Human Gene DDX3X (ENST00000399959.7) from GENCODE V49

Description: Belongs to the DEAD box helicase family. DDX3/DED1 subfamily. (from UniProt A0A2U3TZJ9)
Gencode Transcript: ENST00000399959.7
Gencode Gene: ENSG00000215301.12
Transcript (Including UTRs)
Position: hg38 chrX:41,334,162-41,350,274 Size: 16,113 Total Exon Count: 17 Strand: +
Coding Region
Position: hg38 chrX:41,334,253-41,347,719 Size: 13,467 Coding Exon Count: 17

Page Index	Sequence and Links	Primers	MalaCards	CTD	RNA-Seq Expression
Microarray Expression	RNA Structure	Other Species	mRNA Descriptions	Pathways	Other Names
GeneReviews	Methods

Data last updated at UCSC: 2025-09-17 13:57:07

Sequence and Links to Tools and Databases

Genomic Sequence (chrX:41,334,162-41,350,274)			mRNA (may differ from genome)		Protein (661 aa)
Gene Sorter	Genome Browser	Other Species FASTA	Gene interactions	Table Schema	AlphaFold
BioGPS	Ensembl	ExonPrimer	Gencode	GeneCards	HGNC
Lynx	Malacards	MGI	myGene2	PubMed	UniProtKB
Wikipedia

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

MalaCards Disease Associations


	MalaCards Gene Search: DDX3X Diseases sorted by gene-association score: mental retardation, x-linked 102* (1681), corpus callosum, agenesis of, with facial anomalies and robin sequence* (350), precursor t-cell acute lymphoblastic leukemia* (80), hepatitis b (10), juvenile astrocytoma (8), childhood medulloblastoma (8), hepatitis c virus (7), juvenile pilocytic astrocytoma (5), hiv-1 (3), intellectual disability (2) * = Manually curated disease association

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D001564 Benzo(a)pyrene D002994 Clofibrate D004958 Estradiol D014635 Valproic Acid C086401 pentabromodiphenyl ether C049325 1,2-dithiol-3-thione C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl C023514 2,6-dinitrotoluene D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide D000082 Acetaminophen more ... click here to view the complete list

RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 74.34 RPKM in Fallopian Tube Total median expression: 2173.26 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data

mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-29.10	91	-0.320	Picture	PostScript	Text
3' UTR	-646.10	2555	-0.253	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.

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
Genome Browser	Genome Browser	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details
Gene Sorter
MGI	RGD
Protein Sequence	Protein Sequence
Alignment	Alignment

Descriptions from all associated GenBank mRNAs


	AF000982 - Homo sapiens dead box, X isoform (DBX) mRNA, alternative transcript 2, complete cds. AF000983 - Homo sapiens dead box, X isoform (DBX) mRNA, alternative transcript 1, complete cds. U50553 - Homo sapiens helicase like protein 2 (DDX14) mRNA, complete cds. BC055083 - Homo sapiens cDNA clone IMAGE:4068230, partial cds. AK310891 - Homo sapiens cDNA, FLJ17933. AK304689 - Homo sapiens cDNA FLJ60399 complete cds, highly similar to ATP-dependent RNA helicase DDX3X (EC 3.6.1.-). AK291153 - Homo sapiens cDNA FLJ76819 complete cds, highly similar to Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked (DDX3X), transcript variant 2, mRNA. AK296906 - Homo sapiens cDNA FLJ55031 complete cds, highly similar to ATP-dependent RNA helicase DDX3X (EC 3.6.1.-). AK297159 - Homo sapiens cDNA FLJ60675 complete cds, highly similar to ATP-dependent RNA helicase DDX3X (EC 3.6.1.-). AF086430 - Homo sapiens full length insert cDNA clone ZD79H04. BC007668 - Homo sapiens cDNA clone IMAGE:3138761, containing frame-shift errors. AF061337 - Homo sapiens DEAD box RNA helicase DDX3 (DDX3) mRNA, complete cds. BC011819 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked, mRNA (cDNA clone MGC:20129 IMAGE:3617040), complete cds. AB208983 - Homo sapiens mRNA for DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3 variant protein. JD486384 - Sequence 467408 from Patent EP1572962. AB384807 - Synthetic construct DNA, clone: pF1KB3467, Homo sapiens DDX3X gene for ATP-dependent RNA helicase DDX3X, complete cds, without stop codon, in Flexi system. AB451343 - Homo sapiens DDX3X mRNA for ATP-dependent RNA helicase DDX3X, partial cds, clone: FLJ08002AAAF. AB451220 - Homo sapiens DDX3X mRNA for ATP-dependent RNA helicase DDX3X, complete cds, clone: FLJ08002AAAN. AK304661 - Homo sapiens cDNA FLJ52848 complete cds, highly similar to ATP-dependent RNA helicase DDX3X (EC 3.6.1.-). DQ587475 - Homo sapiens piRNA piR-54587, complete sequence. AY776161 - Homo sapiens clone Ctg007 unknown mRNA. DQ574619 - Homo sapiens piRNA piR-42731, complete sequence. DQ600255 - Homo sapiens piRNA piR-38321, complete sequence. L37696 - Homo sapiens (clone 68) macronuclear mRNA. JD400322 - Sequence 381346 from Patent EP1572962. JD374812 - Sequence 355836 from Patent EP1572962. JD092467 - Sequence 73491 from Patent EP1572962. JD324990 - Sequence 306014 from Patent EP1572962. DM107612 - METHODS FOR GENERATING NEW HAIR FOLLICLES, TREATING BALDNESS, AND HAIR REMOVAL. HW120616 - JP 2013049691-A/171: METHODS FOR GENERATING NEW HAIR FOLLICLES, TREATING BALDNESS, AND HAIR REMOVAL. LF858719 - JP 2015172074-A/171: METHODS FOR GENERATING NEW HAIR FOLLICLES, TREATING BALDNESS, AND HAIR REMOVAL. MA726069 - JP 2017114907-A/171: METHODS FOR GENERATING NEW HAIR FOLLICLES, TREATING BALDNESS, AND HAIR REMOVAL. JD543075 - Sequence 524099 from Patent EP1572962. JD369704 - Sequence 350728 from Patent EP1572962. JD170076 - Sequence 151100 from Patent EP1572962. JD455163 - Sequence 436187 from Patent EP1572962. DQ591868 - Homo sapiens piRNA piR-58980, complete sequence. JD372293 - Sequence 353317 from Patent EP1572962. JD295273 - Sequence 276297 from Patent EP1572962. JD374793 - Sequence 355817 from Patent EP1572962. JD085241 - Sequence 66265 from Patent EP1572962. JD332890 - Sequence 313914 from Patent EP1572962.

Biochemical and Signaling Pathways


	KEGG - Kyoto Encyclopedia of Genes and Genomes hsa04622 - RIG-I-like receptor signaling pathway

Other Names for This Gene


	Alternate Gene Symbols: A0A2U3TZJ9, A0A2U3TZJ9_HUMAN, BC007668, DDX3X , ENST00000399959.1, ENST00000399959.2, ENST00000399959.3, ENST00000399959.4, ENST00000399959.5, ENST00000399959.6, uc286cwg.1 UCSC ID: ENST00000399959.7 RefSeq Accession: NM_001356.5 CCDS: CCDS43931.1, CCDS55404.1

GeneReviews for This Gene


	GeneReviews article(s) related to gene DDX3X: ddx3x-ndd (DDX3X-Related Neurodevelopmental Disorder)

Methods, Credits, and Use Restrictions


	Click here for details on how this gene model was made and data restrictions if any.

GNF Expression Atlas 2 Data from U133A and GNF1H Chips