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Q9Z1N5

- DX39B_MOUSE

UniProt

Q9Z1N5 - DX39B_MOUSE

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Protein

Spliceosome RNA helicase Ddx39b

Gene

Ddx39b

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Involved in nuclear export of spliced and unspliced mRNA. Assembling component of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and specifically associates with spliced mRNA and not with unspliced pre-mRNA. TREX is recruited to spliced mRNAs by a transcription-independent mechanism, binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export to the cytoplasm via the TAP/NFX1 pathway. May undergo several rounds of ATP hydrolysis during assembly of TREX to drive subsequent loading of components such as ALYREF/THOC and CHTOP onto mRNA. Also associates with pre-mRNA independent of ALYREF/THOC4 and the THO complex. Involved in the nuclear export of intronless mRNA; the ATP-bound form is proposed to recruit export adapter ALYREF/THOC4 to intronless mRNA; its ATPase activity is cooperatively stimulated by RNA and ALYREF/THOC4 and ATP hydrolysis is thought to trigger the dissociation from RNA to allow the association of ALYREF/THOC4 and the NXF1-NXT1 heterodimer. Involved in transcription elongation and genome stability By similarity.By similarity
Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. Can unwind 5' or 3' overhangs or blunt end RNA duplexes in vitro. The ATPase and helicase activities are not influenced by U2AF2; the effect of ALYREF/THOC4 is reported conflictingly By similarity.By similarity

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi89 – 968ATPPROSITE-ProRule annotation

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. ATP-dependent RNA helicase activity Source: Ensembl
  3. poly(A) RNA binding Source: Ensembl
  4. U4 snRNA binding Source: Ensembl
  5. U6 snRNA binding Source: Ensembl

GO - Biological processi

  1. negative regulation of DNA damage checkpoint Source: UniProtKB
  2. positive regulation of DNA-templated transcription, elongation Source: UniProtKB
  3. RNA secondary structure unwinding Source: Ensembl
  4. spliceosomal complex assembly Source: Ensembl
  5. viral mRNA export from host cell nucleus Source: Ensembl
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

mRNA processing, mRNA splicing, mRNA transport, Transport

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Spliceosome RNA helicase Ddx39b (EC:3.6.4.13)
Alternative name(s):
56 kDa U2AF65-associated protein
DEAD box protein UAP56
HLA-B-associated transcript 1 protein
Gene namesi
Name:Ddx39b
Synonyms:Bat1, Bat1a, Uap56
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 17

Organism-specific databases

MGIiMGI:99240. Ddx39b.

Subcellular locationi

Nucleus By similarity. Nucleus speckle By similarity. Cytoplasm By similarity
Note: Can translocate to the cytoplasm in the presence of MX1.By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-KW
  2. spliceosomal complex Source: UniProtKB-KW
  3. transcription export complex Source: Ensembl
  4. U4 snRNP Source: Ensembl
  5. U6 snRNP Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedBy similarity
Chaini2 – 428427Spliceosome RNA helicase Ddx39bPRO_0000055073Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineBy similarity
Modified residuei36 – 361N6-acetyllysineBy similarity
Modified residuei38 – 381PhosphoserineBy similarity
Modified residuei172 – 1721PhosphothreonineBy similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiQ9Z1N5.
PaxDbiQ9Z1N5.
PRIDEiQ9Z1N5.

PTM databases

PhosphoSiteiQ9Z1N5.

Expressioni

Gene expression databases

BgeeiQ9Z1N5.
CleanExiMM_BAT1A.
ExpressionAtlasiQ9Z1N5. baseline and differential.
GenevestigatoriQ9Z1N5.

Interactioni

Subunit structurei

Homodimer, and heterodimer with DDX39A. Component of the transcription/export (TREX) complex at least composed of ALYREF/THOC4, DDX39B, SARNP/CIP29, CHTOP and the THO subcomplex; TREX seems to have dynamic structure involving ATP-dependent remodeling; in the complex bridges ALYREF/THOC4 and the THO complex, and, in a ATP-dependent manner, ALYREF/THOC4 and SARNP/CIP29. Component of the spliceosome. Interacts directly with U2AF2. Interacts with RBM8A, RNPS1 and SRRM1, FYTTD1/UIF, THOC1, MX1 and POLDIP3 By similarity.By similarity

Protein-protein interaction databases

BioGridi207488. 4 interactions.
IntActiQ9Z1N5. 3 interactions.
MINTiMINT-1867862.

Structurei

3D structure databases

ProteinModelPortaliQ9Z1N5.
SMRiQ9Z1N5. Positions 46-426.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini76 – 249174Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini261 – 422162Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi45 – 7329Q motifAdd
BLAST
Motifi196 – 1994DECD box

Domaini

The helicase C-terminal domain mediates interaction with ALYREF/THOC4.By similarity

Sequence similaritiesi

Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0513.
GeneTreeiENSGT00760000119343.
HOVERGENiHBG107334.
InParanoidiQ9Z1N5.
KOiK12812.
OMAiFMNNPLE.
OrthoDBiEOG7W154N.
PhylomeDBiQ9Z1N5.
TreeFamiTF300442.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9Z1N5-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAENDVDNEL LDYEDDEVET AAGADGTEAP AKKDVKGSYV SIHSSGFRDF
60 70 80 90 100
LLKPELLRAI VDCGFEHPSE VQHECIPQAI LGMDVLCQAK SGMGKTAVFV
110 120 130 140 150
LATLQQLEPV TGQVSVLVMC HTRELAFQIS KEYERFSKYM PNVKVAVFFG
160 170 180 190 200
GLSIKKDEEV LKKNCPHIVV GTPGRILALA RNKSLNLKHI KHFILDECDK
210 220 230 240 250
MLEQLDMRRD VQEIFRMTPH EKQVMMFSAT LSKEIRPVCR KFMQDPMEIF
260 270 280 290 300
VDDETKLTLH GLQQYYVKLK DNEKNRKLFD LLDVLEFNQV VIFVKSVQRC
310 320 330 340 350
IALAQLLVEQ NFPAIAIHRG MPQEERLSRY QQFKDFQRRI LVATNLFGRG
360 370 380 390 400
MDIERVNIAF NYDMPEDSDT YLHRVARAGR FGTKGLAITF VSDENDAKIL
410 420
NDVQDRFEVN ISELPDEIDI SSYIEQTR
Length:428
Mass (Da):49,035
Last modified:May 1, 1999 - v1
Checksum:iD5AA6B3905FDC968
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF118128 mRNA. Translation: AAD13115.1.
AY255786 mRNA. Translation: AAP91685.1.
AY255787 mRNA. Translation: AAP91686.1.
AC007080 Genomic DNA. Translation: AAD30177.1.
AK088867 mRNA. Translation: BAC40624.1.
AK051034 mRNA. Translation: BAC34505.1.
BC011067 mRNA. Translation: AAH11067.1.
BC024859 mRNA. Translation: AAH24859.1.
CCDSiCCDS28695.1.
RefSeqiNP_001239386.1. NM_001252457.1.
NP_062667.1. NM_019693.3.
UniGeneiMm.439827.

Genome annotation databases

EnsembliENSMUST00000068056; ENSMUSP00000070682; ENSMUSG00000019432.
ENSMUST00000172549; ENSMUSP00000134178; ENSMUSG00000019432.
ENSMUST00000173731; ENSMUSP00000133428; ENSMUSG00000019432.
GeneIDi53817.
KEGGimmu:53817.
UCSCiuc008cha.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF118128 mRNA. Translation: AAD13115.1 .
AY255786 mRNA. Translation: AAP91685.1 .
AY255787 mRNA. Translation: AAP91686.1 .
AC007080 Genomic DNA. Translation: AAD30177.1 .
AK088867 mRNA. Translation: BAC40624.1 .
AK051034 mRNA. Translation: BAC34505.1 .
BC011067 mRNA. Translation: AAH11067.1 .
BC024859 mRNA. Translation: AAH24859.1 .
CCDSi CCDS28695.1.
RefSeqi NP_001239386.1. NM_001252457.1.
NP_062667.1. NM_019693.3.
UniGenei Mm.439827.

3D structure databases

ProteinModelPortali Q9Z1N5.
SMRi Q9Z1N5. Positions 46-426.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 207488. 4 interactions.
IntActi Q9Z1N5. 3 interactions.
MINTi MINT-1867862.

PTM databases

PhosphoSitei Q9Z1N5.

Proteomic databases

MaxQBi Q9Z1N5.
PaxDbi Q9Z1N5.
PRIDEi Q9Z1N5.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000068056 ; ENSMUSP00000070682 ; ENSMUSG00000019432 .
ENSMUST00000172549 ; ENSMUSP00000134178 ; ENSMUSG00000019432 .
ENSMUST00000173731 ; ENSMUSP00000133428 ; ENSMUSG00000019432 .
GeneIDi 53817.
KEGGi mmu:53817.
UCSCi uc008cha.2. mouse.

Organism-specific databases

CTDi 7919.
MGIi MGI:99240. Ddx39b.

Phylogenomic databases

eggNOGi COG0513.
GeneTreei ENSGT00760000119343.
HOVERGENi HBG107334.
InParanoidi Q9Z1N5.
KOi K12812.
OMAi FMNNPLE.
OrthoDBi EOG7W154N.
PhylomeDBi Q9Z1N5.
TreeFami TF300442.

Miscellaneous databases

NextBioi 310679.
PROi Q9Z1N5.
SOURCEi Search...

Gene expression databases

Bgeei Q9Z1N5.
CleanExi MM_BAT1A.
ExpressionAtlasi Q9Z1N5. baseline and differential.
Genevestigatori Q9Z1N5.

Family and domain databases

Gene3Di 3.40.50.300. 2 hits.
InterProi IPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view ]
Pfami PF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view ]
SMARTi SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view ]
SUPFAMi SSF52540. SSF52540. 1 hit.
PROSITEi PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence analysis of a mouse homolog of the human BAT1 gene (nuclear RNA helicase of the DEAD box protein family)."
    Handel-Fernandez M.E., Vincek V.
    Submitted (JAN-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: C57BL/10.
  2. "Characterization of murine Bat1, a putative immunoregulator of Tnfa."
    Dolecki K.J., Wong A.M.L., Price P.
    Submitted (MAR-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: BALB/c and C57BL/10 X DBA/2.
  3. "Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse."
    Xie T., Rowen L., Aguado B., Ahearn M.E., Madan A., Qin S., Campbell R.D., Hood L.
    Genome Res. 13:2621-2636(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 129.
  4. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J and NOD.
    Tissue: Embryo and Thymus.
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: FVB/N.
    Tissue: Eye and Mammary tumor.
  6. Lubec G., Kang S.U.
    Submitted (APR-2007) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 145-155, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: C57BL/6.
    Tissue: Brain.

Entry informationi

Entry nameiDX39B_MOUSE
AccessioniPrimary (citable) accession number: Q9Z1N5
Secondary accession number(s): Q8HW97
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 15, 2005
Last sequence update: May 1, 1999
Last modified: October 29, 2014
This is version 116 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3