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Q9R1R0

- LHX6_MOUSE

UniProt

Q9R1R0 - LHX6_MOUSE

Protein

LIM/homeobox protein Lhx6

Gene

Lhx6

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 119 (01 Oct 2014)
      Sequence version 2 (27 Jul 2011)
      Previous versions | rss
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    Functioni

    Probable transcription factor required for the expression of a subset of genes involved in interneurons migration and development. Functions in the specification of cortical interneuron subtypes and in the migration of GABAergic interneuron precursors from the subpallium to the cerebral cortex.5 Publications

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    DNA bindingi219 – 27860HomeoboxPROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. protein binding Source: UniProtKB
    2. sequence-specific DNA binding Source: InterPro
    3. sequence-specific DNA binding transcription factor activity Source: UniProtKB
    4. zinc ion binding Source: InterPro

    GO - Biological processi

    1. cell maturation Source: MGI
    2. cerebral cortex GABAergic interneuron migration Source: MGI
    3. cerebral cortex neuron differentiation Source: MGI
    4. cerebral cortex radially oriented cell migration Source: MGI
    5. cerebral cortex tangential migration Source: MGI
    6. forebrain neuron development Source: MGI
    7. forebrain neuron fate commitment Source: MGI
    8. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Molecular functioni

    Developmental protein

    Keywords - Biological processi

    Differentiation, Neurogenesis, Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding, Metal-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    LIM/homeobox protein Lhx6
    Short name:
    LIM homeobox protein 6
    Alternative name(s):
    LIM/homeobox protein Lhx6.1
    Gene namesi
    Name:Lhx6
    Synonyms:Lhx6.1
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 2

    Organism-specific databases

    MGIiMGI:1306803. Lhx6.

    Subcellular locationi

    Nucleus Curated

    GO - Cellular componenti

    1. nucleus Source: MGI

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Disruption phenotypei

    Mice lacking Lhx6 fail to thrive, develop general weakness and die within the first 2 weeks after birth.2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 363363LIM/homeobox protein Lhx6PRO_0000075795Add
    BLAST

    Proteomic databases

    PRIDEiQ9R1R0.

    Expressioni

    Tissue specificityi

    Brain specific. Expressed by neurons in the amygdala that are activated by reproductive olfactory stimuli and project in regions of the hypothalamus involved in reproduction (at protein level).2 Publications

    Developmental stagei

    Specifically expressed during brain maturation from E14.5 to P2 by a subset of tangentially migrating interneurons. Barely detectable in adult brain. Isoform 1 expression peaks at P2 and remains high in adulthood compared to isoform 2. Expressed in preoptic area, hypothalamic regions and the first branchial arch at E9.5. Expressed uniformly in the odontogenic mesenchyme of the first branchial arch prior to initiation of tooth development. During odontogenesis expression is restricted to the mesenchyme participating in the formation of individual teeth. Expressed in olfactory bulb, arcuate nucleus, medial glanglionic eminence and preoptic area at E13.5 and E14.5. Expression spread to the cortex and hippocampus at P1.0. Preferentially expressed in parvalbumin or somatostatin positive cortical interneurons.4 Publications

    Gene expression databases

    ArrayExpressiQ9R1R0.
    BgeeiQ9R1R0.
    GenevestigatoriQ9R1R0.

    Interactioni

    Subunit structurei

    Interacts with LDB1 (via the LIM zinc-binding domains).1 Publication

    Structurei

    3D structure databases

    ProteinModelPortaliQ9R1R0.
    SMRiQ9R1R0. Positions 69-187, 214-277.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini70 – 12253LIM zinc-binding 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini131 – 18454LIM zinc-binding 2PROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni55 – 194140Required for interaction with LDB1Add
    BLAST

    Sequence similaritiesi

    Contains 1 homeobox DNA-binding domain.PROSITE-ProRule annotation
    Contains 2 LIM zinc-binding domains.PROSITE-ProRule annotation

    Keywords - Domaini

    Homeobox, LIM domain, Repeat

    Phylogenomic databases

    eggNOGiNOG264882.
    GeneTreeiENSGT00740000114869.
    HOGENOMiHOG000038965.
    HOVERGENiHBG006261.
    InParanoidiQ6P1H2.
    KOiK09375.
    OrthoDBiEOG744T9J.

    Family and domain databases

    Gene3Di1.10.10.60. 1 hit.
    2.10.110.10. 2 hits.
    InterProiIPR017970. Homeobox_CS.
    IPR001356. Homeobox_dom.
    IPR009057. Homeodomain-like.
    IPR001781. Znf_LIM.
    [Graphical view]
    PfamiPF00046. Homeobox. 1 hit.
    PF00412. LIM. 2 hits.
    [Graphical view]
    SMARTiSM00389. HOX. 1 hit.
    SM00132. LIM. 2 hits.
    [Graphical view]
    SUPFAMiSSF46689. SSF46689. 1 hit.
    PROSITEiPS00027. HOMEOBOX_1. 1 hit.
    PS50071. HOMEOBOX_2. 1 hit.
    PS00478. LIM_DOMAIN_1. 2 hits.
    PS50023. LIM_DOMAIN_2. 2 hits.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q9R1R0-1) [UniParc]FASTAAdd to Basket

    Also known as: Lhx6.1a

    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

    MAQPGSGCKA TTRCLEGTAP PAMAQSDAEA LAGALDKDEG RASPCTPSTP    50
    SVCSPPSAAS SVPSAGKNIC SSCGLEILDR YLLKVNNLIW HVRCLECSVC 100
    RTSLRQQNSC YIKNKEIYCK MDYFSRFGTK CARCGRQIYA SDWVRRARGN 150
    AYHLACFACF SCKRQLSTGE EFGLVEEKVL CRIHYDTMIE NLKRAAENGN 200
    GLTLEGAVPS EQDSQPKPAK RARTSFTAEQ LQVMQAQFAQ DNNPDAQTLQ 250
    KLADMTGLSR RVIQVWFQNC RARHKKHTPQ HPVPPSGAPP TRLPSALSDD 300
    IHYSPFSSPE RARMVTLHGY IESQVQCGQV HCRLPYTAPP VHLKADLDGP 350
    LSSRGEKVIL FQY 363
    Length:363
    Mass (Da):40,044
    Last modified:July 27, 2011 - v2
    Checksum:i50A937B64A1AB277
    GO
    Isoform 2 (identifier: Q9R1R0-2) [UniParc]FASTAAdd to Basket

    Also known as: Lhx6.1b

    The sequence of this isoform differs from the canonical sequence as follows:
         324-363: QVQCGQVHCRLPYTAPPVHLKADLDGPLSSRGEKVILFQY → HPFSVLTLPALAHLSMGTTQLPLSR

    Show »
    Length:348
    Mass (Da):38,267
    Checksum:iABB40B2D6216F0E2
    GO

    Sequence cautioni

    The sequence CAA04011.1 differs from that shown. Reason: Several sequencing errors.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti19 – 191A → T in BAA83420. (PubMed:10393337)Curated
    Sequence conflicti19 – 191A → T in BAA83421. (PubMed:10393337)Curated
    Sequence conflicti194 – 1941R → K in BAA83420. (PubMed:10393337)Curated
    Sequence conflicti194 – 1941R → K in BAA83421. (PubMed:10393337)Curated
    Sequence conflicti258 – 2581L → F in BAA83420. (PubMed:10393337)Curated
    Sequence conflicti258 – 2581L → F in BAA83421. (PubMed:10393337)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei324 – 36340QVQCG…ILFQY → HPFSVLTLPALAHLSMGTTQ LPLSR in isoform 2. 1 PublicationVSP_003110Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ000337 mRNA. Translation: CAA04011.1. Sequence problems.
    AB031040 mRNA. Translation: BAA83421.1.
    AB031039 mRNA. Translation: BAA83420.1.
    AL773525 Genomic DNA. Translation: CAM16137.1.
    BC065077 mRNA. Translation: AAH65077.1.
    CCDSiCCDS38111.1. [Q9R1R0-2]
    CCDS38113.1. [Q9R1R0-1]
    RefSeqiNP_001076595.1. NM_001083126.1. [Q9R1R0-1]
    NP_001076596.1. NM_001083127.1. [Q9R1R0-2]
    NP_032526.2. NM_008500.2.
    XP_006497807.1. XM_006497744.1. [Q9R1R0-1]
    UniGeneiMm.12881.

    Genome annotation databases

    EnsembliENSMUST00000112961; ENSMUSP00000108585; ENSMUSG00000026890. [Q9R1R0-1]
    ENSMUST00000112963; ENSMUSP00000108587; ENSMUSG00000026890. [Q9R1R0-1]
    ENSMUST00000112966; ENSMUSP00000108590; ENSMUSG00000026890. [Q9R1R0-2]
    GeneIDi16874.
    KEGGimmu:16874.
    UCSCiuc008jld.1. mouse. [Q9R1R0-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ000337 mRNA. Translation: CAA04011.1 . Sequence problems.
    AB031040 mRNA. Translation: BAA83421.1 .
    AB031039 mRNA. Translation: BAA83420.1 .
    AL773525 Genomic DNA. Translation: CAM16137.1 .
    BC065077 mRNA. Translation: AAH65077.1 .
    CCDSi CCDS38111.1. [Q9R1R0-2 ]
    CCDS38113.1. [Q9R1R0-1 ]
    RefSeqi NP_001076595.1. NM_001083126.1. [Q9R1R0-1 ]
    NP_001076596.1. NM_001083127.1. [Q9R1R0-2 ]
    NP_032526.2. NM_008500.2.
    XP_006497807.1. XM_006497744.1. [Q9R1R0-1 ]
    UniGenei Mm.12881.

    3D structure databases

    ProteinModelPortali Q9R1R0.
    SMRi Q9R1R0. Positions 69-187, 214-277.
    ModBasei Search...
    MobiDBi Search...

    Proteomic databases

    PRIDEi Q9R1R0.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000112961 ; ENSMUSP00000108585 ; ENSMUSG00000026890 . [Q9R1R0-1 ]
    ENSMUST00000112963 ; ENSMUSP00000108587 ; ENSMUSG00000026890 . [Q9R1R0-1 ]
    ENSMUST00000112966 ; ENSMUSP00000108590 ; ENSMUSG00000026890 . [Q9R1R0-2 ]
    GeneIDi 16874.
    KEGGi mmu:16874.
    UCSCi uc008jld.1. mouse. [Q9R1R0-1 ]

    Organism-specific databases

    CTDi 26468.
    MGIi MGI:1306803. Lhx6.

    Phylogenomic databases

    eggNOGi NOG264882.
    GeneTreei ENSGT00740000114869.
    HOGENOMi HOG000038965.
    HOVERGENi HBG006261.
    InParanoidi Q6P1H2.
    KOi K09375.
    OrthoDBi EOG744T9J.

    Miscellaneous databases

    NextBioi 290850.
    PROi Q9R1R0.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q9R1R0.
    Bgeei Q9R1R0.
    Genevestigatori Q9R1R0.

    Family and domain databases

    Gene3Di 1.10.10.60. 1 hit.
    2.10.110.10. 2 hits.
    InterProi IPR017970. Homeobox_CS.
    IPR001356. Homeobox_dom.
    IPR009057. Homeodomain-like.
    IPR001781. Znf_LIM.
    [Graphical view ]
    Pfami PF00046. Homeobox. 1 hit.
    PF00412. LIM. 2 hits.
    [Graphical view ]
    SMARTi SM00389. HOX. 1 hit.
    SM00132. LIM. 2 hits.
    [Graphical view ]
    SUPFAMi SSF46689. SSF46689. 1 hit.
    PROSITEi PS00027. HOMEOBOX_1. 1 hit.
    PS50071. HOMEOBOX_2. 1 hit.
    PS00478. LIM_DOMAIN_1. 2 hits.
    PS50023. LIM_DOMAIN_2. 2 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Expression and regulation of Lhx6 and Lhx7, a novel subfamily of LIM homeodomain encoding genes, suggests a role in mammalian head development."
      Grigoriou M., Tucker A.S., Sharpe P.T., Pachnis V.
      Development 125:2063-2074(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), DEVELOPMENTAL STAGE.
    2. "A brain region-specific gene product Lhx6.1 interacts with Ldb1 through tandem LIM-domains."
      Kimura N., Ueno M., Nakashima K., Taga T.
      J. Biochem. 126:180-187(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), FUNCTION, INTERACTION WITH LDB1, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE (ISOFORMS 1 AND 2).
      Tissue: Fetal brain.
    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 1).
      Strain: C57BL/6.
      Tissue: Brain.
    4. "The medial ganglionic eminence gives rise to a population of early neurons in the developing cerebral cortex."
      Lavdas A.A., Grigoriou M., Pachnis V., Parnavelas J.G.
      J. Neurosci. 19:7881-7888(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: DEVELOPMENTAL STAGE.
    5. "Lhx6 regulates the migration of cortical interneurons from the ventral telencephalon but does not specify their GABA phenotype."
      Alifragis P., Liapi A., Parnavelas J.G.
      J. Neurosci. 24:5643-5648(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    6. "Lhx6 delineates a pathway mediating innate reproductive behaviors from the amygdala to the hypothalamus."
      Choi G.B., Dong H.-W., Murphy A.J., Valenzuela D.M., Yancopoulos G.D., Swanson L.W., Anderson D.J.
      Neuron 46:647-660(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: TISSUE SPECIFICITY.
    7. "Lhx6 activity is required for the normal migration and specification of cortical interneuron subtypes."
      Liodis P., Denaxa M., Grigoriou M., Akufo-Addo C., Yanagawa Y., Pachnis V.
      J. Neurosci. 27:3078-3089(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: DISRUPTION PHENOTYPE, FUNCTION, DEVELOPMENTAL STAGE.
    8. "NKX2.1 specifies cortical interneuron fate by activating Lhx6."
      Du T., Xu Q., Ocbina P.J., Anderson S.A.
      Development 135:1559-1567(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    9. "Distinct molecular pathways for development of telencephalic interneuron subtypes revealed through analysis of Lhx6 mutants."
      Zhao Y., Flandin P., Long J.E., Cuesta M.D., Westphal H., Rubenstein J.L.R.
      J. Comp. Neurol. 510:79-99(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: DISRUPTION PHENOTYPE, FUNCTION, DEVELOPMENTAL STAGE.

    Entry informationi

    Entry nameiLHX6_MOUSE
    AccessioniPrimary (citable) accession number: Q9R1R0
    Secondary accession number(s): O88706, Q6P1H2, Q9R1R1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: July 27, 2011
    Last modified: October 1, 2014
    This is version 119 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