Spdye4 (speedy/RINGO cell cycle regulator family member E4) - Rat Genome Database

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Gene: Spdye4 (speedy/RINGO cell cycle regulator family member E4) Rattus norvegicus
Analyze
Symbol: Spdye4
Name: speedy/RINGO cell cycle regulator family member E4
RGD ID: 1561076
Description: Predicted to enable protein kinase binding activity. Orthologous to human SPDYE4 (speedy/RINGO cell cycle regulator family member E4); INTERACTS WITH atrazine; bisphenol A; N,N-diethyl-m-toluamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: hypothetical protein LOC498146; MGC125213; similar to speedy B isoform; speedy homolog E4; speedy homolog E4 (Xenopus laevis); speedy protein B; speedy protein E4
RGD Orthologs
Human
Mouse
Bonobo
Dog
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81216,450,833 - 16,458,330 (+)NCBIGRCr8
mRatBN7.21211,337,262 - 11,344,753 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1211,337,299 - 11,344,740 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1212,145,092 - 12,152,552 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01212,768,374 - 12,775,833 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01211,794,456 - 11,801,915 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01213,390,831 - 13,398,301 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1213,390,859 - 13,398,295 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01215,431,782 - 15,439,132 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41211,708,689 - 11,716,143 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1213,129,508 - 13,136,688 (+)NCBICelera
Cytogenetic Map12p11NCBI
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

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. 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.
Additional References at PubMed
PMID:15611625  


Genomics

Comparative Map Data
Spdye4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81216,450,833 - 16,458,330 (+)NCBIGRCr8
mRatBN7.21211,337,262 - 11,344,753 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1211,337,299 - 11,344,740 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1212,145,092 - 12,152,552 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01212,768,374 - 12,775,833 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01211,794,456 - 11,801,915 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01213,390,831 - 13,398,301 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1213,390,859 - 13,398,295 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01215,431,782 - 15,439,132 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41211,708,689 - 11,716,143 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1213,129,508 - 13,136,688 (+)NCBICelera
Cytogenetic Map12p11NCBI
SPDYE4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38178,747,532 - 8,758,546 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl178,747,524 - 8,758,559 (-)EnsemblGRCh38hg38GRCh38
GRCh37178,650,850 - 8,661,864 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36178,597,181 - 8,602,556 (-)NCBINCBI36Build 36hg18NCBI36
Celera178,687,309 - 8,692,763 (-)NCBICelera
Cytogenetic Map17p13.1NCBI
HuRef178,555,388 - 8,560,840 (-)NCBIHuRef
CHM1_1178,665,508 - 8,670,961 (-)NCBICHM1_1
T2T-CHM13v2.0178,653,744 - 8,664,766 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2766,082,367 - 66,089,201 (+)NCBI
Spdye4b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395143,166,772 - 143,190,832 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5143,166,772 - 143,190,830 (+)EnsemblGRCm39 Ensembl
GRCm385143,181,017 - 143,205,077 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5143,181,017 - 143,205,075 (+)EnsemblGRCm38mm10GRCm38
MGSCv375143,942,696 - 143,966,747 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365143,446,157 - 143,470,208 (+)NCBIMGSCv36mm8
Celera5140,225,740 - 140,249,569 (+)NCBICelera
Cytogenetic Map5G2NCBI
cM Map581.99NCBI
SPDYE4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21964,988,902 - 65,001,396 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11769,798,181 - 69,810,682 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01742,895,260 - 42,902,399 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11747,628,877 - 47,634,370 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1747,628,877 - 47,634,358 (+)Ensemblpanpan1.1panPan2
LOC607286
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1612,058,028 - 12,065,373 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha618,181,328 - 18,189,900 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0612,057,950 - 12,066,124 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1611,932,206 - 11,941,778 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0611,940,380 - 11,949,878 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0612,138,756 - 12,148,187 (+)NCBIUU_Cfam_GSD_1.0
LOC100520556
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.134,441,881 - 4,448,524 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23144,255,998 - 144,263,077 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SPDYE4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1168,109,933 - 8,117,162 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl168,110,896 - 8,116,145 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605913,266,178 - 13,277,560 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Spdye4
61 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:25
Count of miRNA genes:25
Interacting mature miRNAs:25
Transcripts:ENSRNOT00000066744
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
2312418Kidm41Kidney mass QTL 413.70.0001kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)12119611090Rat
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12122591684Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123297788Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12129333307Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12134851688Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)12142110980Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6556449546669029Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449846669029Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12610757946669029Rat
1600391Edcs2Endometrial carcinoma susceptibility QTL23.50.01uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)12683319017870186Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12719673046669029Rat
2293086Iddm30Insulin dependent diabetes mellitus QTL 303.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)12844949028302290Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)12852542328064601Rat
1331739Hrtrt14Heart rate QTL 143.56232heart pumping trait (VT:2000009)heart rate (CMO:0000002)12931821612829686Rat
1300157Rf21Renal function QTL 214.4renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)12931821632103380Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)12960327746669029Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121047413746669029Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121047413746669029Rat
1331786Kidm11Kidney mass QTL 113.571kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)121107382524234895Rat
1331755Bp219Blood pressure QTL 2193.041arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382528064557Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382545055165Rat

Markers in Region
AU049324  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21211,344,691 - 11,344,871 (+)MAPPERmRatBN7.2
Rnor_6.01213,398,249 - 13,398,430NCBIRnor6.0
Rnor_5.01215,439,080 - 15,439,261UniSTSRnor5.0
RGSC_v3.41211,716,091 - 11,716,272UniSTSRGSC3.4
Celera1213,136,636 - 13,136,814UniSTS
Cytogenetic Map12p11UniSTS


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

circulatory system endocrine system integumental system musculoskeletal system nervous system reproductive system respiratory system appendage
High
Medium 7
Low
Below cutoff 1 1 1 1 1 4 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000066744   ⟹   ENSRNOP00000062723
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1211,337,299 - 11,342,314 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080489   ⟹   ENSRNOP00000071196
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1211,337,299 - 11,344,740 (+)Ensembl
Rnor_6.0 Ensembl1213,390,859 - 13,398,295 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000119664   ⟹   ENSRNOP00000088064
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1211,338,067 - 11,344,740 (+)Ensembl
RefSeq Acc Id: NM_001034153   ⟹   NP_001029325
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81216,450,886 - 16,458,330 (+)NCBI
mRatBN7.21211,337,299 - 11,344,744 (+)NCBI
Rnor_6.01213,390,859 - 13,398,301 (+)NCBI
Rnor_5.01215,431,782 - 15,439,132 (+)NCBI
RGSC_v3.41211,708,689 - 11,716,143 (+)RGD
Celera1213,129,508 - 13,136,688 (+)RGD
Sequence:
RefSeq Acc Id: XM_008768995   ⟹   XP_008767217
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81216,451,743 - 16,458,330 (+)NCBI
mRatBN7.21211,337,877 - 11,344,753 (+)NCBI
Rnor_6.01213,391,699 - 13,398,296 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598437   ⟹   XP_017453926
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81216,450,833 - 16,455,901 (+)NCBI
mRatBN7.21211,337,262 - 11,342,314 (+)NCBI
Rnor_6.01213,390,831 - 13,395,874 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063271576   ⟹   XP_063127646
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81216,451,449 - 16,458,330 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001029325   ⟸   NM_001034153
- UniProtKB: Q3KR78 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008767217   ⟸   XM_008768995
- Peptide Label: isoform X1
- UniProtKB: A0A8I6A4C0 (UniProtKB/TrEMBL),   A6K1M4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017453926   ⟸   XM_017598437
- Peptide Label: isoform X3
- UniProtKB: D3ZEY3 (UniProtKB/TrEMBL),   A6K1M3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000071196   ⟸   ENSRNOT00000080489
RefSeq Acc Id: ENSRNOP00000062723   ⟸   ENSRNOT00000066744
RefSeq Acc Id: ENSRNOP00000088064   ⟸   ENSRNOT00000119664
RefSeq Acc Id: XP_063127646   ⟸   XM_063271576
- Peptide Label: isoform X2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZEY3-F1-model_v2 AlphaFold D3ZEY3 1-201 view protein structure
AF-Q3KR78-F1-model_v2 AlphaFold Q3KR78 1-231 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:1561076 AgrOrtholog
BioCyc Gene G2FUF-19995 BioCyc
Ensembl Genes ENSRNOG00000058563 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066744.4 UniProtKB/TrEMBL
  ENSRNOT00000080489 ENTREZGENE
  ENSRNOT00000080489.2 UniProtKB/TrEMBL
  ENSRNOT00000119664.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7453404 IMAGE-MGC_LOAD
InterPro Cell_cycle_regulatory_Spy1 UniProtKB/TrEMBL
KEGG Report rno:498146 UniProtKB/TrEMBL
MGC_CLONE MGC:125213 IMAGE-MGC_LOAD
NCBI Gene 498146 ENTREZGENE
PANTHER PTHR31156 UniProtKB/TrEMBL
  SPEEDY PROTEIN E4 UniProtKB/TrEMBL
Pfam Spy1 UniProtKB/TrEMBL
PhenoGen Spdye4 PhenoGen
RatGTEx ENSRNOG00000058563 RatGTEx
UniProt A0A8I6A4C0 ENTREZGENE, UniProtKB/TrEMBL
  A6K1M3 ENTREZGENE, UniProtKB/TrEMBL
  A6K1M4 ENTREZGENE, UniProtKB/TrEMBL
  D3ZEY3 ENTREZGENE, UniProtKB/TrEMBL
  Q3KR78 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-15 Spdye4  speedy/RINGO cell cycle regulator family member E4  Spdye4  speedy homolog E4 (Xenopus laevis)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-23 Spdye4  speedy homolog E4 (Xenopus laevis)  MGC125213  similar to speedy B isoform  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 MGC125213  similar to speedy B isoform      Symbol and Name status set to provisional 70820 PROVISIONAL