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Q9Z1N7

- ARI3B_MOUSE

UniProt

Q9Z1N7 - ARI3B_MOUSE

Protein

AT-rich interactive domain-containing protein 3B

Gene

Arid3b

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 80 (01 Oct 2014)
      Sequence version 1 (01 May 1999)
      Previous versions | rss
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    Functioni

    Transcription factor involved in the production of cranial mesenchymal tissues. Favors nuclear targeting of ARID3A.1 Publication

    GO - Molecular functioni

    1. RNA polymerase II core promoter proximal region sequence-specific DNA binding Source: NTNU_SB
    2. RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription Source: NTNU_SB
    3. RNA polymerase II distal enhancer sequence-specific DNA binding Source: NTNU_SB
    4. RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription Source: NTNU_SB

    GO - Biological processi

    1. multicellular organismal development Source: UniProtKB-KW
    2. positive regulation of transcription from RNA polymerase II promoter Source: NTNU_SB

    Keywords - Molecular functioni

    Developmental protein

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    AT-rich interactive domain-containing protein 3B
    Short name:
    ARID domain-containing protein 3B
    Alternative name(s):
    Bright and dead ringer protein
    Bright-like protein
    Gene namesi
    Name:Arid3b
    Synonyms:Bdp, Dril2
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 9

    Organism-specific databases

    MGIiMGI:1930768. Arid3b.

    Subcellular locationi

    Nucleus PROSITE-ProRule annotation

    GO - Cellular componenti

    1. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Disruption phenotypei

    Embryos die before E11.5 and display various abnormalities, including wavy neural tube, small branchial arches and defects of cardiovascular system.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 568568AT-rich interactive domain-containing protein 3BPRO_0000295163Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei1 – 11N-acetylmethionineBy similarity
    Modified residuei87 – 871PhosphoserineBy similarity

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    PRIDEiQ9Z1N7.

    PTM databases

    PhosphoSiteiQ9Z1N7.

    Expressioni

    Tissue specificityi

    Expressed at high levels in testis. Also expressed in prostate, thyroid and thymus.1 Publication

    Developmental stagei

    First detected at E7. Strongly expressed in cranial mesenchyme and caudal mesoderm. Expression in cranial mesenchyme decreases starting from E10.5.1 Publication

    Gene expression databases

    ArrayExpressiQ9Z1N7.
    BgeeiQ9Z1N7.
    CleanExiMM_ARID3B.
    GenevestigatoriQ9Z1N7.

    Interactioni

    Subunit structurei

    Heterodimer with ARID3A. Interacts with unphosphorylated RB1 By similarity.By similarity

    Protein-protein interaction databases

    BioGridi207941. 3 interactions.
    IntActiQ9Z1N7. 1 interaction.
    STRINGi10090.ENSMUSP00000109802.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9Z1N7.
    SMRiQ9Z1N7. Positions 174-326.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini213 – 30593ARIDPROSITE-ProRule annotationAdd
    BLAST
    Domaini425 – 52298REKLESPROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni201 – 374174Interaction with RB1By similarityAdd
    BLAST
    Regioni495 – 51824Interaction with ARID3ABy similarityAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi5 – 3733Gln-richAdd
    BLAST
    Compositional biasi88 – 936Poly-Glu
    Compositional biasi339 – 36224Ala-richAdd
    BLAST
    Compositional biasi528 – 56740Ser-richAdd
    BLAST

    Sequence similaritiesi

    Contains 1 ARID domain.PROSITE-ProRule annotation
    Contains 1 REKLES domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiNOG327790.
    GeneTreeiENSGT00550000074575.
    HOGENOMiHOG000236281.
    HOVERGENiHBG103680.
    InParanoidiQ9Z1N7.
    OMAiFHVQKVA.
    OrthoDBiEOG77DJ6W.
    PhylomeDBiQ9Z1N7.
    TreeFamiTF320364.

    Family and domain databases

    Gene3Di1.10.150.60. 1 hit.
    InterProiIPR001606. ARID/BRIGHT_DNA-bd.
    IPR023334. REKLES_domain.
    [Graphical view]
    PfamiPF01388. ARID. 1 hit.
    [Graphical view]
    SMARTiSM00501. BRIGHT. 1 hit.
    [Graphical view]
    SUPFAMiSSF46774. SSF46774. 1 hit.
    PROSITEiPS51011. ARID. 1 hit.
    PS51486. REKLES. 1 hit.
    [Graphical view]

    Sequences (3)i

    Sequence statusi: Complete.

    This entry describes 3 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q9Z1N7-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MEPLQQQQQQ QQQKQPQQPL LQMDAREKQG PQTRESQFLY ASKLGTQPAL    50
    LSITPGRPSG SSVLGPLARV PPATPVARMS EQSNVNSEPE EEEGGLEDED 100
    GDDDVAEVAE KEAQAASKYF HMQKVTRQEP RATPMSSLLP VPGLSPQGQQ 150
    TKEDHTKDAS KAPPSVPTAG QPSWSLDEQL KQNGALAWSD DADGGRGREI 200
    SRDFAKLYEL DGDPERKEFL DDLFIFMQKR GTPINRIPIM AKQILDLYML 250
    YKLVTEKGGL VEIINKKIWR EITKGLNLPT SITSAAFTLR TQYMKYLYAY 300
    ECEKKALSSP AELQAAIDGN RREGRRPSYS SSLFGYSPAA AAAAAAAAAA 350
    AAASAASAGT PALLSSPKIR FSILGLGSSS GTSASSPRIP PASTLRKGDG 400
    VPVPVPNRLA VSGTLAGQQA GNRPGPLEHL RERLESGEPP EKKASRLSEE 450
    EQRLVQQAFQ RNLFSMARQL PMKIRINGRE DRAEPSAPAL NLTTSNIGSI 500
    NMSVDIDGTT YTGVLFAQKP VVHLIAGSTP QSIGSSASSS NSSSSHCSPS 550
    PTSSRGTPSA EPSTSWSL 568
    Length:568
    Mass (Da):61,015
    Last modified:May 1, 1999 - v1
    Checksum:i70250959E6EAF526
    GO
    Isoform 2 (identifier: Q9Z1N7-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         234-282: INRIPIMAKQ...TKGLNLPTSI → SGASPAGIVL...VIAHGSLGRD
         283-568: Missing.

    Show »
    Length:282
    Mass (Da):30,795
    Checksum:iB18C5EB90DED77C4
    GO
    Isoform 3 (identifier: Q9Z1N7-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         232-287: TPINRIPIMA...LPTSITSAAF → DPAAAAECTA...QADPGPVHAV
         288-568: Missing.

    Show »
    Length:287
    Mass (Da):31,376
    Checksum:i6DFB9E26A48E6A6C
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti99 – 991E → G in BAE24019. (PubMed:16141072)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei232 – 28756TPINR…TSAAF → DPAAAAECTAFLLPSLIVIK YPGTTQLSTIMQKGVWHPNQ PDSHHGQADPGPVHAV in isoform 3. 1 PublicationVSP_026775Add
    BLAST
    Alternative sequencei234 – 28249INRIP…LPTSI → SGASPAGIVLKATWPCGWPG QPPPLLCLVCILTRKKKKNV IAHGSLGRD in isoform 2. 1 PublicationVSP_026776Add
    BLAST
    Alternative sequencei283 – 568286Missing in isoform 2. 1 PublicationVSP_026777Add
    BLAST
    Alternative sequencei288 – 568281Missing in isoform 3. 1 PublicationVSP_026778Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF116847 mRNA. Translation: AAD09134.1.
    AK139455 mRNA. Translation: BAE24019.1.
    BC049776 mRNA. Translation: AAH49776.1.
    CCDSiCCDS23233.1. [Q9Z1N7-1]
    RefSeqiNP_062663.1. NM_019689.2. [Q9Z1N7-1]
    XP_006511354.1. XM_006511291.1. [Q9Z1N7-1]
    UniGeneiMm.425588.

    Genome annotation databases

    EnsembliENSMUST00000004780; ENSMUSP00000004780; ENSMUSG00000004661. [Q9Z1N7-1]
    ENSMUST00000164035; ENSMUSP00000131677; ENSMUSG00000004661. [Q9Z1N7-3]
    ENSMUST00000171444; ENSMUSP00000130173; ENSMUSG00000004661. [Q9Z1N7-1]
    GeneIDi56380.
    KEGGimmu:56380.
    UCSCiuc009pvt.2. mouse. [Q9Z1N7-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF116847 mRNA. Translation: AAD09134.1 .
    AK139455 mRNA. Translation: BAE24019.1 .
    BC049776 mRNA. Translation: AAH49776.1 .
    CCDSi CCDS23233.1. [Q9Z1N7-1 ]
    RefSeqi NP_062663.1. NM_019689.2. [Q9Z1N7-1 ]
    XP_006511354.1. XM_006511291.1. [Q9Z1N7-1 ]
    UniGenei Mm.425588.

    3D structure databases

    ProteinModelPortali Q9Z1N7.
    SMRi Q9Z1N7. Positions 174-326.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 207941. 3 interactions.
    IntActi Q9Z1N7. 1 interaction.
    STRINGi 10090.ENSMUSP00000109802.

    PTM databases

    PhosphoSitei Q9Z1N7.

    Proteomic databases

    PRIDEi Q9Z1N7.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000004780 ; ENSMUSP00000004780 ; ENSMUSG00000004661 . [Q9Z1N7-1 ]
    ENSMUST00000164035 ; ENSMUSP00000131677 ; ENSMUSG00000004661 . [Q9Z1N7-3 ]
    ENSMUST00000171444 ; ENSMUSP00000130173 ; ENSMUSG00000004661 . [Q9Z1N7-1 ]
    GeneIDi 56380.
    KEGGi mmu:56380.
    UCSCi uc009pvt.2. mouse. [Q9Z1N7-1 ]

    Organism-specific databases

    CTDi 10620.
    MGIi MGI:1930768. Arid3b.

    Phylogenomic databases

    eggNOGi NOG327790.
    GeneTreei ENSGT00550000074575.
    HOGENOMi HOG000236281.
    HOVERGENi HBG103680.
    InParanoidi Q9Z1N7.
    OMAi FHVQKVA.
    OrthoDBi EOG77DJ6W.
    PhylomeDBi Q9Z1N7.
    TreeFami TF320364.

    Miscellaneous databases

    NextBioi 312460.
    PROi Q9Z1N7.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q9Z1N7.
    Bgeei Q9Z1N7.
    CleanExi MM_ARID3B.
    Genevestigatori Q9Z1N7.

    Family and domain databases

    Gene3Di 1.10.150.60. 1 hit.
    InterProi IPR001606. ARID/BRIGHT_DNA-bd.
    IPR023334. REKLES_domain.
    [Graphical view ]
    Pfami PF01388. ARID. 1 hit.
    [Graphical view ]
    SMARTi SM00501. BRIGHT. 1 hit.
    [Graphical view ]
    SUPFAMi SSF46774. SSF46774. 1 hit.
    PROSITEi PS51011. ARID. 1 hit.
    PS51486. REKLES. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Bdp, a new member of a family of DNA-binding proteins, associates with the retinoblastoma gene product."
      Numata S., Claudio P.P., Dean C., Giordano A., Croce C.M.
      Cancer Res. 59:3741-3747(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    2. "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] (ISOFORM 3).
      Strain: C57BL/6J.
      Tissue: Brain cortex.
    3. "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] (ISOFORM 2).
      Tissue: Embryo.
    4. "Microarray analysis of PDGFR alpha+ populations in ES cell differentiation culture identifies genes involved in differentiation of mesoderm and mesenchyme including ARID3b that is essential for development of embryonic mesenchymal cells."
      Takebe A., Era T., Okada M., Martin Jakt L., Kuroda Y., Nishikawa S.
      Dev. Biol. 293:25-37(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: DISRUPTION PHENOTYPE, DEVELOPMENTAL STAGE, TISSUE SPECIFICITY, FUNCTION.

    Entry informationi

    Entry nameiARI3B_MOUSE
    AccessioniPrimary (citable) accession number: Q9Z1N7
    Secondary accession number(s): Q3UTG1, Q810L9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 10, 2007
    Last sequence update: May 1, 1999
    Last modified: October 1, 2014
    This is version 80 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, 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