Ddx54 (DEAD-box helicase 54) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Ddx54 (DEAD-box helicase 54) Heterocephalus glaber
Analyze
Symbol: Ddx54
Name: DEAD-box helicase 54
RGD ID: 18923656
Description: ENCODES a protein that exhibits nuclear estrogen receptor binding (ortholog); signaling receptor binding (ortholog); transcription corepressor activity (ortholog); INVOLVED IN RNA metabolic process (ortholog); RNA processing (ortholog); ASSOCIATED WITH epilepsy (ortholog); intellectual disability (ortholog); Liver Neoplasms (ortholog); FOUND IN Golgi apparatus (ortholog); nucleoplasm (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: ATP-dependent RNA helicase DDX54
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: HetGla 1.0 - Naked Mole-Rat female 1.0 Assembly
Position:
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474719,264,888 - 19,278,934 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474719,264,836 - 19,279,251 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (IEA)
Golgi apparatus  (ISO)
nucleolus  (IEA)
nucleoplasm  (ISO)
nucleus  (IEA)

Molecular Function

References
Additional References at PubMed
PMID:21993625   PMID:22301074  


Genomics

Comparative Map Data
Ddx54
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474719,264,888 - 19,278,934 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474719,264,836 - 19,279,251 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2
DDX54
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812113,157,173 - 113,185,478 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl12113,157,173 - 113,185,479 (-)EnsemblGRCh38hg38GRCh38
GRCh3712113,594,978 - 113,623,283 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3612112,079,361 - 112,107,667 (-)NCBINCBI36Build 36hg18NCBI36
Build 3412112,057,698 - 112,086,004NCBI
Celera12113,221,967 - 113,250,107 (-)NCBICelera
Cytogenetic Map12q24.13NCBI
HuRef12110,607,691 - 110,635,997 (-)NCBIHuRef
CHM1_112113,563,241 - 113,591,547 (-)NCBICHM1_1
T2T-CHM13v2.012113,133,817 - 113,162,122 (-)NCBIT2T-CHM13v2.0
Ddx54
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395120,751,182 - 120,766,657 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5120,750,804 - 120,766,657 (+)EnsemblGRCm39 Ensembl
GRCm385120,613,082 - 120,628,592 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5120,612,739 - 120,628,592 (+)EnsemblGRCm38mm10GRCm38
MGSCv375121,063,139 - 121,078,601 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365120,873,747 - 120,889,209 (+)NCBIMGSCv36mm8
Celera5117,698,330 - 117,713,837 (+)NCBICelera
Cytogenetic Map5FNCBI
cM Map560.63NCBI
Ddx54
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81241,595,298 - 41,610,560 (-)NCBIGRCr8
mRatBN7.21235,934,713 - 35,949,956 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1235,934,716 - 35,972,523 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1237,115,128 - 37,129,581 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01237,726,345 - 37,740,799 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01236,778,808 - 36,793,262 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01241,469,642 - 41,484,887 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1241,470,557 - 41,485,122 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01243,327,743 - 43,343,059 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41237,103,084 - 37,117,525 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1237,596,914 - 37,611,356 (-)NCBICelera
Cytogenetic Map12q16NCBI
Ddx54
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554829,494,188 - 9,509,872 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554829,493,840 - 9,509,916 (-)NCBIChiLan1.0ChiLan1.0
DDX54
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v210121,247,419 - 121,274,468 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan112121,243,816 - 121,270,866 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v012110,763,319 - 110,790,364 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.112114,144,659 - 114,173,129 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12114,144,664 - 114,173,127 (-)Ensemblpanpan1.1panPan2
DDX54
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12610,562,773 - 10,568,631 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2610,550,019 - 10,568,763 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2610,669,034 - 10,690,854 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02610,791,136 - 10,812,857 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2610,792,176 - 10,813,194 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12610,764,808 - 10,786,758 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02610,827,627 - 10,849,426 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02610,876,383 - 10,898,344 (-)NCBIUU_Cfam_GSD_1.0
Ddx54
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118148,563,980 - 148,575,846 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366683,061,796 - 3,075,426 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366683,062,868 - 3,074,769 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DDX54
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1438,645,891 - 38,668,265 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11438,650,660 - 38,668,266 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21441,110,096 - 41,123,364 (-)NCBISscrofa10.2Sscrofa10.2susScr3
DDX54
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.111108,407,623 - 108,437,188 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl11108,404,719 - 108,437,168 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037136,661,013 - 136,687,963 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSHGLT00000020333   ⟹   ENSHGLP00000020132
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_00462474719,264,888 - 19,278,934 (+)Ensembl
RefSeq Acc Id: XM_004843746   ⟹   XP_004843803
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462474719,264,837 - 19,279,251 (+)NCBI
RefSeq Acc Id: XM_004843747   ⟹   XP_004843804
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462474719,264,837 - 19,279,251 (+)NCBI
RefSeq Acc Id: XM_004843748   ⟹   XP_004843805
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462474719,264,836 - 19,279,251 (+)NCBI
RefSeq Acc Id: XM_021257448   ⟹   XP_021113107
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462474719,264,836 - 19,278,675 (+)NCBI
Protein Sequences
Protein RefSeqs XP_004843803 (Get FASTA)   NCBI Sequence Viewer  
  XP_004843804 (Get FASTA)   NCBI Sequence Viewer  
  XP_004843805 (Get FASTA)   NCBI Sequence Viewer  
  XP_021113107 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EHA97657 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSHGLP00000020132
GenBank Protein JAN97656 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: XP_004843805   ⟸   XM_004843748
- Peptide Label: isoform X4
- UniProtKB: A0AAX6P5B4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_021113107   ⟸   XM_021257448
- Peptide Label: isoform X2
- UniProtKB: A0AAX6SZ54 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_004843803   ⟸   XM_004843746
- Peptide Label: isoform X1
- UniProtKB: A0AAX6P4X2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_004843804   ⟸   XM_004843747
- Peptide Label: isoform X3
- UniProtKB: G5AKW4 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSHGLP00000020132   ⟸   ENSHGLT00000020333


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSHGLG00000014411 Ensembl, ENTREZGENE
Ensembl Transcript ENSHGLT00000020333 ENTREZGENE
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
InterPro DBP10_C UniProtKB/TrEMBL
  DDX54/DBP10 UniProtKB/TrEMBL
  DEAD/DEAH_box_helicase_dom UniProtKB/TrEMBL
  DEAD_box_RNA_helicase UniProtKB/TrEMBL
  Helicase_ATP-bd UniProtKB/TrEMBL
  Helicase_C UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  RNA-helicase_DEAD-box_CS UniProtKB/TrEMBL
  RNA_helicase_DEAD_Q_motif UniProtKB/TrEMBL
NCBI Gene Ddx54 ENTREZGENE
PANTHER ATP-DEPENDENT RNA HELICASE RHLE-RELATED UniProtKB/TrEMBL
  RNA HELICASE UniProtKB/TrEMBL
Pfam DBP10CT UniProtKB/TrEMBL
  DEAD UniProtKB/TrEMBL
  Helicase_C UniProtKB/TrEMBL
PROSITE DEAD_ATP_HELICASE UniProtKB/TrEMBL
  HELICASE_ATP_BIND_1 UniProtKB/TrEMBL
  HELICASE_CTER UniProtKB/TrEMBL
  Q_MOTIF UniProtKB/TrEMBL
SMART DBP10CT UniProtKB/TrEMBL
  DEXDc UniProtKB/TrEMBL
  HELICc UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A0AAX6P4X2 ENTREZGENE, UniProtKB/TrEMBL
  A0AAX6P5B4 ENTREZGENE, UniProtKB/TrEMBL
  A0AAX6SZ54 ENTREZGENE, UniProtKB/TrEMBL
  G5AKW4 ENTREZGENE, UniProtKB/TrEMBL