Sbspon (somatomedin B and thrombospondin, type 1 domain containing) - Rat Genome Database

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Gene: Sbspon (somatomedin B and thrombospondin, type 1 domain containing) Rattus norvegicus
Analyze
Symbol: Sbspon
Name: somatomedin B and thrombospondin, type 1 domain containing
RGD ID: 1559717
Description: Orthologous to human SBSPON (somatomedin B and thrombospondin type 1 domain containing); INTERACTS WITH 2,2',5,5'-tetrachlorobiphenyl; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC297757; RGD1559717; RPE-spondin; Rpesp; similar to RPE-spondin
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr858,186,004 - 8,216,576 (+)NCBIGRCr8
mRatBN7.253,402,763 - 3,433,338 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl53,402,648 - 3,435,420 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx55,520,177 - 5,550,817 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.057,159,058 - 7,189,701 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.056,856,180 - 6,887,020 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.052,813,004 - 2,847,697 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl52,813,131 - 2,843,483 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.052,802,976 - 2,833,045 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.452,516,220 - 2,547,152 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera52,998,696 - 3,033,376 (+)NCBICelera
Cytogenetic Map5q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Hepatomegaly  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:20551380   PMID:27068509   PMID:27559042  


Genomics

Comparative Map Data
Sbspon
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr858,186,004 - 8,216,576 (+)NCBIGRCr8
mRatBN7.253,402,763 - 3,433,338 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl53,402,648 - 3,435,420 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx55,520,177 - 5,550,817 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.057,159,058 - 7,189,701 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.056,856,180 - 6,887,020 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.052,813,004 - 2,847,697 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl52,813,131 - 2,843,483 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.052,802,976 - 2,833,045 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.452,516,220 - 2,547,152 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera52,998,696 - 3,033,376 (+)NCBICelera
Cytogenetic Map5q11NCBI
SBSPON
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38873,064,543 - 73,093,172 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl873,064,543 - 73,124,088 (-)EnsemblGRCh38hg38GRCh38
GRCh37873,976,778 - 74,005,407 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36874,141,808 - 74,168,061 (-)NCBINCBI36Build 36hg18NCBI36
Celera869,973,957 - 70,002,409 (-)NCBICelera
Cytogenetic Map8q21.11NCBI
HuRef869,467,671 - 69,496,653 (-)NCBIHuRef
CHM1_1874,029,653 - 74,058,364 (-)NCBICHM1_1
T2T-CHM13v2.0873,493,598 - 73,522,530 (-)NCBIT2T-CHM13v2.0
Sbspon
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39115,924,086 - 15,962,946 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl115,924,086 - 15,962,946 (-)EnsemblGRCm39 Ensembl
GRCm38115,853,862 - 15,892,722 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl115,853,862 - 15,892,722 (-)EnsemblGRCm38mm10GRCm38
MGSCv37115,843,943 - 15,882,803 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36115,839,076 - 15,877,936 (-)NCBIMGSCv36mm8
Celera115,798,996 - 15,837,907 (-)NCBICelera
Cytogenetic Map1A3NCBI
cM Map14.89NCBI
Sbspon
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554447,068,906 - 7,094,583 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554447,068,906 - 7,094,583 (+)NCBIChiLan1.0ChiLan1.0
SBSPON
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2788,811,771 - 88,840,669 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1864,441,478 - 64,470,347 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0869,602,230 - 69,632,306 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1871,249,079 - 71,279,468 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl871,249,079 - 71,279,468 (-)Ensemblpanpan1.1panPan2
SBSPON
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12921,710,640 - 21,737,007 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2921,712,267 - 21,736,943 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2921,975,499 - 22,001,657 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02921,820,582 - 21,846,794 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2921,822,209 - 21,846,888 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12921,878,707 - 21,904,840 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02921,915,271 - 21,941,482 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02922,196,170 - 22,222,329 (-)NCBIUU_Cfam_GSD_1.0
Sbspon
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530357,563,328 - 57,599,552 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366481,850,650 - 1,885,120 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366481,850,048 - 1,885,251 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SBSPON
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl462,756,342 - 62,791,609 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1462,756,262 - 62,791,621 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2468,303,793 - 68,336,205 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SBSPON
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1868,665,669 - 68,693,768 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl868,664,538 - 68,693,663 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603972,689,194 - 72,717,272 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sbspon
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474418,086,904 - 18,108,859 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474418,086,842 - 18,109,170 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sbspon
220 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:101
Count of miRNA genes:89
Interacting mature miRNAs:90
Transcripts:ENSRNOT00000009530
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
631551Vetf1Vascular elastic tissue fragility QTL 150.0001aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)522822265904428Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat


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 1 25 11
Low 2 35 25 12 12 12 8 9 52 10 27 11 8
Below cutoff 2 29 26 7 26 2 22 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009530   ⟹   ENSRNOP00000009530
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl53,402,648 - 3,435,420 (+)Ensembl
Rnor_6.0 Ensembl52,813,131 - 2,843,483 (+)Ensembl
RefSeq Acc Id: NM_001399482   ⟹   NP_001386411
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr858,186,004 - 8,216,576 (+)NCBI
mRatBN7.253,402,763 - 3,433,338 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001386411 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM11516 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000009530
  ENSRNOP00000009530.4
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000009530   ⟸   ENSRNOT00000009530
RefSeq Acc Id: NP_001386411   ⟸   NM_001399482
- Peptide Label: precursor
- UniProtKB: D3ZS55 (UniProtKB/TrEMBL),   A6JFC0 (UniProtKB/TrEMBL)
Protein Domains
SMB

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZS55-F1-model_v2 AlphaFold D3ZS55 1-264 view protein structure

Transcriptome

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

Promoters
RGD ID:13693540
Promoter ID:EPDNEW_R4051
Type:initiation region
Name:Sbspon_1
Description:somatomedin B and thrombospondin, type 1 domain containing
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_6.052,813,146 - 2,813,206EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1559717 AgrOrtholog
BioCyc Gene G2FUF-42297 BioCyc
Ensembl Genes ENSRNOG00000007258 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009530 ENTREZGENE
  ENSRNOT00000009530.8 UniProtKB/TrEMBL
Gene3D-CATH 2.20.100.10 UniProtKB/TrEMBL
InterPro SBSPON UniProtKB/TrEMBL
  Somatomedin_B UniProtKB/TrEMBL
  Somatomedin_B-like_dom UniProtKB/TrEMBL
  Thrombospondin_1_rpt UniProtKB/TrEMBL
  TSP1_rpt_sf UniProtKB/TrEMBL
  TSP1_spondin_dom UniProtKB/TrEMBL
KEGG Report rno:297757 UniProtKB/TrEMBL
NCBI Gene 297757 ENTREZGENE
PANTHER PTHR20920 UniProtKB/TrEMBL
  SOMATOMEDIN-B AND THROMBOSPONDIN TYPE-1 DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
Pfam TSP1_spondin UniProtKB/TrEMBL
PhenoGen Sbspon PhenoGen
PROSITE SMB_1 UniProtKB/TrEMBL
  SMB_2 UniProtKB/TrEMBL
  TSP1 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000007258 RatGTEx
Superfamily-SCOP SSF90188 UniProtKB/TrEMBL
  TSP1 UniProtKB/TrEMBL
UniProt A6JFC0 ENTREZGENE, UniProtKB/TrEMBL
  D3ZS55 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-15 Sbspon  somatomedin B and thrombospondin, type 1 domain containing  Rpesp  RPE-spondin  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-28 Rpesp  RPE-spondin  RGD1559717_predicted  similar to RPE-spondin (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1559717_predicted  similar to RPE-spondin (predicted)  LOC297757  similar to RPE-spondin  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC297757  similar to RPE-spondin      Symbol and Name status set to provisional 70820 PROVISIONAL