Cdc40 (cell division cycle 40) - Rat Genome Database

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Gene: Cdc40 (cell division cycle 40) Rattus norvegicus
Analyze
Symbol: Cdc40
Name: cell division cycle 40
RGD ID: 1307063
Description: Predicted to enable mRNA binding activity. Predicted to be involved in embryonic brain development and mRNA splicing, via spliceosome. Predicted to be located in nuclear speck. Predicted to be part of U2-type catalytic step 2 spliceosome. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 15. Orthologous to human CDC40 (cell division cycle 40); PARTICIPATES IN spliceosome pathway; INTERACTS WITH atrazine; bisphenol A; cadmium dichloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cell division cycle 40 homolog; cell division cycle 40 homolog (S. cerevisiae); cell division cycle 40 homolog (yeast); LOC361859; pre-mRNA-processing factor 17
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82045,855,739 - 45,908,239 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2045,855,739 - 45,907,978 (-)EnsemblGRCr8
mRatBN7.22044,273,080 - 44,325,605 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2044,273,089 - 44,325,358 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2046,057,606 - 46,109,850 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02045,716,758 - 45,769,005 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02046,439,399 - 46,491,699 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02048,503,973 - 48,574,546 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2048,503,973 - 48,574,546 (+)Ensemblrn6Rnor6.0
Rnor_5.02050,156,108 - 50,219,888 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42044,952,482 - 44,974,587 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2045,080,203 - 45,130,581 (-)NCBICelera
RGSC_v3.12044,975,493 - 44,998,090 (-)NCBI
Cytogenetic Map20q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9830021   PMID:11991638   PMID:12477932   PMID:22658674   PMID:28076346  


Genomics

Comparative Map Data
Cdc40
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82045,855,739 - 45,908,239 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2045,855,739 - 45,907,978 (-)EnsemblGRCr8
mRatBN7.22044,273,080 - 44,325,605 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2044,273,089 - 44,325,358 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2046,057,606 - 46,109,850 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02045,716,758 - 45,769,005 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02046,439,399 - 46,491,699 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02048,503,973 - 48,574,546 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2048,503,973 - 48,574,546 (+)Ensemblrn6Rnor6.0
Rnor_5.02050,156,108 - 50,219,888 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42044,952,482 - 44,974,587 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2045,080,203 - 45,130,581 (-)NCBICelera
RGSC_v3.12044,975,493 - 44,998,090 (-)NCBI
Cytogenetic Map20q12NCBI
CDC40
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386110,180,427 - 110,232,232 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6110,180,141 - 110,254,275 (+)Ensemblhg38GRCh38
GRCh376110,501,630 - 110,553,435 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366110,608,317 - 110,660,116 (+)NCBIBuild 36Build 36hg18NCBI36
Build 346110,608,316 - 110,660,113NCBI
Celera6111,248,290 - 111,300,016 (+)NCBICelera
Cytogenetic Map6q21NCBI
HuRef6108,068,262 - 108,120,175 (+)NCBIHuRef
CHM1_16110,764,827 - 110,816,626 (+)NCBICHM1_1
T2T-CHM13v2.06111,358,498 - 111,410,681 (+)NCBIT2T-CHM13v2.0
Cdc40
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391040,707,617 - 40,759,139 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1040,707,617 - 40,759,307 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381040,831,621 - 40,883,143 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1040,831,621 - 40,883,311 (-)Ensemblmm10GRCm38
MGSCv371040,552,699 - 40,602,949 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361040,520,036 - 40,571,776 (-)NCBIMGSCv36mm8
Celera1041,729,015 - 41,779,240 (-)NCBICelera
Cytogenetic Map10B1NCBI
cM Map1022.06NCBI
Cdc40
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541134,966,339 - 35,007,558 (+)Ensembl
ChiLan1.0NW_00495541134,966,797 - 35,007,577 (+)NCBIChiLan1.0ChiLan1.0
CDC40
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25130,193,290 - 130,246,419 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16128,079,212 - 128,132,327 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06107,989,176 - 108,040,790 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16112,058,835 - 112,108,985 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6112,058,835 - 112,131,813 (+)EnsemblpanPan2panpan1.1
CDC40
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11266,897,953 - 66,950,131 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1266,897,412 - 66,949,366 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1266,717,460 - 66,769,671 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01267,782,001 - 67,834,254 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1267,780,399 - 67,834,251 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11267,133,353 - 67,185,550 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01266,979,811 - 67,032,023 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01267,251,589 - 67,303,808 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Cdc40
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946101,821,254 - 101,868,091 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365646,096,167 - 6,143,213 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365646,096,180 - 6,143,852 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDC40
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl176,179,164 - 76,232,959 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1176,179,169 - 76,234,690 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2185,659,401 - 85,714,982 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CDC40
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11363,666,294 - 63,718,628 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1363,666,294 - 63,718,521 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604035,954,432 - 36,004,665 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cdc40
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249161,302,420 - 1,352,986 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046249161,302,294 - 1,353,487 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Cdc40
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11840,578,110 - 40,630,406 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Cdc40
431 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:168
Count of miRNA genes:116
Interacting mature miRNAs:140
Transcripts:ENSRNOT00000064081
Prediction methods:Miranda, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202668936256021148Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)20418947649189476Rat
1598858Cm61Cardiac mass QTL 613.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)20821635953216359Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20153308346533083Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202679235356021148Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)201224324249189476Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202668936256021148Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202074558556021148Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202668936256021148Rat
1598870Bp289Blood pressure QTL 2892.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)20821635953216359Rat
70158Bp60Blood pressure QTL 603arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)203215696745978663Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202668936256021148Rat

Markers in Region
BG372291  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22044,264,431 - 44,264,612 (-)MAPPERmRatBN7.2
Rnor_6.02048,583,023 - 48,583,203NCBIRnor6.0
Rnor_6.02048,527,912 - 48,528,092NCBIRnor6.0
Rnor_5.02050,228,362 - 50,228,542UniSTSRnor5.0
Rnor_5.02050,177,706 - 50,177,886UniSTSRnor5.0
RGSC_v3.42044,943,825 - 44,944,005UniSTSRGSC3.4
Celera2045,071,546 - 45,071,726UniSTS
RH 3.4 Map20479.7UniSTS
Cytogenetic Map20q12UniSTS
RH143599  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.02050,196,635 - 50,196,841NCBIRnor5.0
RGSC_v3.42044,975,383 - 44,975,601UniSTSRGSC3.4
Celera2045,102,531 - 45,102,749UniSTS
RH 3.4 Map20469.7UniSTS
Cytogenetic Map20q12UniSTS
RH140230  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22044,306,843 - 44,307,041 (-)MAPPERmRatBN7.2
Rnor_6.02048,523,752 - 48,523,949NCBIRnor6.0
Rnor_5.02050,173,546 - 50,173,743UniSTSRnor5.0
Celera2045,111,846 - 45,112,043UniSTS
RH 3.4 Map20476.3UniSTS
Cytogenetic Map20q12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000064081   ⟹   ENSRNOP00000058923
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2044,273,089 - 44,294,722 (-)Ensembl
Rnor_6.0 Ensembl2048,503,973 - 48,574,546 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000077926   ⟹   ENSRNOP00000069760
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2045,855,739 - 45,907,978 (-)Ensembl
mRatBN7.2 Ensembl2044,273,093 - 44,325,358 (-)Ensembl
Rnor_6.0 Ensembl2048,552,289 - 48,574,538 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000087740   ⟹   ENSRNOP00000071389
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2048,504,264 - 48,573,218 (+)Ensembl
RefSeq Acc Id: NM_001394220   ⟹   NP_001381149
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82045,855,739 - 45,907,978 (-)NCBI
mRatBN7.22044,273,090 - 44,325,335 (-)NCBI
RefSeq Acc Id: XM_063279319   ⟹   XP_063135389
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82045,858,052 - 45,908,239 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001381149 (Get FASTA)   NCBI Sequence Viewer  
  XP_063135389 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI66724 (Get FASTA)   NCBI Sequence Viewer  
  EDL83241 (Get FASTA)   NCBI Sequence Viewer  
  EDL83242 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000069760
  ENSRNOP00000069760.2
Ensembl Acc Id: ENSRNOP00000071389   ⟸   ENSRNOT00000087740
Ensembl Acc Id: ENSRNOP00000069760   ⟸   ENSRNOT00000077926
Ensembl Acc Id: ENSRNOP00000058923   ⟸   ENSRNOT00000064081
RefSeq Acc Id: NP_001381149   ⟸   NM_001394220
- UniProtKB: A0A0G2JW64 (UniProtKB/TrEMBL),   B2RYC1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135389   ⟸   XM_063279319
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K0C5-F1-model_v2 AlphaFold A0A0G2K0C5 1-579 view protein structure

Transcriptome

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

Promoters
RGD ID:13701684
Promoter ID:EPDNEW_R12202
Type:initiation region
Name:Cdc40_1
Description:cell division cycle 40
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_6.02048,504,244 - 48,504,304EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307063 AgrOrtholog
BioCyc Gene G2FUF-3414 BioCyc
Ensembl Genes ENSRNOG00000000581 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000077926 ENTREZGENE
  ENSRNOT00000077926.3 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7933637 IMAGE-MGC_LOAD
InterPro PRPF17 UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom UniProtKB/TrEMBL
  WD40_repeat UniProtKB/TrEMBL
  WD40_repeat_CS UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/TrEMBL
MGC_CLONE MGC:188440 IMAGE-MGC_LOAD
NCBI Gene 361859 ENTREZGENE
PANTHER PRE-MRNA-PROCESSING FACTOR 17 UniProtKB/TrEMBL
  PTHR43979 UniProtKB/TrEMBL
Pfam WD40 UniProtKB/TrEMBL
PhenoGen Cdc40 PhenoGen
PROSITE WD_REPEATS_1 UniProtKB/TrEMBL
  WD_REPEATS_2 UniProtKB/TrEMBL
  WD_REPEATS_REGION UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000581 RatGTEx
SMART WD40 UniProtKB/TrEMBL
Superfamily-SCOP WD40_like UniProtKB/TrEMBL
UniProt A0A0G2JW64 ENTREZGENE
  B2RYC1 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary A0A0G2JW64 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-01-23 Cdc40  cell division cycle 40  Cdc40  cell division cycle 40 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-26 Cdc40  cell division cycle 40 homolog (S. cerevisiae)  Cdc40  cell division cycle 40 homolog (yeast)   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Cdc40  cell division cycle 40 homolog (yeast)   Cdc40_predicted  cell division cycle 40 homolog (yeast) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Cdc40_predicted  cell division cycle 40 homolog (yeast) (predicted)      Symbol and Name status set to approved 70820 APPROVED