Shisa3 (shisa family member 3) - Rat Genome Database

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Gene: Shisa3 (shisa family member 3) Rattus norvegicus
Analyze
Symbol: Shisa3
Name: shisa family member 3
RGD ID: 1565710
Description: Predicted to act upstream of or within negative regulation of canonical Wnt signaling pathway. Orthologous to human SHISA3 (shisa family member 3); INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC498356; protein shisa-3 homolog; RGD1565710; shisa homolog 3; shisa homolog 3 (Xenopus laevis); similar to MGC68837 protein
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
GRCr81440,917,563 - 40,922,135 (-)NCBIGRCr8
mRatBN7.21440,563,672 - 40,568,244 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1440,563,673 - 40,568,244 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1440,910,502 - 40,915,074 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01442,210,574 - 42,215,146 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01440,691,360 - 40,695,932 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01442,216,653 - 42,221,225 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1442,216,654 - 42,221,225 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01442,013,406 - 42,017,978 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41443,175,486 - 43,180,058 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1439,721,342 - 39,725,914 (-)NCBICelera
Cytogenetic Map14p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
membrane  (IEA)

Molecular Function

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:12477932  


Genomics

Comparative Map Data
Shisa3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81440,917,563 - 40,922,135 (-)NCBIGRCr8
mRatBN7.21440,563,672 - 40,568,244 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1440,563,673 - 40,568,244 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1440,910,502 - 40,915,074 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01442,210,574 - 42,215,146 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01440,691,360 - 40,695,932 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01442,216,653 - 42,221,225 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1442,216,654 - 42,221,225 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01442,013,406 - 42,017,978 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41443,175,486 - 43,180,058 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1439,721,342 - 39,725,914 (-)NCBICelera
Cytogenetic Map14p11NCBI
SHISA3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38442,397,488 - 42,402,487 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl442,397,488 - 42,402,487 (+)EnsemblGRCh38hg38GRCh38
GRCh37442,399,505 - 42,404,504 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36442,094,613 - 42,099,261 (+)NCBINCBI36Build 36hg18NCBI36
Celera442,847,702 - 42,852,350 (+)NCBICelera
Cytogenetic Map4p13NCBI
HuRef441,721,064 - 41,725,712 (+)NCBIHuRef
CHM1_1442,400,127 - 42,404,775 (+)NCBICHM1_1
T2T-CHM13v2.0442,371,349 - 42,376,348 (+)NCBIT2T-CHM13v2.0
Shisa3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39567,765,226 - 67,771,330 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl567,765,225 - 67,780,895 (+)EnsemblGRCm39 Ensembl
GRCm38567,607,883 - 67,613,987 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl567,607,882 - 67,623,552 (+)EnsemblGRCm38mm10GRCm38
MGSCv37567,999,122 - 68,003,511 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36567,887,018 - 67,891,407 (+)NCBIMGSCv36mm8
Celera564,899,945 - 64,905,332 (+)NCBICelera
Cytogenetic Map5C3.1NCBI
cM Map536.15NCBI
Shisa3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554435,365,791 - 5,372,108 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554435,367,306 - 5,372,091 (-)NCBIChiLan1.0ChiLan1.0
SHISA3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2342,580,469 - 42,585,747 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1442,771,347 - 42,776,625 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0436,718,938 - 36,723,924 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1442,566,944 - 42,572,098 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl442,567,291 - 42,572,098 (+)Ensemblpanpan1.1panPan2
SHISA3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11339,358,206 - 39,360,723 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1339,358,607 - 39,359,730 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1339,333,616 - 39,338,124 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01339,847,323 - 39,851,823 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1339,846,741 - 39,851,805 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11339,535,571 - 39,540,095 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01339,648,613 - 39,653,152 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01340,113,373 - 40,117,919 (+)NCBIUU_Cfam_GSD_1.0
Shisa3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528536,741,476 - 36,745,878 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364829,551,933 - 9,556,794 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364829,551,933 - 9,556,763 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHISA3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl833,374,265 - 33,378,951 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1833,373,633 - 33,379,039 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2835,095,667 - 35,096,819 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SHISA3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1277,939,248 - 7,946,897 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl277,940,285 - 7,943,677 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604754,236,396 - 54,241,498 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Shisa3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476124,511,759 - 24,519,251 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476124,514,251 - 24,519,253 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Shisa3
6 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:459
Count of miRNA genes:258
Interacting mature miRNAs:308
Transcripts:ENSRNOT00000036103
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
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)143999825175582726Rat

Markers in Region
BE095714  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21440,564,376 - 40,564,528 (+)MAPPERmRatBN7.2
Rnor_6.01442,217,358 - 42,217,509NCBIRnor6.0
Rnor_5.01442,014,111 - 42,014,262UniSTSRnor5.0
RGSC_v3.41443,176,191 - 43,176,342UniSTSRGSC3.4
Celera1439,722,047 - 39,722,198UniSTS
Cytogenetic Map14p11UniSTS


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 14 14 14 23 18 18
Low 2 18 39 25 11 25 7 8 47 17 17 9 7
Below cutoff 22 4 2 8 2 1 3 4 3 2 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000036103   ⟹   ENSRNOP00000033959
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1440,563,673 - 40,568,244 (-)Ensembl
Rnor_6.0 Ensembl1442,216,654 - 42,221,225 (-)Ensembl
RefSeq Acc Id: NM_001109087   ⟹   NP_001102557
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81440,917,563 - 40,922,135 (-)NCBI
mRatBN7.21440,563,672 - 40,568,244 (-)NCBI
Rnor_6.01442,216,653 - 42,221,225 (-)NCBI
Rnor_5.01442,013,406 - 42,017,978 (-)NCBI
RGSC_v3.41443,175,486 - 43,180,058 (-)RGD
Celera1439,721,342 - 39,725,914 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102557 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI68960 (Get FASTA)   NCBI Sequence Viewer  
  EDL90024 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000033959
  ENSRNOP00000033959.3
Reference Protein Sequences
RefSeq Acc Id: NP_001102557   ⟸   NM_001109087
- Peptide Label: precursor
- UniProtKB: B5DF81 (UniProtKB/TrEMBL),   F7FMB1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000033959   ⟸   ENSRNOT00000036103

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B5DF81-F1-model_v2 AlphaFold B5DF81 1-238 view protein structure

Transcriptome

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

Promoters
RGD ID:13699303
Promoter ID:EPDNEW_R9828
Type:single initiation site
Name:Shisa3_1
Description:shisa family member 3
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_6.01442,221,243 - 42,221,303EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565710 AgrOrtholog
BioCyc Gene G2FUF-15788 BioCyc
Ensembl Genes ENSRNOG00000025670 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000036103 ENTREZGENE
  ENSRNOT00000036103.4 UniProtKB/TrEMBL
InterPro Shisa UniProtKB/TrEMBL
KEGG Report rno:498356 UniProtKB/TrEMBL
NCBI Gene 498356 ENTREZGENE
PANTHER PROTEIN SHISA-3 HOMOLOG UniProtKB/TrEMBL
  PTHR31395 UniProtKB/TrEMBL
Pfam Shisa UniProtKB/TrEMBL
PhenoGen Shisa3 PhenoGen
RatGTEx ENSRNOG00000025670 RatGTEx
UniProt B5DF81 ENTREZGENE, UniProtKB/TrEMBL
  F7FMB1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-07 Shisa3  shisa family member 3  Shisa3  shisa homolog 3 (Xenopus laevis)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-02 Shisa3  shisa homolog 3 (Xenopus laevis)  RGD1565710  similar to MGC68837 protein   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1565710  similar to MGC68837 protein   RGD1565710_predicted  similar to MGC68837 protein (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1565710_predicted  similar to MGC68837 protein (predicted)  LOC498356  similar to MGC68837 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498356  similar to MGC68837 protein      Symbol and Name status set to provisional 70820 PROVISIONAL