Ccdc54 (coiled-coil domain containing 54) - Rat Genome Database

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Gene: Ccdc54 (coiled-coil domain containing 54) Rattus norvegicus
Analyze
Symbol: Ccdc54
Name: coiled-coil domain containing 54
RGD ID: 1559779
Description: Orthologous to human CCDC54 (coiled-coil domain containing 54); INTERACTS WITH acrylamide; bisphenol A; benzene-1,2,4-triol (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: coiled-coil domain-containing protein 54; LOC498073; RGD1559779; similar to testes development-related NYD-SP17
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
GRCr81163,693,017 - 63,696,114 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1163,692,105 - 63,722,348 (+)EnsemblGRCr8
mRatBN7.21150,224,216 - 50,227,313 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1150,224,190 - 50,227,431 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1158,993,172 - 58,996,269 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01151,654,854 - 51,657,951 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01150,778,927 - 50,782,024 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01152,826,062 - 52,829,159 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1152,828,116 - 52,829,105 (+)Ensemblrn6Rnor6.0
Rnor_5.01155,997,628 - 55,998,894 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41151,401,013 - 51,402,056 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1149,873,824 - 49,876,921 (+)NCBICelera
Cytogenetic Map11q21NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Ccdc54
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81163,693,017 - 63,696,114 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1163,692,105 - 63,722,348 (+)EnsemblGRCr8
mRatBN7.21150,224,216 - 50,227,313 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1150,224,190 - 50,227,431 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1158,993,172 - 58,996,269 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01151,654,854 - 51,657,951 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01150,778,927 - 50,782,024 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01152,826,062 - 52,829,159 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1152,828,116 - 52,829,105 (+)Ensemblrn6Rnor6.0
Rnor_5.01155,997,628 - 55,998,894 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41151,401,013 - 51,402,056 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1149,873,824 - 49,876,921 (+)NCBICelera
Cytogenetic Map11q21NCBI
CCDC54
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383107,377,439 - 107,378,635 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3107,377,439 - 107,378,635 (+)Ensemblhg38GRCh38
GRCh373107,096,286 - 107,097,482 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363108,578,878 - 108,580,171 (+)NCBIBuild 36Build 36hg18NCBI36
Celera3105,492,535 - 105,493,828 (+)NCBICelera
Cytogenetic Map3q13.12NCBI
HuRef3104,469,653 - 104,470,946 (+)NCBIHuRef
CHM1_13107,060,506 - 107,061,799 (+)NCBICHM1_1
T2T-CHM13v2.03110,097,142 - 110,098,338 (+)NCBIT2T-CHM13v2.0
Ccdc54
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391650,410,222 - 50,411,517 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1650,410,220 - 50,411,517 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381650,589,859 - 50,591,154 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1650,589,857 - 50,591,154 (-)Ensemblmm10GRCm38
MGSCv371650,589,972 - 50,591,267 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361650,509,207 - 50,510,502 (-)NCBIMGSCv36mm8
Celera1650,936,873 - 50,938,137 (-)NCBICelera
Cytogenetic Map16B5NCBI
cM Map1631.5NCBI
Ccdc54
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554278,082,515 - 8,083,798 (+)NCBIChiLan1.0ChiLan1.0
CCDC54
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22105,358,651 - 105,364,601 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan13105,363,429 - 105,367,523 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03104,508,649 - 104,511,730 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13111,445,384 - 111,446,680 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3111,445,645 - 111,446,619 (+)EnsemblpanPan2panpan1.1
CCDC54
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13312,684,359 - 12,685,632 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3312,684,585 - 12,685,571 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3312,790,595 - 12,791,866 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03312,850,062 - 12,851,333 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3312,850,286 - 12,851,272 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13312,719,843 - 12,721,114 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03312,785,721 - 12,786,992 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03313,197,782 - 13,199,053 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ccdc54
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602142,100,791 - 142,102,051 (-)NCBIHiC_Itri_2
SpeTri2.0NW_004936645743,784 - 744,770 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCDC54
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13152,158,280 - 152,159,257 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.113152,157,578 - 152,159,927 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
CCDC54
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12273,407,623 - 73,409,100 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2273,407,684 - 73,408,670 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604193,081,511 - 93,082,803 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccdc54
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473142,239,261 - 42,240,845 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Ccdc54
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1434,973,485 - 34,974,477 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ccdc54
37 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:119
Count of miRNA genes:102
Interacting mature miRNAs:108
Transcripts:ENSRNOT00000035340
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)112252474682951192Rat
1598841Memor7Memory QTL 7exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)113330600878306008Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)114644316891443168Rat
1598811Bp291Blood pressure QTL 2911.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)113330600878306008Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)115827236396350770Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)115892833699753367Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)113674945981749459Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)113294306789836615Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)113191546976915469Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)113642841681428416Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)113461876079618760Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)115441539196071021Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)115893182292356038Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)115775483796071021Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112019354996351019Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)113674945981749459Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)113674945981749459Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)113674945981749459Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)115827236396350770Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)115107102196071021Rat
631510Spl2Serum phospholipid level QTL 24.1blood phospholipid amount (VT:0006084)serum phospholipid level (CMO:0001171)112755668572556685Rat

Markers in Region
AI644412  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21150,227,126 - 50,227,235 (+)MAPPERmRatBN7.2
Rnor_6.01152,828,973 - 52,829,081NCBIRnor6.0
Rnor_5.01155,998,708 - 55,998,816UniSTSRnor5.0
RGSC_v3.41151,401,870 - 51,401,978UniSTSRGSC3.4
Celera1149,876,735 - 49,876,843UniSTS
Cytogenetic Map11q21UniSTS


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
4 9 7 64 36 38 16 31 16 2 86 50 2 52 9 34 22 9 9

Sequence


Ensembl Acc Id: ENSRNOT00000035340   ⟹   ENSRNOP00000030424
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1163,692,115 - 63,713,680 (+)Ensembl
mRatBN7.2 Ensembl1150,224,190 - 50,227,431 (+)Ensembl
Rnor_6.0 Ensembl1152,828,116 - 52,829,105 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000162422   ⟹   ENSRNOP00000108551
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1163,692,105 - 63,722,348 (+)Ensembl
RefSeq Acc Id: NM_001398860   ⟹   NP_001385789
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81163,693,017 - 63,696,114 (+)NCBI
mRatBN7.21150,224,216 - 50,227,313 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001385789 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000030424
  ENSRNOP00000030424.3
  ENSRNOP00000108551.1
GenBank Protein QTQ94996 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Acc Id: ENSRNOP00000030424   ⟸   ENSRNOT00000035340
RefSeq Acc Id: NP_001385789   ⟸   NM_001398860
- UniProtKB: D4A958 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000108551   ⟸   ENSRNOT00000162422

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A958-F1-model_v2 AlphaFold D4A958 1-330 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:1559779 AgrOrtholog
BioCyc Gene G2FUF-21447 BioCyc
Ensembl Genes ENSRNOG00000028005 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000035340 ENTREZGENE
  ENSRNOT00000035340.6 UniProtKB/TrEMBL
  ENSRNOT00000162422.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.340 UniProtKB/TrEMBL
InterPro Ccdc54 UniProtKB/TrEMBL
NCBI Gene 498073 ENTREZGENE
PANTHER COILED-COIL DOMAIN-CONTAINING PROTEIN 54 UniProtKB/TrEMBL
  PTHR37880 UniProtKB/TrEMBL
PhenoGen Ccdc54 PhenoGen
RatGTEx ENSRNOG00000028005 RatGTEx
Superfamily-SCOP Bacterial hemolysins UniProtKB/TrEMBL
UniProt D4A958 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-28 Ccdc54  coiled-coil domain containing 54  RGD1559779_predicted  similar to testes development-related NYD-SP17 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1559779_predicted  similar to testes development-related NYD-SP17 (predicted)  LOC498073  similar to testes development-related NYD-SP17  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498073  similar to testes development-related NYD-SP17      Symbol and Name status set to provisional 70820 PROVISIONAL