Ripply3 (ripply transcriptional repressor 3) - Rat Genome Database

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Gene: Ripply3 (ripply transcriptional repressor 3) Rattus norvegicus
Analyze
Symbol: Ripply3
Name: ripply transcriptional repressor 3
RGD ID: 1308788
Description: Predicted to be involved in several processes, including embryonic pattern specification; negative regulation of transcription by RNA polymerase II; and pharyngeal system development. Predicted to act upstream of or within negative regulation of cell population proliferation. Predicted to be active in nucleus. Orthologous to human RIPPLY3 (ripply transcriptional repressor 3); INTERACTS WITH 1,3-dinitrobenzene; 6-propyl-2-thiouracil; all-trans-retinoic acid.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Down syndrome critical region gene 6; Down syndrome critical region homolog 6; Down syndrome critical region homolog 6 (human); Dscr6; LOC288239; ripply3 homolog; ripply3 homolog (zebrafish)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
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
GRCr81147,118,147 - 47,126,244 (+)NCBIGRCr8
mRatBN7.21133,648,471 - 33,656,587 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1133,648,486 - 33,656,584 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1142,303,306 - 42,311,405 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01134,974,670 - 34,982,769 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01134,123,066 - 34,131,163 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01134,557,679 - 34,565,776 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1134,557,679 - 34,565,776 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01138,145,428 - 38,153,525 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41134,575,083 - 34,583,180 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11134,631,403 - 34,639,055 (+)NCBI
Celera1134,793,208 - 34,801,305 (-)NCBICelera
Cytogenetic Map11q11NCBI
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

Cellular Component
nucleus  (IBA)

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:21177346   PMID:25053427  


Genomics

Comparative Map Data
Ripply3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81147,118,147 - 47,126,244 (+)NCBIGRCr8
mRatBN7.21133,648,471 - 33,656,587 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1133,648,486 - 33,656,584 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1142,303,306 - 42,311,405 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01134,974,670 - 34,982,769 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01134,123,066 - 34,131,163 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01134,557,679 - 34,565,776 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1134,557,679 - 34,565,776 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01138,145,428 - 38,153,525 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41134,575,083 - 34,583,180 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11134,631,403 - 34,639,055 (+)NCBI
Celera1134,793,208 - 34,801,305 (-)NCBICelera
Cytogenetic Map11q11NCBI
RIPPLY3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382137,006,150 - 37,019,662 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2137,006,150 - 37,019,662 (+)EnsemblGRCh38hg38GRCh38
GRCh372138,378,450 - 38,391,962 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362137,300,733 - 37,313,829 (+)NCBINCBI36Build 36hg18NCBI36
Build 342137,300,732 - 37,313,826NCBI
Celera2123,577,251 - 23,590,347 (+)NCBICelera
Cytogenetic Map21q22.13NCBI
HuRef2123,854,553 - 23,867,647 (+)NCBIHuRef
CHM1_12137,940,236 - 37,953,313 (+)NCBICHM1_1
T2T-CHM13v2.02135,388,362 - 35,401,872 (+)NCBIT2T-CHM13v2.0
Ripply3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391694,129,281 - 94,137,794 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1694,129,279 - 94,137,794 (+)EnsemblGRCm39 Ensembl
GRCm381694,328,422 - 94,336,935 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1694,328,420 - 94,336,935 (+)EnsemblGRCm38mm10GRCm38
MGSCv371694,550,029 - 94,558,542 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361694,437,218 - 94,445,733 (+)NCBIMGSCv36mm8
Celera1695,415,747 - 95,424,097 (+)NCBICelera
Cytogenetic Map16C4NCBI
cM Map1655.17NCBI
Ripply3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540736,101,206 - 36,108,808 (+)NCBIChiLan1.0ChiLan1.0
RIPPLY3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22233,118,522 - 33,130,950 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12127,979,071 - 27,991,153 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02123,368,472 - 23,379,560 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12136,723,931 - 36,734,886 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2136,723,931 - 36,734,382 (+)Ensemblpanpan1.1panPan2
RIPPLY3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13132,150,768 - 32,188,604 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3132,150,882 - 32,188,436 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3131,239,163 - 31,249,248 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03131,481,096 - 31,491,184 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3131,481,116 - 31,506,328 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13131,349,063 - 31,359,184 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03131,362,083 - 31,372,228 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03131,852,602 - 31,862,690 (+)NCBIUU_Cfam_GSD_1.0
RIPPLY3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.113200,642,802 - 200,652,401 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213210,717,930 - 210,727,520 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RIPPLY3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1280,992,876 - 81,001,956 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660548,835,299 - 8,847,263 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ripply3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474526,636,307 - 26,658,373 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ripply3
40 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:121
Count of miRNA genes:92
Interacting mature miRNAs:108
Transcripts:ENSRNOT00000002289
Prediction methods: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
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11135331169Rat
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11843667453436674Rat
724517Uae18Urinary albumin excretion QTL 183.7urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)111647204744285911Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112295940367959403Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112328045668280456Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112328045668280456Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)112952841860324829Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat

Markers in Region
RH140735  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21133,655,489 - 33,655,707 (+)MAPPERmRatBN7.2
Rnor_6.01134,564,683 - 34,564,900NCBIRnor6.0
Rnor_5.01138,152,432 - 38,152,649UniSTSRnor5.0
RGSC_v3.41134,582,087 - 34,582,304UniSTSRGSC3.4
Celera1134,794,084 - 34,794,301UniSTS
Cytogenetic Map11q11UniSTS


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 8 11
Low 3 36 27 18 3 18 1 1 65 27 40 1
Below cutoff 7 29 22 16 22 6 8 9 1 6

Sequence


RefSeq Acc Id: ENSRNOT00000002289   ⟹   ENSRNOP00000002289
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1133,648,486 - 33,656,584 (+)Ensembl
Rnor_6.0 Ensembl1134,557,679 - 34,565,776 (+)Ensembl
RefSeq Acc Id: NM_001105892   ⟹   NP_001099362
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81147,118,147 - 47,126,244 (+)NCBI
mRatBN7.21133,648,486 - 33,656,584 (+)NCBI
Rnor_6.01134,557,679 - 34,565,776 (+)NCBI
Rnor_5.01138,145,428 - 38,153,525 (+)NCBI
RGSC_v3.41134,575,083 - 34,583,180 (+)RGD
Celera1134,793,208 - 34,801,305 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001099362 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL76722 (Get FASTA)   NCBI Sequence Viewer  
  EDL76723 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000002289
  ENSRNOP00000002289.4
RefSeq Acc Id: NP_001099362   ⟸   NM_001105892
- UniProtKB: D4AA46 (UniProtKB/TrEMBL),   A6KPY0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002289   ⟸   ENSRNOT00000002289

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AA46-F1-model_v2 AlphaFold D4AA46 1-149 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:1308788 AgrOrtholog
BioCyc Gene G2FUF-21770 BioCyc
Ensembl Genes ENSRNOG00000001684 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002289 ENTREZGENE
  ENSRNOT00000002289.6 UniProtKB/TrEMBL
InterPro Ripply_fam UniProtKB/TrEMBL
KEGG Report rno:288239 UniProtKB/TrEMBL
NCBI Gene 288239 ENTREZGENE
PANTHER PROTEIN RIPPLY3 UniProtKB/TrEMBL
  PTHR16770 UniProtKB/TrEMBL
Pfam Ripply UniProtKB/TrEMBL
PhenoGen Ripply3 PhenoGen
RatGTEx ENSRNOG00000001684 RatGTEx
UniProt A6KPY0 ENTREZGENE, UniProtKB/TrEMBL
  D4AA46 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-07 Ripply3  ripply transcriptional repressor 3  Ripply3  ripply3 homolog (zebrafish)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-06-14 Ripply3  ripply3 homolog (zebrafish)  Dscr6  Down syndrome critical region gene 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-01-14 Dscr6  Down syndrome critical region gene 6  Dscr6  Down syndrome critical region homolog 6 (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Dscr6  Down syndrome critical region homolog 6 (human)   Dscr6_predicted  Down syndrome critical region homolog 6 (human) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Dscr6_predicted  Down syndrome critical region homolog 6 (human) (predicted)    Down syndrome critical region gene 6 (predicted)  Name updated 1299863 APPROVED
2005-01-12 Dscr6_predicted  Down syndrome critical region gene 6 (predicted)      Symbol and Name status set to approved 70820 APPROVED