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P81067

- IRX3_MOUSE

UniProt

P81067 - IRX3_MOUSE

Protein

Iroquois-class homeodomain protein IRX-3

Gene

Irx3

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 101 (01 Oct 2014)
      Sequence version 2 (03 Nov 2009)
      Previous versions | rss
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    Functioni

    Transcription factor. Involved in SHH-dependent neural patterning. Together with NKX2-2 and NKX6-1 acts to restrict the generation of motor neurons to the appropriate region of the neural tube. Belongs to the class I proteins of neuronal progenitor factors, which are repressed by SHH signals. Involved in the transcriptional repression of MNX1 in non-motor neuron cells.2 Publications

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    DNA bindingi130 – 19263Homeobox; TALE-typePROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. sequence-specific DNA binding Source: InterPro
    2. sequence-specific DNA binding transcription factor activity Source: InterPro

    GO - Biological processi

    1. mesoderm development Source: MGI
    2. metanephros development Source: UniProtKB
    3. negative regulation of neuron differentiation Source: MGI
    4. positive regulation of neuron differentiation Source: MGI
    5. proximal/distal pattern formation involved in nephron development Source: UniProtKB
    6. specification of loop of Henle identity Source: UniProtKB
    7. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Molecular functioni

    Developmental protein, Repressor

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Iroquois-class homeodomain protein IRX-3
    Alternative name(s):
    Homeodomain protein IRXB1
    Iroquois homeobox protein 3
    Gene namesi
    Name:Irx3
    Synonyms:Irxb1
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 8

    Organism-specific databases

    MGIiMGI:1197522. Irx3.

    Subcellular locationi

    Nucleus Curated

    GO - Cellular componenti

    1. axon Source: MGI
    2. cytoplasm Source: MGI
    3. nucleus Source: MGI

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 507507Iroquois-class homeodomain protein IRX-3PRO_0000049156Add
    BLAST

    Proteomic databases

    PRIDEiP81067.

    PTM databases

    PhosphoSiteiP81067.

    Expressioni

    Tissue specificityi

    Expressed by neural progenitor cells in discrete domains of the ventral neural tube. Also expressed in specific and overlapping patterns with Irx1 and Irx2 in the developing and adult metanephric kidney. In the adult metanephros, renal expression is confined to the S3 segment of the proximal tubule, in the loop of Henle.2 Publications

    Developmental stagei

    The earliest expressed of the Irx family, with expression seen in trophectoderm-derived extraembryonic tissues from E6.5, including expression in the chorionic ectoderm at E8.0. Embryonic expression starts at the end of gastrulation (E7.5) in the ectodermal layer which gives rise to the nervous system. At E8.0, expression is confined to the thickening neural ectoderm corresponding to the future mesencephalon (midbrain) and rhombencephalon (hindbrain) and from E8.5 onwards, expression also includes the rostral part of the closing neural tube. After neural tube closure at E9.5, expression predominates in the CNS in the midbrain, hindbrain and spinal cord. Also expressed in a number of tissues outside of the CNS including ectodermal layer of the branchial arches. Expressed in the prospective limb buds of the lateral plate mesoderm, and from E10.5 onwards a gradient exists along the dorsoventral and proximodistal axes of developing limbs. Expressed in the notochord at stage E9.0. At E9.5 found in the cephalic mesoderm surrounding the optic vesicle. Around E10.5, expression in the head mesoderm extends into the nasal pits. By E12.5, still expressed in the mesenchyme, and expressions begins in specific subsets of post-mitotic cells in the neuroretina. As development ensues, expression increases in the neuroretina and mesenchymal expression gradually decreases. At E16.5, expressed exclusively in the inner neuroblast layers of the neuroretina. In the developing heart, first expressed in the trabecules of embryonic ventricles at E9.5, and from then onwards localizes specifically to the trabeculated myocardium of the ventricles.4 Publications

    Gene expression databases

    BgeeiP81067.
    CleanExiMM_IRX3.
    GenevestigatoriP81067.

    Structurei

    3D structure databases

    ProteinModelPortaliP81067.
    SMRiP81067. Positions 139-188.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi24 – 296Poly-Gly
    Compositional biasi64 – 7310Poly-Ala
    Compositional biasi204 – 26057Glu-richAdd
    BLAST
    Compositional biasi315 – 429115Pro-richAdd
    BLAST
    Compositional biasi379 – 46183Ala-richAdd
    BLAST

    Sequence similaritiesi

    Belongs to the TALE/IRO homeobox family.Curated
    Contains 1 homeobox DNA-binding domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Homeobox

    Phylogenomic databases

    eggNOGiNOG315186.
    GeneTreeiENSGT00750000117717.
    HOGENOMiHOG000234546.
    HOVERGENiHBG006180.
    InParanoidiQ3UPZ3.
    OMAiGPISDSK.
    OrthoDBiEOG7RV9HC.
    PhylomeDBiP81067.
    TreeFamiTF319371.

    Family and domain databases

    Gene3Di1.10.10.60. 1 hit.
    InterProiIPR017970. Homeobox_CS.
    IPR001356. Homeobox_dom.
    IPR008422. Homeobox_KN_domain.
    IPR009057. Homeodomain-like.
    IPR003893. Iroquois_homeo.
    [Graphical view]
    PfamiPF05920. Homeobox_KN. 1 hit.
    [Graphical view]
    SMARTiSM00389. HOX. 1 hit.
    SM00548. IRO. 1 hit.
    [Graphical view]
    SUPFAMiSSF46689. SSF46689. 1 hit.
    PROSITEiPS00027. HOMEOBOX_1. 1 hit.
    PS50071. HOMEOBOX_2. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: P81067-1) [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

    MSFPQLGYQY IRPLYPPERP GAAGGGGGGS SAGGRSGPGA GASELAASGS    50
    LSNVLSSVYG APYAAAAAAA AAAQGYGAFL PYATELPIFP QLGAQYELKD 100
    SPGVQHPATA AAFPHPHPAF YPYGQYQFGD PSRPKNATRE STSTLKAWLN 150
    EHRKNPYPTK GEKIMLAIIT KMTLTQVSTW FANARRRLKK ENKMTWAPRS 200
    RTDEEGNAYG SEREEEDEEE DEEESKRELE MEEEELAGEE EDTGGEGLAD 250
    DDEDEEIDLE NLDSAAAGSE LTLAGAAHRN GDFGLGPISD CKTSDSDDSS 300
    EGLEDRPLSV LSLAPPPPPV ARAPASPPSP PSSLDPCAPA PAPSSALQKP 350
    KIWSLAETAT SPDNPRRSPP GAGGSPPGAA VAPPTLQLSP AAAAAAAAAH 400
    RLVSAPLGKF PAWTNRPFPG PPAGPRPHPL SMLGSAPQHL LGLPGAAGHP 450
    AAAAAAYARP AEPESGTDRC SALEVEKKLL KTAFQPVPRR PQNHLDAALV 500
    LSALSSS 507
    Length:507
    Mass (Da):52,693
    Last modified:November 3, 2009 - v2
    Checksum:i04FD67E8F5C29AB6
    GO
    Isoform 2 (identifier: P81067-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         468-507: DRCSALEVEK...ALVLSALSSS → GDKKNIAVVP...NFSTIFKSLY

    Note: No experimental confirmation available.

    Show »
    Length:522
    Mass (Da):54,893
    Checksum:i65929DB6FC66C07E
    GO

    Sequence cautioni

    The sequence CAA75233.1 differs from that shown. Reason: Frameshift at positions 239 and 254.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti494 – 4941H → R in CAA75233. (PubMed:9486539)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei468 – 50740DRCSA…ALSSS → GDKKNIAVVPWKWRKSYSRQ LSSRCQGGHRTIWTLLWSYQ LSPRLNFSTIFKSLY in isoform 2. 1 PublicationVSP_038351Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y15001 mRNA. Translation: CAA75233.1. Frameshift.
    AK143023 mRNA. Translation: BAE25251.1.
    CH466525 Genomic DNA. Translation: EDL11081.1.
    BC085500 mRNA. Translation: AAH85500.1.
    CCDSiCCDS57630.1. [P81067-2]
    CCDS57631.1. [P81067-1]
    RefSeqiNP_001240751.1. NM_001253822.1. [P81067-2]
    NP_032419.2. NM_008393.3. [P81067-1]
    UniGeneiMm.238044.

    Genome annotation databases

    EnsembliENSMUST00000093312; ENSMUSP00000091002; ENSMUSG00000031734. [P81067-2]
    ENSMUST00000175795; ENSMUSP00000135488; ENSMUSG00000031734. [P81067-1]
    GeneIDi16373.
    KEGGimmu:16373.
    UCSCiuc009msu.2. mouse. [P81067-1]
    uc009msv.2. mouse. [P81067-2]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y15001 mRNA. Translation: CAA75233.1 . Frameshift.
    AK143023 mRNA. Translation: BAE25251.1 .
    CH466525 Genomic DNA. Translation: EDL11081.1 .
    BC085500 mRNA. Translation: AAH85500.1 .
    CCDSi CCDS57630.1. [P81067-2 ]
    CCDS57631.1. [P81067-1 ]
    RefSeqi NP_001240751.1. NM_001253822.1. [P81067-2 ]
    NP_032419.2. NM_008393.3. [P81067-1 ]
    UniGenei Mm.238044.

    3D structure databases

    ProteinModelPortali P81067.
    SMRi P81067. Positions 139-188.
    ModBasei Search...
    MobiDBi Search...

    PTM databases

    PhosphoSitei P81067.

    Proteomic databases

    PRIDEi P81067.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000093312 ; ENSMUSP00000091002 ; ENSMUSG00000031734 . [P81067-2 ]
    ENSMUST00000175795 ; ENSMUSP00000135488 ; ENSMUSG00000031734 . [P81067-1 ]
    GeneIDi 16373.
    KEGGi mmu:16373.
    UCSCi uc009msu.2. mouse. [P81067-1 ]
    uc009msv.2. mouse. [P81067-2 ]

    Organism-specific databases

    CTDi 79191.
    MGIi MGI:1197522. Irx3.

    Phylogenomic databases

    eggNOGi NOG315186.
    GeneTreei ENSGT00750000117717.
    HOGENOMi HOG000234546.
    HOVERGENi HBG006180.
    InParanoidi Q3UPZ3.
    OMAi GPISDSK.
    OrthoDBi EOG7RV9HC.
    PhylomeDBi P81067.
    TreeFami TF319371.

    Miscellaneous databases

    NextBioi 289504.
    PROi P81067.
    SOURCEi Search...

    Gene expression databases

    Bgeei P81067.
    CleanExi MM_IRX3.
    Genevestigatori P81067.

    Family and domain databases

    Gene3Di 1.10.10.60. 1 hit.
    InterProi IPR017970. Homeobox_CS.
    IPR001356. Homeobox_dom.
    IPR008422. Homeobox_KN_domain.
    IPR009057. Homeodomain-like.
    IPR003893. Iroquois_homeo.
    [Graphical view ]
    Pfami PF05920. Homeobox_KN. 1 hit.
    [Graphical view ]
    SMARTi SM00389. HOX. 1 hit.
    SM00548. IRO. 1 hit.
    [Graphical view ]
    SUPFAMi SSF46689. SSF46689. 1 hit.
    PROSITEi PS00027. HOMEOBOX_1. 1 hit.
    PS50071. HOMEOBOX_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Identification of the vertebrate Iroquois homeobox gene family with overlapping expression during early development of the nervous system."
      Bosse A., Zulch A., Becker M.B., Torres M., Gomez-Skarmeta J.-L., Modolell J., Gruss P.
      Mech. Dev. 69:169-181(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), DEVELOPMENTAL STAGE.
    2. "Patterning the embryonic heart: identification of five mouse Iroquois homeobox genes in the developing heart."
      Christoffels V.M., Keijser A.G.M., Houweling A.C., Clout D.E.W., Moorman A.F.M.
      Dev. Biol. 224:263-274(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), DEVELOPMENTAL STAGE.
      Strain: FVB/N.
      Tissue: Embryonic heart.
    3. "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 2).
      Strain: C57BL/6J.
      Tissue: Lung.
    4. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
      Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    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] (ISOFORM 1).
      Strain: C57BL/6.
      Tissue: Eye.
    6. "Xiro3 encodes a Xenopus homolog of the Drosophila Iroquois genes and functions in neural specification."
      Bellefroid E.J., Kobbe A., Gruss P., Pieler T., Gurdon J.B., Papalopulu N.
      EMBO J. 17:191-203(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: DEVELOPMENTAL STAGE.
    7. "A homeodomain protein code specifies progenitor cell identity and neuronal fate in the ventral neural tube."
      Briscoe J., Pierani A., Jessell T.M., Ericson J.
      Cell 101:435-445(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, TISSUE SPECIFICITY.
    8. "Expression of two novel mouse Iroquois-class homeobox genes during neurogenesis."
      Cohen D.R., Cheng C.W., Cheng S.H., Hui C.-C.
      Mech. Dev. 91:317-321(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: DEVELOPMENTAL STAGE.
    9. "Analysis of embryonic motoneuron gene regulation: derepression of general activators function in concert with enhancer factors."
      Lee S.K., Jurata L.W., Funahashi J., Ruiz E.C., Pfaff S.L.
      Development 131:3295-3306(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS TRANSCRIPTIONAL REPRESSOR.
    10. "The prepattern transcription factor Irx3 directs nephron segment identity."
      Reggiani L., Raciti D., Airik R., Kispert A., Braendli A.W.
      Genes Dev. 21:2358-2370(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: TISSUE SPECIFICITY.

    Entry informationi

    Entry nameiIRX3_MOUSE
    AccessioniPrimary (citable) accession number: P81067
    Secondary accession number(s): Q3UPZ3, Q5U3K8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1998
    Last sequence update: November 3, 2009
    Last modified: October 1, 2014
    This is version 101 of the entry and version 2 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