CDC40 (cell division cycle 40) - Rat Genome Database
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Gene: CDC40 (cell division cycle 40) Homo sapiens
Analyze
Symbol: CDC40
Name: cell division cycle 40
RGD ID: 1316032
HGNC Page HGNC
Description: Exhibits RNA binding activity. Involved in mRNA splicing, via spliceosome. Localizes to U2-type catalytic step 2 spliceosome and nuclear speck.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: cell division cycle 40 homolog; cell division cycle 40 homolog (yeast); EH-binding protein 3; EHB3; FLJ10564; hPRP17; MGC102802; pre-mRNA splicing factor 17; pre-mRNA-processing factor 17; PRP17; PRP17 homolog; PRPF17
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6110,180,141 - 110,254,275 (+)EnsemblGRCh38hg38GRCh38
GRCh386110,180,427 - 110,232,232 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh376110,501,624 - 110,553,423 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366110,608,317 - 110,660,116 (+)NCBINCBI36hg18NCBI36
Build 346110,608,316 - 110,660,113NCBI
Celera6111,248,290 - 111,300,016 (+)NCBI
Cytogenetic Map6q21NCBI
HuRef6108,068,262 - 108,120,175 (+)NCBIHuRef
CHM1_16110,764,827 - 110,816,626 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Additional References at PubMed
PMID:7568168   PMID:8125298   PMID:8889548   PMID:9303539   PMID:9524131   PMID:9769104   PMID:9830021   PMID:11102353   PMID:11991638   PMID:12226669   PMID:12477932   PMID:14574404  
PMID:14702039   PMID:15489334   PMID:15761153   PMID:17081983   PMID:18976975   PMID:19420964   PMID:20360068   PMID:20508642   PMID:21873635   PMID:22365833   PMID:22658674   PMID:23084401  
PMID:24457600   PMID:26186194   PMID:26344197   PMID:26496610   PMID:26949251   PMID:27349221   PMID:28076346   PMID:28077445   PMID:28431233   PMID:28514442   PMID:28561026   PMID:29298432  
PMID:29395067   PMID:29467282   PMID:29509190   PMID:29773831   PMID:30033366   PMID:30404004   PMID:30463901   PMID:30804502   PMID:30948266   PMID:31091453   PMID:31300519   PMID:31586073  
PMID:32780723   PMID:32877691  


Genomics

Comparative Map Data
CDC40
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6110,180,141 - 110,254,275 (+)EnsemblGRCh38hg38GRCh38
GRCh386110,180,427 - 110,232,232 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh376110,501,624 - 110,553,423 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366110,608,317 - 110,660,116 (+)NCBINCBI36hg18NCBI36
Build 346110,608,316 - 110,660,113NCBI
Celera6111,248,290 - 111,300,016 (+)NCBI
Cytogenetic Map6q21NCBI
HuRef6108,068,262 - 108,120,175 (+)NCBIHuRef
CHM1_16110,764,827 - 110,816,626 (+)NCBICHM1_1
Cdc40
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391040,707,617 - 40,759,139 (-)NCBIGRCm39mm39
GRCm381040,831,621 - 40,883,143 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1040,831,621 - 40,883,311 (-)EnsemblGRCm38mm10GRCm38
MGSCv371040,552,699 - 40,602,949 (-)NCBIGRCm37mm9NCBIm37
MGSCv361040,520,036 - 40,571,776 (-)NCBImm8
Celera1041,729,015 - 41,779,240 (-)NCBICelera
Cytogenetic Map10B1NCBI
Cdc40
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.02048,503,973 - 48,574,546 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2048,503,973 - 48,574,546 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02050,156,108 - 50,219,888 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42044,952,482 - 44,974,587 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12044,975,493 - 44,998,090 (-)NCBI
Celera2045,080,203 - 45,130,581 (-)NCBICelera
Cytogenetic Map20q13NCBI
Cdc40
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541134,966,339 - 35,007,558 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541134,966,797 - 35,007,577 (+)NCBIChiLan1.0ChiLan1.0
CDC40
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16112,058,835 - 112,108,985 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6112,058,835 - 112,131,813 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06107,989,176 - 108,040,790 (+)NCBIMhudiblu_PPA_v0panPan3
CDC40
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1266,897,412 - 66,949,366 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11266,897,953 - 66,950,131 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Cdc40
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1176,179,169 - 76,234,690 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2185,659,401 - 85,714,982 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CDC40
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11363,666,294 - 63,718,628 (-)NCBI
ChlSab1.1 Ensembl1363,666,294 - 63,718,521 (-)Ensembl
Cdc40
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249161,302,294 - 1,353,487 (+)NCBI

Position Markers
CDC40_2301  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh376110,552,722 - 110,553,463UniSTSGRCh37
Build 366110,659,415 - 110,660,156RGDNCBI36
Celera6111,299,315 - 111,300,056RGD
HuRef6108,119,474 - 108,120,215UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:2154
Count of miRNA genes:685
Interacting mature miRNAs:781
Transcripts:ENST00000307731, ENST00000368930, ENST00000368932, ENST00000431461, ENST00000445340, ENST00000453107, ENST00000606893
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.


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 sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 811 1153 1063 122 1176 69 2355 369 1595 193 1101 1265 68 1 657 1447 5 2
Low 1628 1830 663 502 773 396 2002 1822 2137 225 359 348 106 547 1341 1
Below cutoff 8 2 6 2 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000307731   ⟹   ENSP00000304370
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl6110,180,427 - 110,232,232 (+)Ensembl
RefSeq Acc Id: ENST00000368930   ⟹   ENSP00000357926
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl6110,180,421 - 110,254,275 (+)Ensembl
RefSeq Acc Id: ENST00000368932   ⟹   ENSP00000357928
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl6110,180,141 - 110,232,223 (+)Ensembl
RefSeq Acc Id: ENST00000431461
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl6110,201,605 - 110,209,316 (+)Ensembl
RefSeq Acc Id: ENST00000445340
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl6110,224,296 - 110,231,671 (+)Ensembl
RefSeq Acc Id: ENST00000453107
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl6110,198,975 - 110,209,112 (+)Ensembl
RefSeq Acc Id: ENST00000606893
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl6110,180,141 - 110,230,333 (+)Ensembl
RefSeq Acc Id: NM_015891   ⟹   NP_056975
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh386110,180,427 - 110,232,232 (+)NCBI
GRCh376110,501,624 - 110,553,423 (+)RGD
Build 366110,608,317 - 110,660,116 (+)NCBI Archive
Celera6111,248,290 - 111,300,016 (+)RGD
HuRef6108,068,262 - 108,120,175 (+)ENTREZGENE
CHM1_16110,764,827 - 110,816,626 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_056975   ⟸   NM_015891
- UniProtKB: O60508 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000304370   ⟸   ENST00000307731
RefSeq Acc Id: ENSP00000357926   ⟸   ENST00000368930
RefSeq Acc Id: ENSP00000357928   ⟸   ENST00000368932
Protein Domains
WD_REPEATS_REGION

Promoters
RGD ID:7208879
Promoter ID:EPDNEW_H10185
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:
Human AssemblyChrPosition (strand)Source
GRCh386110,180,427 - 110,180,487EPDNEW
RGD ID:6804026
Promoter ID:HG_KWN:54622
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   K562,   Lymphoblastoid,   NB4
Transcripts:ENST00000265601,   ENST00000368930,   ENST00000368932,   ENST00000368933,   ENST00000368938,   ENST00000392586,   NM_001024934,   NM_001024935,   NM_001024936,   NM_003931,   OTTHUMT00000041785,   OTTHUMT00000041787,   OTTHUMT00000041788,   UC003PTZ.1,   UC003PUA.1
Position:
Human AssemblyChrPosition (strand)Source
Build 366110,606,726 - 110,608,477 (-)MPROMDB

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 6q21-23.2(chr6:108944899-132067720)x1 copy number loss See cases [RCV000051196] Chr6:108944899..132067720 [GRCh38]
Chr6:109266102..132388860 [GRCh37]
Chr6:109372795..132430553 [NCBI36]
Chr6:6q21-23.2
pathogenic
GRCh38/hg38 6q16.3-21(chr6:102356502-111049879)x1 copy number loss See cases [RCV000134806] Chr6:102356502..111049879 [GRCh38]
Chr6:102804377..111371082 [GRCh37]
Chr6:102911070..111477775 [NCBI36]
Chr6:6q16.3-21
pathogenic
GRCh38/hg38 6q21-22.1(chr6:107370141-115827482)x1 copy number loss See cases [RCV000138006] Chr6:107370141..115827482 [GRCh38]
Chr6:107691345..116148646 [GRCh37]
Chr6:107798038..116255339 [NCBI36]
Chr6:6q21-22.1
pathogenic
GRCh38/hg38 6q21(chr6:109780913-110202309)x1 copy number loss See cases [RCV000140325] Chr6:109780913..110202309 [GRCh38]
Chr6:110102116..110523512 [GRCh37]
Chr6:110208809..110630205 [NCBI36]
Chr6:6q21
uncertain significance
GRCh38/hg38 6q13-24.1(chr6:74382807-142040500)x3 copy number gain See cases [RCV000139729] Chr6:74382807..142040500 [GRCh38]
Chr6:75092523..142361637 [GRCh37]
Chr6:75149243..142403330 [NCBI36]
Chr6:6q13-24.1
pathogenic
GRCh38/hg38 6q16.1-22.31(chr6:96609994-122161548)x1 copy number loss See cases [RCV000139465] Chr6:96609994..122161548 [GRCh38]
Chr6:97057870..122482694 [GRCh37]
Chr6:97164591..122524393 [NCBI36]
Chr6:6q16.1-22.31
pathogenic
GRCh38/hg38 6q21(chr6:107445281-110547907)x1 copy number loss See cases [RCV000141382] Chr6:107445281..110547907 [GRCh38]
Chr6:107766485..110869110 [GRCh37]
Chr6:107873178..110975803 [NCBI36]
Chr6:6q21
pathogenic
GRCh38/hg38 6q21-22.31(chr6:106503719-125781219)x1 copy number loss See cases [RCV000141587] Chr6:106503719..125781219 [GRCh38]
Chr6:106951594..126102365 [GRCh37]
Chr6:107058287..126144058 [NCBI36]
Chr6:6q21-22.31
pathogenic
GRCh38/hg38 6q21(chr6:110020558-111200711)x3 copy number gain See cases [RCV000141546] Chr6:110020558..111200711 [GRCh38]
Chr6:110341761..111521914 [GRCh37]
Chr6:110448454..111628607 [NCBI36]
Chr6:6q21
uncertain significance
GRCh38/hg38 6q16.3-21(chr6:103279465-113934239)x1 copy number loss See cases [RCV000142287] Chr6:103279465..113934239 [GRCh38]
Chr6:103727340..114255403 [GRCh37]
Chr6:103834033..114362096 [NCBI36]
Chr6:6q16.3-21
pathogenic
GRCh38/hg38 6q16.3-22.31(chr6:100054889-120488154)x1 copy number loss See cases [RCV000143227] Chr6:100054889..120488154 [GRCh38]
Chr6:100502765..120809300 [GRCh37]
Chr6:100609486..120850999 [NCBI36]
Chr6:6q16.3-22.31
pathogenic
GRCh37/hg19 6q21(chr6:109564793-112223595)x1 copy number loss See cases [RCV000447293] Chr6:109564793..112223595 [GRCh37]
Chr6:6q21
uncertain significance
GRCh37/hg19 6q14.3-22.31(chr6:85988428-120548687)x1 copy number loss See cases [RCV000445666] Chr6:85988428..120548687 [GRCh37]
Chr6:6q14.3-22.31
pathogenic
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482)x3 copy number gain See cases [RCV000512067] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27
pathogenic
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482) copy number gain See cases [RCV000510595] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27
pathogenic
GRCh37/hg19 6q21(chr6:110419878-111698827)x1 copy number loss not provided [RCV000682707] Chr6:110419878..111698827 [GRCh37]
Chr6:6q21
uncertain significance
GRCh37/hg19 6q16.1-22.1(chr6:95549951-116684929)x1 copy number loss not provided [RCV000682693] Chr6:95549951..116684929 [GRCh37]
Chr6:6q16.1-22.1
pathogenic
GRCh37/hg19 6p25.3-q27(chr6:108666-170980171)x3 copy number gain not provided [RCV000745403] Chr6:108666..170980171 [GRCh37]
Chr6:6p25.3-q27
pathogenic
GRCh37/hg19 6p25.3-q27(chr6:60107-171054786)x3 copy number gain not provided [RCV000745400] Chr6:60107..171054786 [GRCh37]
Chr6:6p25.3-q27
pathogenic
GRCh37/hg19 6p25.3-q27(chr6:165632-170919470)x3 copy number gain not provided [RCV000745404] Chr6:165632..170919470 [GRCh37]
Chr6:6p25.3-q27
pathogenic
GRCh37/hg19 6q21(chr6:109564694-112232351)x1 copy number loss not provided [RCV001007557] Chr6:109564694..112232351 [GRCh37]
Chr6:6q21
uncertain significance
GRCh37/hg19 6q16.3-22.1(chr6:101296547-117004249)x3 copy number gain Microcephaly [RCV001251053] Chr6:101296547..117004249 [GRCh37]
Chr6:6q16.3-22.1
pathogenic
GRCh37/hg19 6q16.1-21(chr6:98949950-114533905)x1 copy number loss Deletion 6q16 q21 [RCV001263224] Chr6:98949950..114533905 [GRCh37]
Chr6:6q16.1-21
pathogenic
GRCh37/hg19 6q21(chr6:110288308-110768384)x3 copy number gain not provided [RCV001259394] Chr6:110288308..110768384 [GRCh37]
Chr6:6q21
uncertain significance

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:17350 AgrOrtholog
COSMIC CDC40 COSMIC
Ensembl Genes ENSG00000168438 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000304370 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000357926 UniProtKB/TrEMBL
  ENSP00000357928 UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000307731 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000368930 UniProtKB/TrEMBL
  ENST00000368932 UniProtKB/Swiss-Prot
Gene3D-CATH 2.130.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000168438 GTEx
HGNC ID HGNC:17350 ENTREZGENE
Human Proteome Map CDC40 Human Proteome Map
InterPro PRPF17 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WD40_repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WD40_repeat_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WD40_repeat_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:51362 UniProtKB/Swiss-Prot
NCBI Gene 51362 ENTREZGENE
OMIM 605585 OMIM
PANTHER PTHR43979 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam WD40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA134891332 PharmGKB
PROSITE WD_REPEATS_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WD_REPEATS_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WD_REPEATS_REGION UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART WD40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50978 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt H0UI46_HUMAN UniProtKB/TrEMBL
  O60508 ENTREZGENE, UniProtKB/Swiss-Prot
  Q2TA76_HUMAN UniProtKB/TrEMBL
  Q5SRN1_HUMAN UniProtKB/TrEMBL
UniProt Secondary B2RBC5 UniProtKB/Swiss-Prot
  O75471 UniProtKB/Swiss-Prot
  Q5SRN0 UniProtKB/Swiss-Prot
  Q9UPG1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-01-22 CDC40  cell division cycle 40    cell division cycle 40 homolog (S. cerevisiae)  Symbol and/or name change 5135510 APPROVED
2011-09-01 CDC40  cell division cycle 40 homolog (S. cerevisiae)  CDC40  cell division cycle 40 homolog (S. cerevisiae)  Symbol and/or name change 5135510 APPROVED