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   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Smoc2 (SPARC related modular calcium binding 2) Chinchilla lanigera
Analyze
Symbol: Smoc2
Name: SPARC related modular calcium binding 2
RGD ID: 8786245
Description: ENCODES a protein that exhibits calcium ion binding (ortholog); glycosaminoglycan binding (ortholog); heparin binding (ortholog); INVOLVED IN extracellular matrix organization (ortholog); positive regulation of angiogenesis (ortholog); positive regulation of cell-substrate adhesion (ortholog); ASSOCIATED WITH Dentin Dysplasia, Type 1 (ortholog); Experimental Liver Cirrhosis (ortholog); schizophrenia (ortholog); FOUND IN basement membrane (ortholog); cell periphery (ortholog); extracellular matrix (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: SPARC-related modular calcium-binding protein 2
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: ChiLan1.0 - Chinchilla ChiLan1.0 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. Transitive Annotation Pipeline Automated assignment of GO, PW and RDO ISO annotations across species
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386168,441,184 - 168,667,992 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6168,441,151 - 168,673,445 (+)EnsemblGRCh38hg38GRCh38
GRCh376168,841,864 - 169,068,672 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366168,584,880 - 168,810,596 (+)NCBINCBI36Build 36hg18NCBI36
Build 346168,660,586 - 168,886,303NCBI
Celera6169,559,437 - 169,782,279 (+)NCBICelera
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 (+)NCBIT2T-CHM13v2.0
Smoc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391714,499,768 - 14,625,052 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1714,499,768 - 14,625,052 (+)EnsemblGRCm39 Ensembl
GRCm381714,279,490 - 14,404,790 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1714,279,506 - 14,404,790 (+)EnsemblGRCm38mm10GRCm38
MGSCv371714,416,513 - 14,541,797 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361714,016,132 - 14,141,361 (+)NCBIMGSCv36mm8
Celera1715,080,624 - 15,205,897 (+)NCBICelera
Cytogenetic Map17A2NCBI
cM Map178.95NCBI
Smoc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8163,935,627 - 64,064,952 (+)NCBIGRCr8
mRatBN7.2155,262,472 - 55,391,804 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl155,262,530 - 55,391,693 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx160,133,640 - 60,262,572 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0168,790,717 - 68,919,413 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0162,043,596 - 62,172,525 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1153,168,675 - 53,298,175 (+)NCBI
Celera151,480,576 - 51,609,313 (+)NCBICelera
Cytogenetic Map1q12NCBI
SMOC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25188,680,006 - 188,916,951 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16186,561,388 - 186,795,664 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06166,430,178 - 166,664,577 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16171,366,929 - 171,588,320 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6171,366,929 - 171,589,084 (+)Ensemblpanpan1.1panPan2
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 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0156,009,740 - 56,168,234 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl156,009,366 - 56,168,233 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1155,906,584 - 56,065,183 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0155,753,833 - 55,912,398 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0156,380,993 - 56,539,474 (+)NCBIUU_Cfam_GSD_1.0
Smoc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946150,202,183 - 150,342,912 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648917,454,270 - 17,594,901 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
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 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1396,264,181 - 96,477,491 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604068,107,603 - 68,398,081 (+)NCBIVero_WHO_p1.0Vero_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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248504,510,700 - 4,658,579 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSCLAT00000021096   ⟹   ENSCLAP00000020895
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_0049554114,729,706 - 4,822,140 (-)Ensembl
RefSeq Acc Id: XM_005377922   ⟹   XP_005377979
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554114,729,753 - 4,822,140 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005377979 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCLAP00000020895
  ENSCLAP00000020895.1
RefSeq Acc Id: XP_005377979   ⟸   XM_005377922
- UniProtKB: A0A8C2VUM4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSCLAP00000020895   ⟸   ENSCLAT00000021096
Protein Domains
EF-hand   Kazal-like   Thyroglobulin type-1


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCLAG00000014318 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCLAT00000021096 ENTREZGENE
  ENSCLAT00000021096.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.60.30 UniProtKB/TrEMBL
  4.10.800.10 UniProtKB/TrEMBL
  EF-hand UniProtKB/TrEMBL
InterPro Dev_reg/Prot_inhib UniProtKB/TrEMBL
  EF-hand-dom_pair UniProtKB/TrEMBL
  EF_Hand_1_Ca_BS UniProtKB/TrEMBL
  EF_hand_dom UniProtKB/TrEMBL
  Kazal_dom UniProtKB/TrEMBL
  Kazal_dom_sf UniProtKB/TrEMBL
  SMOC2_EC UniProtKB/TrEMBL
  SPARC/Testican_Ca-bd-dom UniProtKB/TrEMBL
  Thyroglobulin_1 UniProtKB/TrEMBL
  Thyroglobulin_1_sf UniProtKB/TrEMBL
NCBI Gene Smoc2 ENTREZGENE
PANTHER SECRETED MODULAR CALCIUM-BINDING PROTEIN UniProtKB/TrEMBL
  SPARC-RELATED MODULAR CALCIUM-BINDING PROTEIN 2 UniProtKB/TrEMBL
Pfam Kazal_2 UniProtKB/TrEMBL
  SPARC_Ca_bdg UniProtKB/TrEMBL
  Thyroglob_assoc UniProtKB/TrEMBL
  Thyroglobulin_1 UniProtKB/TrEMBL
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
  SSF57610 UniProtKB/TrEMBL
UniProt A0A8C2VUM4 ENTREZGENE, UniProtKB/TrEMBL