Human Gene DDX23 (uc001rsm.3) Description and Page Index
  Description: Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 23 (DDX23), mRNA.
RefSeq Summary (NM_004818): 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 protein encoded by this gene is a component of the U5 snRNP complex; it may facilitate conformational changes in the spliceosome during nuclear pre-mRNA splicing. An alternatively spliced transcript variant has been found for this gene, but its biological validity has not been determined. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AF026402.1, SRR1660805.154689.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000308025.8/ ENSP00000310723.2 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr12:49,223,539-49,245,957 Size: 22,419 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg19 chr12:49,224,252-49,239,565 Size: 15,314 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:49,223,539-49,245,957)mRNA (may differ from genome)Protein (820 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: DDX23_HUMAN
DESCRIPTION: RecName: Full=Probable ATP-dependent RNA helicase DDX23; EC=3.6.4.13; AltName: Full=100 kDa U5 snRNP-specific protein; AltName: Full=DEAD box protein 23; AltName: Full=PRP28 homolog; AltName: Full=U5-100kD;
FUNCTION: Involved in pre-mRNA splicing and its phosphorylated form (by SRPK2) is required for spliceosomal B complex formation.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: The phosphorylated form (by SRPK2) associates wth tri- snRNP (U4/U6-U5 tri-small nuclear ribonucleoproteins). Identified in the spliceosome C complex. Interacts with ERBB4.
SUBCELLULAR LOCATION: Nucleus.
PTM: In vitro phosphorylated by CLK1 and U1 snRNP-associated protein kinase. Phosphorylated by SRPK2 and this phosphorylation is required for its association with the tri-snRNP (U4/U6-U5 tri- small nuclear ribonucleoproteins) and subsequent spliceosomal B complex formation.
SIMILARITY: Belongs to the DEAD box helicase family. DDX23/PRP28 subfamily.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.

-  MalaCards Disease Associations
  MalaCards Gene Search: DDX23
Diseases sorted by gene-association score: distal hereditary motor neuropathy, type ii (3)

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 36.85 RPKM in Spleen
Total median expression: 1184.44 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -31.2091-0.343 Picture PostScript Text
3' UTR -272.20713-0.382 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
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

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

ModBase Predicted Comparative 3D Structure on Q9BUQ8
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0004004 ATP-dependent RNA helicase activity
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0008026 ATP-dependent helicase activity

Biological Process:
GO:0000354 cis assembly of pre-catalytic spliceosome
GO:0000375 RNA splicing, via transesterification reactions
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0010501 RNA secondary structure unwinding

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005682 U5 snRNP
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0070062 extracellular exosome
GO:0071013 catalytic step 2 spliceosome


-  Descriptions from all associated GenBank mRNAs
  AF026402 - Homo sapiens U5 snRNP 100 kD protein mRNA, complete cds.
AK128428 - Homo sapiens cDNA FLJ46571 fis, clone THYMU3041428, highly similar to Probable ATP-dependent RNA helicase DDX23 (EC 3.6.1.-).
BC002366 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 23, mRNA (cDNA clone MGC:8416 IMAGE:2820898), complete cds.
JD546628 - Sequence 527652 from Patent EP1572962.
JD061035 - Sequence 42059 from Patent EP1572962.
JD332850 - Sequence 313874 from Patent EP1572962.
AK292921 - Homo sapiens cDNA FLJ77678 complete cds, highly similar to Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 23, mRNA.
JD314646 - Sequence 295670 from Patent EP1572962.
JD137800 - Sequence 118824 from Patent EP1572962.
JD196600 - Sequence 177624 from Patent EP1572962.
JD250976 - Sequence 232000 from Patent EP1572962.
JD218612 - Sequence 199636 from Patent EP1572962.
JD278481 - Sequence 259505 from Patent EP1572962.
JD283045 - Sequence 264069 from Patent EP1572962.
JD043500 - Sequence 24524 from Patent EP1572962.
AK312379 - Homo sapiens cDNA, FLJ92706, highly similar to Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 23 (DDX23),mRNA.
KJ892765 - Synthetic construct Homo sapiens clone ccsbBroadEn_02159 DDX23 gene, encodes complete protein.
DQ891425 - Synthetic construct clone IMAGE:100004055; FLH176808.01X; RZPDo839H07122D DEAD (Asp-Glu-Ala-Asp) box polypeptide 23 (DDX23) gene, encodes complete protein.
DQ894599 - Synthetic construct Homo sapiens clone IMAGE:100009059; FLH176804.01L; RZPDo839H07121D DEAD (Asp-Glu-Ala-Asp) box polypeptide 23 (DDX23) gene, encodes complete protein.
JD024103 - Sequence 5127 from Patent EP1572962.
JD034317 - Sequence 15341 from Patent EP1572962.
AK294877 - Homo sapiens cDNA FLJ54028 complete cds, highly similar to Probable ATP-dependent RNA helicase DDX23 (EC 3.6.1.-).
CU677932 - Synthetic construct Homo sapiens gateway clone IMAGE:100023253 5' read DDX23 mRNA.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03040 - Spliceosome

Reactome (by CSHL, EBI, and GO)

Protein Q9BUQ8 (Reactome details) participates in the following event(s):

R-HSA-75083 ATAC spliceosome mediated 3' splice site cleavage, exon ligation
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-75081 Formation of AT-AC B Complex
R-HSA-75082 ATAC spliceosome mediated Lariat formation,5' splice site cleavage
R-HSA-75079 Formation of AT-AC C complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72165 mRNA Splicing - Minor Pathway
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: B2R600, DDX23_HUMAN, NM_004818, NP_004809, O43188, Q9BUQ8
UCSC ID: uc001rsm.3
RefSeq Accession: NM_004818
Protein: Q9BUQ8 (aka DDX23_HUMAN)
CCDS: CCDS8770.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_004818.2
exon count: 17CDS single in 3' UTR: no RNA size: 3288
ORF size: 2463CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5102.00frame shift in genome: no % Coverage: 99.36
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.