Human Gene DHX38 (uc002fcb.3) Description and Page Index
  Description: Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 38 (DHX38), mRNA.
RefSeq Summary (NM_014003): 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 member of the DEAD/H box family of splicing factors. This protein resembles yeast Prp16 more closely than other DEAD/H family members. It is an ATPase and essential for the catalytic step II in pre-mRNA splicing process. [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 :: SRR1803617.261139.1, SRR1660809.36002.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000268482.8/ ENSP00000268482.3 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr16:72,127,615-72,146,811 Size: 19,197 Total Exon Count: 27 Strand: +
Coding Region
   Position: hg19 chr16:72,130,057-72,146,396 Size: 16,340 Coding Exon Count: 26 

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

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr16:72,127,615-72,146,811)mRNA (may differ from genome)Protein (1227 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedReactomeStanford SOURCETreefam

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16; EC=; AltName: Full=ATP-dependent RNA helicase DHX38; AltName: Full=DEAH box protein 38;
FUNCTION: Probable ATP-binding RNA helicase involved in pre-mRNA splicing.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: Identified in the spliceosome C complex.
SUBCELLULAR LOCATION: Nucleus (By similarity).
SIMILARITY: Belongs to the DEAD box helicase family. DEAH subfamily. PRP16 sub-subfamily.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.
SEQUENCE CAUTION: Sequence=BAA13213.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  MalaCards Disease Associations
  MalaCards Gene Search: DHX38
Diseases sorted by gene-association score: coloboma (2), retinitis pigmentosa (1)

-  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: 28.26 RPKM in Ovary
Total median expression: 939.20 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 -134.90355-0.380 Picture PostScript Text
3' UTR -152.20415-0.367 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
IPR002464 - DNA/RNA_helicase_DEAH_CS
IPR011709 - DUF1605
IPR007502 - Helicase-assoc_dom
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C

Pfam Domains:
PF00270 - DEAD/DEAH box helicase
PF00271 - Helicase conserved C-terminal domain
PF04408 - Helicase associated domain (HA2)
PF07717 - Oligonucleotide/oligosaccharide-binding (OB)-fold

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

ModBase Predicted Comparative 3D Structure on Q92620
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence

-  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

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0006405 RNA export from nucleus
GO:0006406 mRNA export from nucleus
GO:0008380 RNA splicing
GO:0031124 mRNA 3'-end processing

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005737 cytoplasm
GO:0016020 membrane
GO:0071013 catalytic step 2 spliceosome

-  Descriptions from all associated GenBank mRNAs
  AK301074 - Homo sapiens cDNA FLJ51112 complete cds, highly similar to Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 (EC 3.6.1.-).
AK297269 - Homo sapiens cDNA FLJ50987 complete cds, highly similar to Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 (EC 3.6.1.-).
AK291634 - Homo sapiens cDNA FLJ76871 complete cds, highly similar to Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 38 (DHX38), mRNA.
AK293776 - Homo sapiens cDNA FLJ55900 complete cds, highly similar to Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 (EC 3.6.1.-).
AK311169 - Homo sapiens cDNA, FLJ18211.
D86977 - Homo sapiens mRNA for KIAA0224 gene.
AK309391 - Homo sapiens cDNA, FLJ99432.
BC004235 - Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 38, mRNA (cDNA clone MGC:757 IMAGE:3504632), complete cds.
BC008340 - Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 38, mRNA (cDNA clone MGC:15850 IMAGE:3508917), complete cds.
AK297791 - Homo sapiens cDNA FLJ50999 complete cds, highly similar to Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 (EC 3.6.1.-).
AF038391 - Homo sapiens pre-mRNA splicing factor (PRP16) mRNA, complete cds.
CU678622 - Synthetic construct Homo sapiens gateway clone IMAGE:100020560 5' read DHX38 mRNA.
AB383811 - Synthetic construct DNA, clone: pF1KSDA0224, Homo sapiens DHX38 gene for pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16, complete cds, without stop codon, in Flexi system.
DQ891886 - Synthetic construct clone IMAGE:100004516; FLH180947.01X; RZPDo839H09134D DEAH (Asp-Glu-Ala-His) box polypeptide 38 (DHX38) gene, encodes complete protein.
DQ895072 - Synthetic construct Homo sapiens clone IMAGE:100009532; FLH180943.01L; RZPDo839H09133D DEAH (Asp-Glu-Ala-His) box polypeptide 38 (DHX38) gene, encodes complete protein.
KJ906009 - Synthetic construct Homo sapiens clone ccsbBroadEn_15679 DHX38 gene, encodes complete protein.
KJ898091 - Synthetic construct Homo sapiens clone ccsbBroadEn_07485 DHX38 gene, encodes complete protein.
JD462871 - Sequence 443895 from Patent EP1572962.
JD275037 - Sequence 256061 from Patent EP1572962.
JD474400 - Sequence 455424 from Patent EP1572962.
JD205881 - Sequence 186905 from Patent EP1572962.
JD444018 - Sequence 425042 from Patent EP1572962.
JD222372 - Sequence 203396 from Patent EP1572962.

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

Reactome (by CSHL, EBI, and GO)

Protein Q92620 (Reactome details) participates in the following event(s):

R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-75096 Docking of the TAP:EJC Complex with the NPC
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-8849157 TREX complex binds spliced, capped mRNA:CBC:EJC cotranscriptionally
R-HSA-72185 mRNA polyadenylation
R-HSA-72180 Cleavage of mRNA at the 3'-end
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-159101 NXF1:NXT1 (TAP:p15) binds capped mRNA:CBC:EJC:TREX (minus DDX39B)
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-159236 Transport of Mature mRNA derived from an Intron-Containing Transcript
R-HSA-72187 mRNA 3'-end processing
R-HSA-109688 Cleavage of Growing Transcript in the Termination Region
R-HSA-72172 mRNA Splicing
R-HSA-72202 Transport of Mature Transcript to Cytoplasm
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-73856 RNA Polymerase II Transcription Termination
R-HSA-8953854 Metabolism of RNA
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: D3DWS7, DDX38, KIAA0224, NM_014003, NP_054722, O75212, PRP16, PRP16_HUMAN, Q92620, Q96HN7
UCSC ID: uc002fcb.3
RefSeq Accession: NM_014003
Protein: Q92620 (aka PRP16_HUMAN or PR16_HUMAN)
CCDS: CCDS10907.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene DHX38:
rp-overview (Nonsyndromic Retinitis Pigmentosa Overview)

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_014003.3
exon count: 27CDS single in 3' UTR: no RNA size: 4470
ORF size: 3684CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 7505.00frame shift in genome: no % Coverage: 99.64
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.