Sntn (sentan, cilia apical structure protein) - Rat Genome Database

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Gene: Sntn (sentan, cilia apical structure protein) Rattus norvegicus
Analyze
Symbol: Sntn
Name: sentan, cilia apical structure protein
RGD ID: 1562356
Description: Predicted to enable calcium ion binding activity and calcium-dependent protein binding activity. Predicted to be located in cilium. Orthologous to human SNTN (sentan, cilia apical structure protein); INTERACTS WITH bisphenol A; Cuprizon; furan.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC498456; RGD1562356; sentan; similar to hypothetical protein A430083B19
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
GRCr81513,943,052 - 13,956,109 (-)NCBIGRCr8
mRatBN7.21511,512,563 - 11,525,608 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1511,512,563 - 11,525,603 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1513,626,907 - 13,640,013 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01514,588,819 - 14,601,924 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01512,840,191 - 12,853,297 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01514,497,770 - 14,510,828 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1514,497,770 - 14,510,828 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01518,501,194 - 18,514,256 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41513,073,259 - 13,086,693 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1511,514,566 - 11,527,178 (-)NCBICelera
Cytogenetic Map15p16NCBI
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
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:29916806  


Genomics

Comparative Map Data
Sntn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81513,943,052 - 13,956,109 (-)NCBIGRCr8
mRatBN7.21511,512,563 - 11,525,608 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1511,512,563 - 11,525,603 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1513,626,907 - 13,640,013 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01514,588,819 - 14,601,924 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01512,840,191 - 12,853,297 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01514,497,770 - 14,510,828 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1514,497,770 - 14,510,828 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01518,501,194 - 18,514,256 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41513,073,259 - 13,086,693 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1511,514,566 - 11,527,178 (-)NCBICelera
Cytogenetic Map15p16NCBI
SNTN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38363,652,675 - 63,665,212 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl363,652,675 - 63,679,020 (+)EnsemblGRCh38hg38GRCh38
GRCh37363,638,351 - 63,650,888 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36363,613,384 - 63,625,933 (+)NCBINCBI36Build 36hg18NCBI36
Celera363,655,601 - 63,668,154 (+)NCBICelera
Cytogenetic Map3p14.2NCBI
HuRef363,735,531 - 63,748,076 (+)NCBIHuRef
CHM1_1363,589,797 - 63,602,351 (+)NCBICHM1_1
T2T-CHM13v2.0363,696,298 - 63,708,831 (+)NCBIT2T-CHM13v2.0
Sntn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39148,786,615 - 8,798,887 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl148,786,615 - 8,798,887 (-)EnsemblGRCm39 Ensembl
GRCm381413,670,876 - 13,683,148 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1413,670,876 - 13,683,148 (+)EnsemblGRCm38mm10GRCm38
MGSCv371414,503,390 - 14,515,662 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361412,464,143 - 12,476,415 (+)NCBIMGSCv36mm8
Celera149,314,695 - 9,327,135 (+)NCBICelera
Cytogenetic Map14A1NCBI
cM Map146.93NCBI
Sntn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555172,209,843 - 2,234,113 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555172,210,700 - 2,233,760 (-)NCBIChiLan1.0ChiLan1.0
SNTN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2263,578,041 - 63,590,634 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1363,582,828 - 63,595,402 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0363,560,204 - 63,572,211 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1364,941,058 - 64,952,774 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl364,941,058 - 64,964,255 (+)Ensemblpanpan1.1panPan2
SNTN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12027,532,916 - 27,548,331 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2027,533,739 - 27,547,972 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2027,457,119 - 27,472,179 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02027,769,816 - 27,784,898 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2027,769,807 - 27,784,905 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12027,266,816 - 27,281,849 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02027,616,443 - 27,631,469 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02027,719,787 - 27,734,858 (-)NCBIUU_Cfam_GSD_1.0
Sntn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118164,348,246 - 164,362,752 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366372,738,068 - 2,745,909 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366372,738,068 - 2,753,610 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SNTN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1345,187,379 - 45,200,718 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11345,187,385 - 45,200,586 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21349,668,180 - 49,681,418 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SNTN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12224,697,324 - 24,709,576 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666041142,113,490 - 142,125,952 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sntn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248882,278,004 - 2,289,695 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248882,277,215 - 2,290,237 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sntn
162 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:304
Count of miRNA genes:190
Interacting mature miRNAs:217
Transcripts:ENSRNOT00000039347
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15129912054Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
5684946Bss98Bone structure and strength QTL 983.90.0026tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)15105825014481294Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)colorectal tumor number (CMO:0001794)15226636822711984Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15226636822711984Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat


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 5
Low 2 2 6
Below cutoff 1 4 3 1 2 1 1 2 9 10 6 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000039347   ⟹   ENSRNOP00000034316
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1511,512,563 - 11,525,603 (-)Ensembl
Rnor_6.0 Ensembl1514,497,770 - 14,510,828 (-)Ensembl
RefSeq Acc Id: NM_001109098   ⟹   NP_001102568
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81513,943,052 - 13,956,090 (-)NCBI
mRatBN7.21511,512,563 - 11,525,603 (-)NCBI
Rnor_6.01514,497,770 - 14,510,828 (-)NCBI
Rnor_5.01518,501,194 - 18,514,256 (-)NCBI
RGSC_v3.41513,073,259 - 13,086,693 (-)RGD
Celera1511,514,566 - 11,527,178 (-)RGD
Sequence:
RefSeq Acc Id: XM_039093578   ⟹   XP_038949506
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81513,943,750 - 13,956,089 (-)NCBI
mRatBN7.21511,513,267 - 11,525,602 (-)NCBI
RefSeq Acc Id: XM_039093579   ⟹   XP_038949507
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81513,943,750 - 13,956,015 (-)NCBI
mRatBN7.21511,513,267 - 11,525,571 (-)NCBI
RefSeq Acc Id: XM_039093580   ⟹   XP_038949508
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81513,946,655 - 13,956,109 (-)NCBI
mRatBN7.21511,516,438 - 11,525,608 (-)NCBI
RefSeq Acc Id: XM_039093581   ⟹   XP_038949509
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81513,943,750 - 13,956,109 (-)NCBI
mRatBN7.21511,513,249 - 11,525,608 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001102568   ⟸   NM_001109098
- UniProtKB: F1LX90 (UniProtKB/TrEMBL),   A6K081 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000034316   ⟸   ENSRNOT00000039347
RefSeq Acc Id: XP_038949509   ⟸   XM_039093581
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038949506   ⟸   XM_039093578
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038949507   ⟸   XM_039093579
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038949508   ⟸   XM_039093580
- Peptide Label: isoform X2
Protein Domains
S100/CaBP-9k-type calcium binding subdomain

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LX90-F1-model_v2 AlphaFold F1LX90 1-143 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562356 AgrOrtholog
BioCyc Gene G2FUF-14368 BioCyc
Ensembl Genes ENSRNOG00000027383 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000039347 ENTREZGENE
  ENSRNOT00000039347.5 UniProtKB/TrEMBL
Gene3D-CATH EF-hand UniProtKB/TrEMBL
InterPro EF-hand-like_dom UniProtKB/TrEMBL
  S-100_dom UniProtKB/TrEMBL
  S100_Ca-bd_sub UniProtKB/TrEMBL
KEGG Report rno:498456 UniProtKB/TrEMBL
NCBI Gene 498456 ENTREZGENE
PANTHER PTHR11639:SF134 UniProtKB/TrEMBL
  S100 CALCIUM-BINDING PROTEIN UniProtKB/TrEMBL
Pfam S_100 UniProtKB/TrEMBL
PhenoGen Sntn PhenoGen
RatGTEx ENSRNOG00000027383 RatGTEx
SMART S_100 UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/TrEMBL
UniProt A6K081 ENTREZGENE, UniProtKB/TrEMBL
  F1LX90 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-06-12 Sntn  sentan, cilia apical structure protein  RGD1562356  similar to hypothetical protein A430083B19   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1562356  similar to hypothetical protein A430083B19   RGD1562356_predicted  similar to hypothetical protein A430083B19 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1562356_predicted  similar to hypothetical protein A430083B19 (predicted)  LOC498456  similar to hypothetical protein A430083B19  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498456  similar to hypothetical protein A430083B19      Symbol and Name status set to provisional 70820 PROVISIONAL