Shisa9 (shisa family member 9) - Rat Genome Database

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Gene: Shisa9 (shisa family member 9) Rattus norvegicus
Analyze
Symbol: Shisa9
Name: shisa family member 9
RGD ID: 2320726
Description: Predicted to enable PDZ domain binding activity. Predicted to be involved in regulation of short-term neuronal synaptic plasticity. Predicted to be located in dendritic spine membrane; postsynaptic density; and postsynaptic membrane. Predicted to be part of AMPA glutamate receptor complex. Predicted to be active in glutamatergic synapse and postsynaptic density membrane. Orthologous to human SHISA9 (shisa family member 9); INTERACTS WITH atrazine; bisphenol A; methoxychlor.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC100361134; shisa homolog 9; shisa homolog 9 (Xenopus laevis); shisa homolog 9-like
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
GRCr8103,842,625 - 4,135,618 (-)NCBIGRCr8
mRatBN7.2103,335,616 - 3,629,334 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl103,337,979 - 3,627,773 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0102,777,675 - 3,072,842 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0101,658,327 - 1,940,603 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4103,152,124 - 3,177,530 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera102,370,352 - 2,661,832 (-)NCBICelera
Cytogenetic Map10q11NCBI
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

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:20185686   PMID:22632720   PMID:24498314  


Genomics

Comparative Map Data
Shisa9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8103,842,625 - 4,135,618 (-)NCBIGRCr8
mRatBN7.2103,335,616 - 3,629,334 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl103,337,979 - 3,627,773 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0102,777,675 - 3,072,842 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0101,658,327 - 1,940,603 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4103,152,124 - 3,177,530 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera102,370,352 - 2,661,832 (-)NCBICelera
Cytogenetic Map10q11NCBI
SHISA9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381612,901,598 - 13,563,017 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1612,901,598 - 13,240,416 (+)EnsemblGRCh38hg38GRCh38
GRCh371612,995,455 - 13,334,273 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361613,083,744 - 13,236,767 (+)NCBINCBI36Build 36hg18NCBI36
Celera1613,170,353 - 13,509,146 (+)NCBICelera
Cytogenetic Map16p13.12NCBI
HuRef1612,912,276 - 13,251,427 (+)NCBIHuRef
CHM1_11612,995,403 - 13,332,162 (+)NCBICHM1_1
T2T-CHM13v2.01612,938,717 - 13,600,679 (+)NCBIT2T-CHM13v2.0
Shisa9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391611,801,457 - 12,088,768 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1611,801,977 - 12,088,766 (+)EnsemblGRCm39 Ensembl
GRCm381611,983,593 - 12,270,904 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1611,984,113 - 12,270,902 (+)EnsemblGRCm38mm10GRCm38
MGSCv371611,984,206 - 12,270,997 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361611,897,726 - 12,183,527 (+)NCBIMGSCv36mm8
Celera1612,611,680 - 12,899,218 (+)NCBICelera
Cytogenetic Map16A1NCBI
cM Map166.89NCBI
Shisa9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554425,540,779 - 5,816,865 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554425,537,372 - 5,817,076 (-)NCBIChiLan1.0ChiLan1.0
SHISA9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21813,441,011 - 14,105,824 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11617,211,861 - 17,880,067 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01611,833,062 - 12,494,972 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11613,258,949 - 13,596,352 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1613,258,945 - 13,591,356 (+)Ensemblpanpan1.1panPan2
SHISA9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1629,801,919 - 30,083,397 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl629,801,904 - 30,083,420 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha631,166,674 - 31,453,618 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0629,968,383 - 30,255,994 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl629,971,854 - 30,256,117 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1629,783,451 - 30,070,591 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0629,658,618 - 29,945,558 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0630,080,489 - 30,368,103 (-)NCBIUU_Cfam_GSD_1.0
Shisa9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344113,397,030 - 113,643,014 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365011,494,885 - 1,737,439 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365011,491,869 - 1,738,118 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHISA9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl329,969,122 - 30,272,943 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1329,966,481 - 30,272,800 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2331,242,556 - 31,253,704 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SHISA9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1512,347,832 - 12,687,382 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606817,384,857 - 17,755,670 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Shisa9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247825,214,341 - 5,500,967 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247825,210,878 - 5,501,438 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Shisa9
2047 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:100
Count of miRNA genes:52
Interacting mature miRNAs:57
Transcripts:ENSRNOT00000065554, ENSRNOT00000073479
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
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
1549898Neuinf3Neuroinflammation QTL 326.4nervous system integrity trait (VT:0010566)MHC Class II RT1A-positive spinal cord ventral horn area to total spinal cord ventral horn area ratio (CMO:0001980)1034063205387112Rat

Markers in Region
D10Got6  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2103,406,320 - 3,406,594 (+)MAPPERmRatBN7.2
Rnor_6.0102,847,625 - 2,847,898NCBIRnor6.0
Rnor_5.0101,728,277 - 1,728,550UniSTSRnor5.0
RGSC_v3.4103,219,701 - 3,219,975RGDRGSC3.4
RGSC_v3.4103,219,702 - 3,219,975UniSTSRGSC3.4
RGSC_v3.1103,219,701 - 3,219,975RGD
Celera102,440,770 - 2,441,043UniSTS
BE106220  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2103,491,492 - 3,491,646 (+)MAPPERmRatBN7.2
Rnor_6.0102,936,348 - 2,936,501NCBIRnor6.0
Rnor_5.0101,815,885 - 1,816,038UniSTSRnor5.0
RGSC_v3.4103,306,799 - 3,306,952UniSTSRGSC3.4
Celera102,527,266 - 2,527,419UniSTS
RH 3.4 Map1043.2UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000101218   ⟹   ENSRNOP00000097822
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl103,337,979 - 3,627,773 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107136   ⟹   ENSRNOP00000089969
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl103,337,979 - 3,627,773 (-)Ensembl
RefSeq Acc Id: XM_039087032   ⟹   XP_038942960
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8103,842,625 - 4,135,618 (-)NCBI
mRatBN7.2103,335,616 - 3,629,320 (-)NCBI
RefSeq Acc Id: XM_039087033   ⟹   XP_038942961
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8103,842,625 - 4,135,485 (-)NCBI
mRatBN7.2103,335,616 - 3,629,317 (-)NCBI
RefSeq Acc Id: XM_039087034   ⟹   XP_038942962
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8103,864,912 - 4,135,485 (-)NCBI
mRatBN7.2103,357,907 - 3,629,320 (-)NCBI
RefSeq Acc Id: XM_039087035   ⟹   XP_038942963
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8104,062,446 - 4,135,485 (-)NCBI
mRatBN7.2103,593,674 - 3,629,322 (-)NCBI
RefSeq Acc Id: XM_039087036   ⟹   XP_038942964
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8104,124,701 - 4,135,485 (-)NCBI
mRatBN7.2103,617,718 - 3,629,334 (-)NCBI
RefSeq Acc Id: XM_063270075   ⟹   XP_063126145
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8104,128,688 - 4,135,485 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_038942960   ⟸   XM_039087032
- Peptide Label: isoform X1
- UniProtKB: A0A8I6ACW8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038942961   ⟸   XM_039087033
- Peptide Label: isoform X2
- UniProtKB: A0A8I6ATC9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038942962   ⟸   XM_039087034
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038942963   ⟸   XM_039087035
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038942964   ⟸   XM_039087036
- Peptide Label: isoform X5
RefSeq Acc Id: ENSRNOP00000089969   ⟸   ENSRNOT00000107136
RefSeq Acc Id: ENSRNOP00000097822   ⟸   ENSRNOT00000101218
RefSeq Acc Id: XP_063126145   ⟸   XM_063270075
- Peptide Label: isoform X6

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:2320726 AgrOrtholog
BioCyc Gene G2FUF-26184 BioCyc
Ensembl Genes ENSRNOG00000063400 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000101218.1 UniProtKB/TrEMBL
  ENSRNOT00000107136.1 UniProtKB/TrEMBL
InterPro Shisa UniProtKB/TrEMBL
NCBI Gene 100361134 ENTREZGENE
PANTHER PROTEIN SHISA-9 UniProtKB/TrEMBL
  PTHR31774 UniProtKB/TrEMBL
Pfam Shisa UniProtKB/TrEMBL
PhenoGen Shisa9 PhenoGen
RatGTEx ENSRNOG00000063400 RatGTEx
UniProt A0A8I6ACW8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6ATC9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Shisa9  shisa family member 9  Shisa9  shisa family member 9  Data merged from RGD:149736190 737654 PROVISIONAL
2021-08-09 Shisa9  shisa family member 9      Symbol and Name status set to provisional 45752 PROVISIONAL
2013-08-07 Shisa9  shisa family member 9  Shisa9  shisa homolog 9 (Xenopus laevis)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-08-10 Shisa9  shisa homolog 9 (Xenopus laevis)  LOC100361134  shisa homolog 9-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-05 LOC100361134  shisa homolog 9-like      Symbol and Name status set to provisional 70820 PROVISIONAL