Human Gene DDX54 (uc001tup.3) Description and Page Index
  Description: Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 54 (DDX54), transcript variant 2, mRNA.
RefSeq Summary (NM_024072): This gene encodes a member of the DEAD box protein family. DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. The nucleolar protein encoded by this gene interacts in a hormone-dependent manner with nuclear receptors, and represses their transcriptional activity. Alternative splice variants that encode different isoforms have been found for this gene. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr12:113,594,978-113,623,284 Size: 28,307 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr12:113,596,682-113,623,256 Size: 26,575 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:113,594,978-113,623,284)mRNA (may differ from genome)Protein (881 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIneXtProt
OMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: DDX54_HUMAN
DESCRIPTION: RecName: Full=ATP-dependent RNA helicase DDX54; EC=3.6.4.13; AltName: Full=ATP-dependent RNA helicase DP97; AltName: Full=DEAD box RNA helicase 97 kDa; AltName: Full=DEAD box protein 54;
FUNCTION: Has RNA-dependent ATPase activity. Represses the transcriptional activity of nuclear receptors.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: Interacts in a hormone-dependent manner with nuclear receptors.
SUBCELLULAR LOCATION: Nucleus, nucleolus.
SIMILARITY: Belongs to the DEAD box helicase family. DDX54/DBP10 subfamily.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.
SEQUENCE CAUTION: Sequence=AAN59978.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the N-terminal part;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 34.12 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 840.01 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -6.5028-0.232 Picture PostScript Text
3' UTR -697.361704-0.409 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR012541 - DBP10CT
IPR011545 - DNA/RNA_helicase_DEAD/DEAH_N
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR000629 - RNA-helicase_DEAD-box_CS
IPR014014 - RNA_helicase_DEAD_Q_motif

Pfam Domains:
PF00270 - DEAD/DEAH box helicase
PF00271 - Helicase conserved C-terminal domain
PF04851 - Type III restriction enzyme, res subunit
PF08147 - DBP10CT (NUC160) domain

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases

ModBase Predicted Comparative 3D Structure on Q8TDD1
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene Details   Gene Details 
Gene Sorter   Gene Sorter 
    WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003714 transcription corepressor activity
GO:0003723 RNA binding
GO:0004004 ATP-dependent RNA helicase activity
GO:0004386 helicase activity
GO:0005102 receptor binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0030331 estrogen receptor binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006396 RNA processing
GO:0010501 RNA secondary structure unwinding
GO:0016070 RNA metabolic process
GO:0030520 intracellular estrogen receptor signaling pathway
GO:1903507 negative regulation of nucleic acid-templated transcription

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  BC005848 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 54, mRNA (cDNA clone IMAGE:2958804), partial cds.
AF478457 - Homo sapiens ATP-dependent RNA helicase mRNA, complete cds.
JD273161 - Sequence 254185 from Patent EP1572962.
JD051251 - Sequence 32275 from Patent EP1572962.
JD323446 - Sequence 304470 from Patent EP1572962.
JD182882 - Sequence 163906 from Patent EP1572962.
JD447914 - Sequence 428938 from Patent EP1572962.
JD175772 - Sequence 156796 from Patent EP1572962.
JD067784 - Sequence 48808 from Patent EP1572962.
JD193597 - Sequence 174621 from Patent EP1572962.
JD212075 - Sequence 193099 from Patent EP1572962.
JD108766 - Sequence 89790 from Patent EP1572962.
JD492706 - Sequence 473730 from Patent EP1572962.
JD132683 - Sequence 113707 from Patent EP1572962.
JD324574 - Sequence 305598 from Patent EP1572962.
JD040160 - Sequence 21184 from Patent EP1572962.
JD528983 - Sequence 510007 from Patent EP1572962.
JD419043 - Sequence 400067 from Patent EP1572962.
JD209829 - Sequence 190853 from Patent EP1572962.
JD093585 - Sequence 74609 from Patent EP1572962.
JD391356 - Sequence 372380 from Patent EP1572962.
JD108485 - Sequence 89509 from Patent EP1572962.
JD465977 - Sequence 447001 from Patent EP1572962.
JD190694 - Sequence 171718 from Patent EP1572962.
JD099850 - Sequence 80874 from Patent EP1572962.
JD148827 - Sequence 129851 from Patent EP1572962.
JD469860 - Sequence 450884 from Patent EP1572962.
JD361717 - Sequence 342741 from Patent EP1572962.
JD457632 - Sequence 438656 from Patent EP1572962.
JD335501 - Sequence 316525 from Patent EP1572962.
JD483597 - Sequence 464621 from Patent EP1572962.
JD278537 - Sequence 259561 from Patent EP1572962.
JD072139 - Sequence 53163 from Patent EP1572962.
JD402438 - Sequence 383462 from Patent EP1572962.
JD408244 - Sequence 389268 from Patent EP1572962.
JD093472 - Sequence 74496 from Patent EP1572962.
JD117488 - Sequence 98512 from Patent EP1572962.
JD089478 - Sequence 70502 from Patent EP1572962.
JD296572 - Sequence 277596 from Patent EP1572962.
LF206951 - JP 2014500723-A/14454: Polycomb-Associated Non-Coding RNAs.
AY148094 - Homo sapiens DEAD box RNA helicase DP97 mRNA, complete cds.
BC001132 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 54, mRNA (cDNA clone IMAGE:2966536), containing frame-shift errors.
BC001848 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 54, mRNA (cDNA clone IMAGE:2966536), containing frame-shift errors.
JD273449 - Sequence 254473 from Patent EP1572962.
JD560384 - Sequence 541408 from Patent EP1572962.
JD074926 - Sequence 55950 from Patent EP1572962.
JD118703 - Sequence 99727 from Patent EP1572962.
JD360912 - Sequence 341936 from Patent EP1572962.
JD045769 - Sequence 26793 from Patent EP1572962.
JD236755 - Sequence 217779 from Patent EP1572962.
JD185495 - Sequence 166519 from Patent EP1572962.
JD231302 - Sequence 212326 from Patent EP1572962.
JD401111 - Sequence 382135 from Patent EP1572962.
JD368307 - Sequence 349331 from Patent EP1572962.
JD396752 - Sequence 377776 from Patent EP1572962.
JD186188 - Sequence 167212 from Patent EP1572962.
JD111069 - Sequence 92093 from Patent EP1572962.
BC156669 - Synthetic construct Homo sapiens clone IMAGE:100062142, MGC:190178 DEAD (Asp-Glu-Ala-Asp) box polypeptide 54 (DDX54) mRNA, encodes complete protein.
JD096504 - Sequence 77528 from Patent EP1572962.
CU674568 - Synthetic construct Homo sapiens gateway clone IMAGE:100018054 5' read DDX54 mRNA.
KJ903140 - Synthetic construct Homo sapiens clone ccsbBroadEn_12534 DDX54 gene, encodes complete protein.
LF359553 - JP 2014500723-A/167056: Polycomb-Associated Non-Coding RNAs.
LF359552 - JP 2014500723-A/167055: Polycomb-Associated Non-Coding RNAs.
LF359551 - JP 2014500723-A/167054: Polycomb-Associated Non-Coding RNAs.
MA442528 - JP 2018138019-A/14454: Polycomb-Associated Non-Coding RNAs.
MA595130 - JP 2018138019-A/167056: Polycomb-Associated Non-Coding RNAs.
MA595129 - JP 2018138019-A/167055: Polycomb-Associated Non-Coding RNAs.
MA595128 - JP 2018138019-A/167054: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: DDX54_HUMAN, NM_024072, NP_076977, Q86YT8, Q8TDD1, Q9BRZ1
UCSC ID: uc001tup.3
RefSeq Accession: NM_024072
Protein: Q8TDD1 (aka DDX54_HUMAN or DX54_HUMAN)
CCDS: CCDS31907.1, CCDS44984.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_024072.3
exon count: 20CDS single in 3' UTR: no RNA size: 4401
ORF size: 2646CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5492.00frame shift in genome: no % Coverage: 99.48
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.