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Aliases for DDX23 Gene

Aliases for DDX23 Gene

  • DEAD-Box Helicase 23 2 3 5
  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 23 2 3
  • 100 KDa U5 SnRNP-Specific Protein 3 4
  • PRP28 Homolog, Yeast 2 3
  • DEAD Box Protein 23 3 4
  • U5-100KD 3 4
  • Probable ATP-Dependent RNA Helicase DDX23 3
  • U5 SnRNP 100 KD Protein 3
  • PRP28p Homolog 3
  • PRP28 Homolog 4
  • EC 3.6.4.13 4
  • SNRNP100 3
  • EC 3.6.1 58
  • U5-100K 3
  • PRPF28 3
  • Prp28 3

External Ids for DDX23 Gene

Previous GeneCards Identifiers for DDX23 Gene

  • GC12M048940
  • GC12M047509
  • GC12M049223
  • GC12M046256

Summaries for DDX23 Gene

Entrez Gene Summary for DDX23 Gene

  • 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]

GeneCards Summary for DDX23 Gene

DDX23 (DEAD-Box Helicase 23) is a Protein Coding gene. Diseases associated with DDX23 include Distal Hereditary Motor Neuropathy, Type Ii. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. GO annotations related to this gene include nucleic acid binding and ATP-dependent RNA helicase activity.

UniProtKB/Swiss-Prot for DDX23 Gene

  • Involved in pre-mRNA splicing and its phosphorylated form (by SRPK2) is required for spliceosomal B complex formation.

Gene Wiki entry for DDX23 Gene

Additional gene information for DDX23 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DDX23 Gene

Genomics for DDX23 Gene

Regulatory Elements for DDX23 Gene

Enhancers for DDX23 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH12H048865 1.1 ENCODE 144 -13.4 -13389 2 HDGF PKNOX1 FOXA2 ZFP64 ARID4B SIN3A FEZF1 ZNF2 YY1 SLC30A9 DDX23 KMT2D KANSL2 LOC390314 CCNT1 LMBR1L SENP1 BCDIN3D PRPF40B ENSG00000257964
GH12H049055 1.7 FANTOM5 ENCODE dbSUPER 84.5 -205.7 -205661 6 FEZF1 DMAP1 YY1 ZNF416 ZNF143 ZNF548 SP3 NFYC ZFP41 MEF2D DDX23 LOC390314 LMBR1L CCNT1 KANSL2 KMT2D SENP1 LOC100422296 PRPF40B OR5BK1P
GH12H049129 1.5 ENCODE dbSUPER 92.3 -278.5 -278525 4 MLX FEZF1 DMAP1 YBX1 YY1 SLC30A9 ZNF416 ZNF143 ZNF548 SP3 DDX23 SMARCD1 LMBR1L LOC390314 KMT2D BCDIN3D PRPF40B KANSL2 CCNT1 LOC100422296
GH12H049263 1.4 ENCODE dbSUPER 76.4 -413.7 -413687 6 DMAP1 YY1 ZNF143 SP3 NFYC ZFP41 MEF2D GLIS1 NBN NR2C1 DDX23 CCNT1 KMT2D LMBR1L KANSL2 LOC390314 SMARCD1 BCDIN3D ENSG00000257298 ENSG00000257964
GH12H048714 1.4 ENCODE dbSUPER 53.4 +136.4 136386 3 MLX DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC MEF2D SSRP1 ZNF610 KANSL2 DDX23 LMBR1L SENP1 KMT2D CCNT1 LOC390314 CCDC184 OR11M1P LALBA
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around DDX23 on UCSC Golden Path with GeneCards custom track

Promoters for DDX23 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000268265 -458 201 TBP HDGF RB1 TBL1XR1 ARID4B DNMT3B RAD21 RFX5 GATA2 ZNF366
ENSR00000051535 842 1601 HDGF PKNOX1 ARNT ARID4B SIN3A YBX1 DMAP1 ZNF2 ZBTB7B YY1

Genomic Location for DDX23 Gene

Chromosome:
12
Start:
48,829,756 bp from pter
End:
48,852,842 bp from pter
Size:
23,087 bases
Orientation:
Minus strand

Genomic View for DDX23 Gene

Genes around DDX23 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DDX23 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DDX23 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DDX23 Gene

Proteins for DDX23 Gene

  • Protein details for DDX23 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BUQ8-DDX23_HUMAN
    Recommended name:
    Probable ATP-dependent RNA helicase DDX23
    Protein Accession:
    Q9BUQ8
    Secondary Accessions:
    • B2R600
    • B4DH15
    • O43188

    Protein attributes for DDX23 Gene

    Size:
    820 amino acids
    Molecular mass:
    95583 Da
    Quaternary structure:
    • The phosphorylated form (by SRPK2) is a component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, WDR57, SNRNP40, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39. Identified in the spliceosome C complex. Interacts with ERBB4.

    Three dimensional structures from OCA and Proteopedia for DDX23 Gene

    Alternative splice isoforms for DDX23 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DDX23 Gene

Selected DME Specific Peptides for DDX23 Gene

Q9BUQ8:
  • PTRELAQQ
  • VLDEADRM
  • VSMVVNYD
  • AETGSGKT
  • HRIGRTGR
  • VIATPGR
  • DEADRMID
  • GVAITFL
  • LAPTREL
  • TGSGKTAAF
  • TPGRLID
  • GRTGRAG
  • APTRELA
  • IATPGRL
  • YIHRIGR

Post-translational modifications for DDX23 Gene

  • 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.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for DDX23 Gene

Domains & Families for DDX23 Gene

Gene Families for DDX23 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for DDX23 Gene

Graphical View of Domain Structure for InterPro Entry

Q9BUQ8

UniProtKB/Swiss-Prot:

DDX23_HUMAN :
  • Belongs to the DEAD box helicase family. DDX23/PRP28 subfamily.
Family:
  • Belongs to the DEAD box helicase family. DDX23/PRP28 subfamily.
genes like me logo Genes that share domains with DDX23: view

Function for DDX23 Gene

Molecular function for DDX23 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.
UniProtKB/Swiss-Prot Function:
Involved in pre-mRNA splicing and its phosphorylated form (by SRPK2) is required for spliceosomal B complex formation.

Enzyme Numbers (IUBMB) for DDX23 Gene

Phenotypes From GWAS Catalog for DDX23 Gene

Gene Ontology (GO) - Molecular Function for DDX23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IDA 22681889
GO:0004004 ATP-dependent RNA helicase activity TAS 9409622
GO:0004386 helicase activity IEA --
GO:0005515 protein binding IPI 20858735
genes like me logo Genes that share ontologies with DDX23: view
genes like me logo Genes that share phenotypes with DDX23: view

Animal Model Products

  • Taconic Biosciences Mouse Models for DDX23

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for DDX23
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for DDX23 Gene

Localization for DDX23 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DDX23 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for DDX23 gene
Compartment Confidence
extracellular 5
nucleus 5
plasma membrane 2
mitochondrion 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for DDX23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,TAS --
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005682 U5 snRNP IDA 9539711
GO:0005730 nucleolus IDA,IBA --
genes like me logo Genes that share ontologies with DDX23: view

Pathways & Interactions for DDX23 Gene

genes like me logo Genes that share pathways with DDX23: view

Pathways by source for DDX23 Gene

Gene Ontology (GO) - Biological Process for DDX23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000354 cis assembly of pre-catalytic spliceosome IC 9539711
GO:0000375 RNA splicing, via transesterification reactions TAS 9409622
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing TAS 9409622
genes like me logo Genes that share ontologies with DDX23: view

No data available for SIGNOR curated interactions for DDX23 Gene

Drugs & Compounds for DDX23 Gene

(3) Drugs for DDX23 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
ATP Nutra Agonist 0

(1) Additional Compounds for DDX23 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
genes like me logo Genes that share compounds with DDX23: view

Transcripts for DDX23 Gene

mRNA/cDNA for DDX23 Gene

(1) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(4) Selected AceView cDNA sequences:
(18) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for DDX23 Gene

DEAD (Asp-Glu-Ala-Asp) box polypeptide 23:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for DDX23
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for DDX23 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^
SP1: - - - -
SP2: - - - - - -
SP3: - - - - -
SP4: - - - - - -
SP5: -
SP6: - -
SP7: - - -
SP8:
SP9: -
SP10: -
SP11:
SP12:
SP13:

ExUns: 16 ^ 17a · 17b ^ 18a · 18b ^ 19a · 19b ^ 20a · 20b ^ 21a · 21b
SP1: - -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12: -
SP13: -

Relevant External Links for DDX23 Gene

GeneLoc Exon Structure for
DDX23
ECgene alternative splicing isoforms for
DDX23

Expression for DDX23 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for DDX23 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for DDX23 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (14.1) and CD8 Tcells (8.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for DDX23 Gene



Protein tissue co-expression partners for DDX23 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of DDX23 Gene:

DDX23

SOURCE GeneReport for Unigene cluster for DDX23 Gene:

Hs.130098

Evidence on tissue expression from TISSUES for DDX23 Gene

  • Nervous system(4.9)
  • Lung(4.6)
genes like me logo Genes that share expression patterns with DDX23: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for DDX23 Gene

Orthologs for DDX23 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for DDX23 Gene

Organism Taxonomy Gene Similarity Type Details
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 100 (a)
OneToMany
-- 34
  • 99 (a)
OneToMany
-- 34
  • 91 (a)
OneToMany
-- 34
  • 87 (a)
OneToMany
chimpanzee
(Pan troglodytes)
Mammalia DDX23 33 34
  • 99.63 (n)
oppossum
(Monodelphis domestica)
Mammalia DDX23 34
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia DDX23 33 34
  • 94.02 (n)
cow
(Bos Taurus)
Mammalia DDX23 33 34
  • 92.97 (n)
mouse
(Mus musculus)
Mammalia Ddx23 33 16 34
  • 90.96 (n)
rat
(Rattus norvegicus)
Mammalia Ddx23 33
  • 90.92 (n)
chicken
(Gallus gallus)
Aves -- 34
  • 98 (a)
OneToMany
-- 34
  • 98 (a)
OneToMany
DDX23 33
  • 82.49 (n)
lizard
(Anolis carolinensis)
Reptilia DDX23 34
  • 91 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.24773 33
zebrafish
(Danio rerio)
Actinopterygii ddx23 33 34
  • 77.13 (n)
wufi39b12 33
fruit fly
(Drosophila melanogaster)
Insecta CG10333 33 34
  • 64.86 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007825 33
  • 54.6 (n)
worm
(Caenorhabditis elegans)
Secernentea ddx-23 33 34
  • 62.75 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PRP28 34 36
  • 38 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G33730 33
  • 57.38 (n)
soybean
(Glycine max)
eudicotyledons Gma.3548 33
rice
(Oryza sativa)
Liliopsida Os03g0708600 33
  • 57.69 (n)
Os.3228 33
barley
(Hordeum vulgare)
Liliopsida Hv.2391 33
wheat
(Triticum aestivum)
Liliopsida Ta.3307 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 68 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU02803 33
  • 57.78 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes prp28 33
  • 53.22 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.11344 33
Species where no ortholog for DDX23 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)

Evolution for DDX23 Gene

ENSEMBL:
Gene Tree for DDX23 (if available)
TreeFam:
Gene Tree for DDX23 (if available)

Paralogs for DDX23 Gene

(11) SIMAP similar genes for DDX23 Gene using alignment to 6 proteins:

Pseudogenes.org Pseudogenes for DDX23 Gene

genes like me logo Genes that share paralogs with DDX23: view

No data available for Paralogs for DDX23 Gene

Variants for DDX23 Gene

Sequence variations from dbSNP and Humsavar for DDX23 Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs1000050240 -- 48,847,295(+) GCAGA(C/T)CATGA intron-variant
rs1000079795 -- 48,849,451(+) GAGGT(C/G)AGGAG intron-variant
rs1000202162 -- 48,834,199(+) AAATA(A/G)CACAT intron-variant
rs1000221416 -- 48,847,034(+) TTAAG(C/T)TTTAG intron-variant
rs1000447660 -- 48,852,935(+) CCCCA(C/G)ATTCC downstream-variant-500B, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for DDX23 Gene

Variant ID Type Subtype PubMed ID
nsv826363 CNV gain 20364138
nsv976609 CNV duplication 23825009

Variation tolerance for DDX23 Gene

Residual Variation Intolerance Score: 2.91% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.57; 12.25% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for DDX23 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
DDX23

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DDX23 Gene

Disorders for DDX23 Gene

MalaCards: The human disease database

(1) MalaCards diseases for DDX23 Gene - From: GeneCards

Disorder Aliases PubMed IDs
distal hereditary motor neuropathy, type ii
  • dsma2
- elite association - COSMIC cancer census association via MalaCards
Search DDX23 in MalaCards View complete list of genes associated with diseases

Relevant External Links for DDX23

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
DDX23
genes like me logo Genes that share disorders with DDX23: view

No data available for UniProtKB/Swiss-Prot and Genatlas for DDX23 Gene

Publications for DDX23 Gene

  1. The human U5 snRNP-specific 100-kD protein is an RS domain-containing, putative RNA helicase with significant homology to the yeast splicing factor Prp28p. (PMID: 9409622) Teigelkamp S … Lührmann R (RNA (New York, N.Y.) 1997) 2 3 4 22 60
  2. Phosphorylation of human PRP28 by SRPK2 is required for integration of the U4/U6-U5 tri-snRNP into the spliceosome. (PMID: 18425142) Mathew R … Lührmann R (Nature structural & molecular biology 2008) 3 4 22 60
  3. The human U5-200kD DEXH-box protein unwinds U4/U6 RNA duplices in vitro. (PMID: 9539711) Laggerbauer B … Lührmann R (Proceedings of the National Academy of Sciences of the United States of America 1998) 2 3 22 60
  4. Interactions of ErbB4 and Kap1 connect the growth factor and DNA damage response pathways. (PMID: 20858735) Gilmore-Hebert M … Stern DF (Molecular cancer research : MCR 2010) 3 4 60
  5. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 60

Products for DDX23 Gene

Sources for DDX23 Gene

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