Ddx39a MGI Mouse Gene Detail - MGI:1915528

Symbol

Ddx39a
Name

DEAD box helicase 39a
Synonyms

2610307C23Rik, BAT1, Ddx39

Feature Type

protein coding gene
IDs

MGI:1915528
NCBI Gene: 68278
Alliance

genome feature page
Transcription Start Sites

5 TSS

Sequence Map

Chr8:84441806-84453521 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 8, 40.22 cM
Mapping Data

1 experiment

SNPs within 2kb

258 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1915528	protein coding gene	Chr8:84441806-84453533 (+)
129S1/SvImJ	ENSMUSG00200023493	protein coding gene	Chr8:78812999-78824699 (+)
A/J	ENSMUSG00195015678	protein coding gene	Chr8:79169719-79181433 (+)
AKR/J	ENSMUSG00220023096	protein coding gene	Chr8:79210433-79222133 (+)
BALB/cJ	ENSMUSG00180017472	protein coding gene	Chr8:79011666-79023367 (+)
C3H/HeJ	ENSMUSG00175010303	protein coding gene	Chr8:79100606-79112318 (+)
C57BL/6NJ	ENSMUSG00215018392	protein coding gene	Chr8:78736267-78747983 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0031277	protein coding gene	Chr8:75039424-75050718 (+)
CAST/EiJ	ENSTCUG00005031872	protein coding gene	Chr8:78624239-78635942 (+)
CBA/J	ENSMUSG00210020181	protein coding gene	Chr8:79092904-79104617 (+)
DBA/2J	ENSMUSG00185033607	protein coding gene	Chr8:85201715-85213428 (+)
FVB/NJ	ENSMUSG00205036319	protein coding gene	Chr8:78147766-78159483 (+)
JF1/MsJ	ENSUMUG00000032630	protein coding gene	Chr8:87492446-87504178 (+)
LP/J	ENSMUSG00230025039	protein coding gene	Chr8:88809852-88821551 (+)
NOD/ShiLtJ	ENSMUSG00190022596	protein coding gene	Chr8:79159024-79170737 (+)
NZO/HlLtJ	ENSMUSG00225038827	protein coding gene	Chr8:92197420-92209135 (+)
PWK/PhJ	ENSLUMG00010025725	protein coding gene	Chr8:78850290-78862002 (+)
SPRET/EiJ	no annotation
WSB/EiJ	ENSIUOG00005014866	protein coding gene	Chr8:79902247-79913947 (+)

Human Ortholog

DDX39A, DExD-box helicase 39A

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

DDX39A, DExD-box helicase 39A
Synonyms

BAT1, BAT1L, DDX39, DDXL, URH49
Links

HGNC:17821

NCBI Gene ID: 10212

UniProt: O00148
Chr Location

19p13.12; chr19:14408798-14419383 (-) GRCh38

MGI Vertebrate Homology

Ddx39a stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: DDX39A
Gene Tree

Ddx39a

less

Phenotype Summary

10 phenotypes from 1 allele in 1 genetic background
45 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

55
Chemically induced (other)

1
Endonuclease-mediated

5
Gene trapped

45
Radiation induced

1
Targeted

3
Genomic Mutations

2 involving Ddx39a
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

60 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

less

All GO Annotations

35
GO References

9

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

less

Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

669
Tissues

63
cDNA Data

185
Literature Summary

5

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase ddx39a

ZFIN ddx39aa, ddx39ab

less

All Sequences

75
RefSeq

9
UniProt

8
CCDS

CCDS22460.1

Ensembl

ENSMUSG00000005481 (Evidence)
NCBI Gene

68278

			Length	Strain/Species	Flank
genomic	ENSMUSG00000005481	Ensembl Gene Model \| MGI Sequence Detail	11716	C57BL/6J	± kb
transcript	ENSMUST00000172396	Ensembl \| MGI Sequence Detail	3836	Not Applicable
polypeptide	ENSMUSP00000132222	Ensembl \| MGI Sequence Detail	427	Not Applicable

less

UniProt

8 Sequences
Protein Ontology

PR:000006363 ATP-dependent RNA helicase DDX39

(term hierarchy)
EC

3.6.4.13
InterPro Domains

IPR011545 DEAD/DEAH-box helicase domain

IPR001650 Helicase, C-terminal domain-like

IPR014001 Helicase superfamily 1/2, ATP-binding domain

IPR027417 P-loop containing nucleoside triphosphate hydrolase

IPR014014 RNA helicase, DEAD-box type, Q motif
GlyGen

Q8VDW0 2 sites, 1 O-linked glycan (1 site)

less

All nucleic 189

cDNA 188

Primer pair 1

Microarray probesets 4

less

MGI:6393445

Summaries

All 84

Developmental Gene Expression 5

Gene Ontology 9

Phenotypes 45
Earliest

J:13049 Gruneberg H, Genetical studies on the skeleton of the mouse. XVIII. Three genes for syndactylism. J Genet. 1956;54(1):113-145
Latest

J:384798 Rayee D, et al., RNA-binding proteins in the mouse lens: Functional classifications, expression profiling, and interaction studies of Carhsp1 with crystallin mRNAs. Dev Biol. 2026 Apr 28;

TSS for Ddx39a:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr78284	Chr8:84441820-84441833 (+)	21 bp
Tssr78285	Chr8:84441856-84441867 (+)	56 bp
Tssr78286	Chr8:84441868-84441917 (+)	87 bp
Tssr78287	Chr8:84441934-84441941 (+)	132 bp
Tssr78288	Chr8:84442133-84442153 (+)	337 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 09/01/2026 MGI 6.24