Spdye4c (speedy/RINGO cell cycle regulator family, member E4C) - Rat Genome Database

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Gene: Spdye4c (speedy/RINGO cell cycle regulator family, member E4C) Rattus norvegicus
Analyze
Symbol: Spdye4c
Name: speedy/RINGO cell cycle regulator family, member E4C
RGD ID: 1561675
Description: Predicted to enable protein kinase binding activity. Orthologous to human SPDYE18 (speedy/RINGO cell cycle regulator family member E18).
Type: protein-coding
RefSeq Status: PREDICTED
Previously known as: hypothetical protein LOC499886; LOC499886; similar to hypothetical protein 4933411G11; uncharacterized protein LOC499886
RGD Orthologs
Mouse
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83136,284,234 - 136,291,586 (+)NCBIGRCr8
mRatBN7.23115,830,999 - 115,838,358 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3115,831,090 - 115,838,354 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3119,728,259 - 119,735,534 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03128,323,807 - 128,331,082 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03125,984,313 - 125,991,590 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03121,128,312 - 121,135,720 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3121,128,368 - 121,135,718 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03128,876,440 - 128,883,834 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43116,192,994 - 116,200,262 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera3114,660,649 - 114,667,918 (+)NCBICelera
Cytogenetic Map3q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

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
4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Genomics

Comparative Map Data
Spdye4c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83136,284,234 - 136,291,586 (+)NCBIGRCr8
mRatBN7.23115,830,999 - 115,838,358 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3115,831,090 - 115,838,354 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3119,728,259 - 119,735,534 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03128,323,807 - 128,331,082 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03125,984,313 - 125,991,590 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03121,128,312 - 121,135,720 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3121,128,368 - 121,135,718 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03128,876,440 - 128,883,834 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43116,192,994 - 116,200,262 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera3114,660,649 - 114,667,918 (+)NCBICelera
Cytogenetic Map3q36NCBI
Spdye4c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392128,433,121 - 128,443,483 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2128,433,129 - 128,440,384 (+)EnsemblGRCm39 Ensembl
GRCm382128,591,201 - 128,601,662 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2128,591,209 - 128,598,464 (+)EnsemblGRCm38mm10GRCm38
MGSCv372128,418,077 - 128,422,579 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362128,283,782 - 128,288,284 (+)NCBIMGSCv36mm8
Celera2129,823,111 - 129,827,613 (+)NCBICelera
Cytogenetic Map2F1NCBI
cM Map262.63NCBI

Variants

.
Variants in Spdye4c
37 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:96
Count of miRNA genes:77
Interacting mature miRNAs:79
Transcripts:ENSRNOT00000055882
Prediction methods: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
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)361017749121056321Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)370348525121056321Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)370653097121056321Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)373376539118376539Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)389772419134772419Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)391797474136797474Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)395735366140735366Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)397084464142084464Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat
1331758Bp207Blood pressure QTL 2072.848arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3112287552135181505Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)3115638168135181505Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)3115638168135181505Rat


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

integumental system musculoskeletal system nervous system reproductive system appendage
High
Medium 5
Low 2
Below cutoff 1 1 2 2 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000055882   ⟹   ENSRNOP00000052735
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3115,831,090 - 115,838,354 (+)Ensembl
Rnor_6.0 Ensembl3121,128,368 - 121,135,718 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000094284   ⟹   ENSRNOP00000092400
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3115,831,090 - 115,838,354 (+)Ensembl
RefSeq Acc Id: NM_001024312   ⟹   NP_001019483
RefSeq Status: PREDICTED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83136,284,318 - 136,291,586 (+)NCBI
mRatBN7.23115,831,090 - 115,838,358 (+)NCBI
Rnor_6.03121,128,368 - 121,135,720 (+)NCBI
Rnor_5.03128,876,440 - 128,883,834 (-)NCBI
RGSC_v3.43116,192,994 - 116,200,262 (+)RGD
Celera3114,660,649 - 114,667,918 (+)RGD
Sequence:
RefSeq Acc Id: XM_008762192   ⟹   XP_008760414
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83136,284,234 - 136,291,267 (+)NCBI
mRatBN7.23115,830,999 - 115,837,207 (+)NCBI
Rnor_6.03121,128,312 - 121,134,721 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017591985   ⟹   XP_017447474
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83136,284,236 - 136,291,267 (+)NCBI
mRatBN7.23115,831,007 - 115,837,207 (+)NCBI
Rnor_6.03121,128,312 - 121,134,721 (+)NCBI
Sequence:
RefSeq Acc Id: XR_001837047
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83136,284,234 - 136,291,267 (+)NCBI
mRatBN7.23115,830,999 - 115,837,207 (+)NCBI
Rnor_6.03121,128,312 - 121,134,721 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001019483 (Get FASTA)   NCBI Sequence Viewer  
  XP_008760414 (Get FASTA)   NCBI Sequence Viewer  
  XP_017447474 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH86511 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000052735
  ENSRNOP00000052735.2
  ENSRNOP00000092400.1
Reference Protein Sequences
RefSeq Acc Id: NP_001019483   ⟸   NM_001024312
- UniProtKB: Q5RJT3 (UniProtKB/TrEMBL),   A0A8I6AHI5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760414   ⟸   XM_008762192
- Peptide Label: isoform X1
- UniProtKB: Q5RJT3 (UniProtKB/TrEMBL),   A0A8I6AHI5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017447474   ⟸   XM_017591985
- Peptide Label: isoform X2
- UniProtKB: A0A8I6AHI5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000052735   ⟸   ENSRNOT00000055882
RefSeq Acc Id: ENSRNOP00000092400   ⟸   ENSRNOT00000094284

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5RJT3-F1-model_v2 AlphaFold Q5RJT3 1-340 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:1561675 AgrOrtholog
BioCyc Gene G2FUF-47941 BioCyc
Ensembl Genes ENSRNOG00000037081 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000055882 ENTREZGENE
  ENSRNOT00000055882.4 UniProtKB/TrEMBL
  ENSRNOT00000094284.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7132989 IMAGE-MGC_LOAD
InterPro Cell_cycle_regulatory_Spy1 UniProtKB/TrEMBL
KEGG Report rno:499886 UniProtKB/TrEMBL
MGC_CLONE MGC:105895 IMAGE-MGC_LOAD
NCBI Gene 499886 ENTREZGENE
PANTHER PTHR31156 UniProtKB/TrEMBL
  SPEEDY/RINGO CELL CYCLE REGULATOR FAMILY, MEMBER E4C UniProtKB/TrEMBL
Pfam Spy1 UniProtKB/TrEMBL
PhenoGen Spdye4c PhenoGen
RatGTEx ENSRNOG00000037081 RatGTEx
UniProt A0A8I6AHI5 ENTREZGENE, UniProtKB/TrEMBL
  Q5RJT3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-10-04 Spdye4c  speedy/RINGO cell cycle regulator family, member E4C  LOC499886  similar to hypothetical protein 4933411G11  Name and Symbol changed 629549 APPROVED
2006-02-09 LOC499886  similar to hypothetical protein 4933411G11      Symbol and Name status set to provisional 70820 PROVISIONAL