,427 - 55,300,635 (+)MAPPERmRatBN7.2
Rnor_6.0156,282,757 - 56,282,964NCBIRnor6.0
Rnor_5.0157,473,569 - 57,473,776UniSTSRnor5.0
RGSC_v3.4153,203,564 - 53,203,820RGDRGSC3.4
RGSC_v3.4153,203,603 - 53,203,810UniSTSRGSC3.4
RGSC_v3.1153,206,548 - 53,206,755RGD
Celera151,518,460 - 51,518,667UniSTS
RH 3.4 Map1672.2RGD
RH 3.4 Map1672.2UniSTS
RH 2.0 Map1391.3RGD
FHH x ACI Map130.3199RGD
Cytogenetic Map1q12UniSTS
D17Jcs34  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2155,313,802 - 55,314,071 (+)MAPPERmRatBN7.2
Rnor_6.0156,296,133 - 56,296,401NCBIRnor6.0
Rnor_5.0157,486,945 - 57,487,213UniSTSRnor5.0
RGSC_v3.4153,216,979 - 53,217,247UniSTSRGSC3.4
Celera151,531,828 - 51,532,096UniSTS
Cytogenetic Map1q12UniSTS
RH130327  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2155,391,499 - 55,391,693 (+)MAPPERmRatBN7.2
Rnor_6.0156,373,791 - 56,373,984NCBIRnor6.0
Rnor_5.0157,565,121 - 57,565,314UniSTSRnor5.0
RGSC_v3.4153,294,929 - 53,295,122UniSTSRGSC3.4
Celera151,609,097 - 51,609,290UniSTS
RH 3.4 Map1673.0UniSTS
Cytogenetic Map1q12UniSTS
BM387775  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2155,380,237 - 55,380,411 (+)MAPPERmRatBN7.2
Rnor_6.0156,362,532 - 56,362,705NCBIRnor6.0
Rnor_5.0157,553,862 - 57,554,035UniSTSRnor5.0
RGSC_v3.4153,283,670 - 53,283,843UniSTSRGSC3.4
Celera151,597,838 - 51,598,011UniSTS
RH 3.4 Map1675.2UniSTS
Cytogenetic Map1q12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11099206555992065Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11148131275088344Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11148131282174945Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)11183518156835181Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)11933357156983283Rat
724520Bp145Blood pressure QTL 1452.10.0024arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12078482865784828Rat
1357400Bw62Body weight QTL624.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)12234064767340647Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)12887978078430678Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13273727390665040Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
1354599Bw29Body weight QTL 293.460.001body mass (VT:0001259)body weight (CMO:0000012)13344984878449848Rat
1354643Foco2Food consumption QTL 27.170.0001eating behavior trait (VT:0001431)food intake rate (CMO:0000427)13344984878449848Rat
8552900Pigfal1Plasma insulin-like growth factor 1 level QTL 17.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
8552948Pigfal11Plasma insulin-like growth factor 1 level QTL 114.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
9589820Insglur3Insulin/glucose ratio QTL 310.750.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)13483685879836858Rat
1331732Srn4Serum renin concentration QTL 44.467renin activity (VT:0005581)plasma renin activity level (CMO:0000116)13523959878430678Rat
1331792Rf29Renal function QTL 294.589urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)13523959878430678Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143284731118944897Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14333300288333002Rat
1331778Rf28Renal function QTL 284.66urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)14580314078430678Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14936146582174945Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14939317294393172Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15386304190532583Rat
4889919Bss86Bone structure and strength QTL 864.1tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)15389511782174945Rat
4889929Bss87Bone structure and strength QTL 876.7tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)15389511782174945Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:455
Count of miRNA genes:245
Interacting mature miRNAs:301
Transcripts:ENSRNOT00000019317
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 3 22 6 4 3 4 8 11 32 30 10 8
Low 21 51 37 16 37 67 3 8 1
Below cutoff 7 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000019317   ⟹   ENSRNOP00000019317
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl155,262,530 - 55,391,693 (+)Ensembl
Rnor_6.0 Ensembl156,242,346 - 56,373,984 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000079718   ⟹   ENSRNOP00000071488
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl155,306,478 - 55,391,693 (+)Ensembl
Rnor_6.0 Ensembl156,288,832 - 56,374,120 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000109266   ⟹   ENSRNOP00000089764
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl155,262,530 - 55,307,228 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000113274   ⟹   ENSRNOP00000078071
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl155,306,478 - 55,386,655 (+)Ensembl
RefSeq Acc Id: NM_001106215   ⟹   NP_001099685
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2155,262,530 - 55,391,716 (+)NCBI
Rnor_6.0156,242,346 - 56,374,007 (+)NCBI
Rnor_5.0157,434,118 - 57,565,436 (+)NCBI
RGSC_v3.4153,165,792 - 53,295,145 (+)RGD
Celera151,480,576 - 51,609,313 (+)RGD
Sequence:
RefSeq Acc Id: XM_006227958   ⟹   XP_006228020
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2155,262,472 - 55,391,804 (+)NCBI
Rnor_6.0156,242,289 - 56,374,106 (+)NCBI
Rnor_5.0157,434,118 - 57,565,436 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001099685 (Get FASTA)   NCBI Sequence Viewer  
  XP_006228020 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI68953 (Get FASTA)   NCBI Sequence Viewer  
  EDL99844 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001099685   ⟸   NM_001106215
- Peptide Label: precursor
- UniProtKB: B5DF75 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006228020   ⟸   XM_006227958
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000071488   ⟸   ENSRNOT00000079718
RefSeq Acc Id: ENSRNOP00000019317   ⟸   ENSRNOT00000019317
RefSeq Acc Id: ENSRNOP00000089764   ⟸   ENSRNOT00000109266
RefSeq Acc Id: ENSRNOP00000078071   ⟸   ENSRNOT00000113274
Protein Domains
EF-hand   Kazal-like   Thyroglobulin type-1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K0K9-F1-model_v2 AlphaFold A0A0G2K0K9 1-457 view protein structure

Transcriptome

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

Promoters
RGD ID:13689636
Promoter ID:EPDNEW_R161
Type:multiple initiation site
Name:Smoc2_1
Description:SPARC related modular calcium binding 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_6.0156,242,332 - 56,242,392EPDNEW

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:1306681 AgrOrtholog
BioCyc Gene G2FUF-61337 BioCyc
Ensembl Genes ENSRNOG00000014166 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000019317 ENTREZGENE
  ENSRNOP00000019317.6 UniProtKB/TrEMBL
  ENSRNOP00000071488 ENTREZGENE
  ENSRNOP00000071488.1 UniProtKB/TrEMBL
  ENSRNOP00000078071.1 UniProtKB/TrEMBL
  ENSRNOP00000089764.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019317 ENTREZGENE
  ENSRNOT00000019317.8 UniProtKB/TrEMBL
  ENSRNOT00000079718 ENTREZGENE
  ENSRNOT00000079718.2 UniProtKB/TrEMBL
  ENSRNOT00000109266.1 UniProtKB/TrEMBL
  ENSRNOT00000113274.1 UniProtKB/TrEMBL
Gene3D-CATH 4.10.800.10 UniProtKB/TrEMBL
InterPro EF-hand-like_dom UniProtKB/TrEMBL
  EF_Hand_1_Ca_BS UniProtKB/TrEMBL
  EF_hand_Ca-bd UniProtKB/TrEMBL
  Kazal_dom_sf UniProtKB/TrEMBL
  Prot_inh_Kazal UniProtKB/TrEMBL
  SMOC2_EC UniProtKB/TrEMBL
  SPARC/Testican_Ca-bd-dom UniProtKB/TrEMBL
  Thyroglobulin_1 UniProtKB/TrEMBL
  Thyroglobulin_1_sf UniProtKB/TrEMBL
KEGG Report rno:292401 UniProtKB/TrEMBL
NCBI Gene 292401 ENTREZGENE
Pfam Kazal_2 UniProtKB/TrEMBL
  SPARC_Ca_bdg UniProtKB/TrEMBL
  Thyroglobulin_1 UniProtKB/TrEMBL
PhenoGen Smoc2 PhenoGen
PROSITE EF_HAND_1 UniProtKB/TrEMBL
  EF_HAND_2 UniProtKB/TrEMBL
  KAZAL_2 UniProtKB/TrEMBL
  THYROGLOBULIN_1_1 UniProtKB/TrEMBL
  THYROGLOBULIN_1_2 UniProtKB/TrEMBL
SMART KAZAL UniProtKB/TrEMBL
  SM00211 UniProtKB/TrEMBL
Superfamily-SCOP SSF100895 UniProtKB/TrEMBL
  SSF47473 UniProtKB/TrEMBL
  Thyroglobulin_1 UniProtKB/TrEMBL
UniProt A0A0G2K0K9_RAT UniProtKB/TrEMBL
  A0A8I5Y6U6_RAT UniProtKB/TrEMBL
  A0A8I6A7Z3_RAT UniProtKB/TrEMBL
  B5DF75 ENTREZGENE, UniProtKB/TrEMBL
  F7FPL2_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Smoc2  SPARC related modular calcium binding 2   Smoc2_predicted  SPARC related modular calcium binding 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Smoc2_predicted  SPARC related modular calcium binding 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED