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Q9R1R0

- LHX6_MOUSE

UniProt

Q9R1R0 - LHX6_MOUSE

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Protein

LIM/homeobox protein Lhx6

Gene

Lhx6

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

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. sequence-specific DNA binding Source: InterPro
  2. sequence-specific DNA binding transcription factor activity Source: UniProtKB
  3. 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
Complete GO annotation...

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
Complete GO annotation...

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

BgeeiQ9R1R0.
ExpressionAtlasiQ9R1R0. baseline and differential.
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.
GeneTreeiENSGT00760000118921.
HOGENOMiHOG000038965.
HOVERGENiHBG006261.
InParanoidiQ9R1R0.
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

        10         20         30         40         50
MAQPGSGCKA TTRCLEGTAP PAMAQSDAEA LAGALDKDEG RASPCTPSTP
60 70 80 90 100
SVCSPPSAAS SVPSAGKNIC SSCGLEILDR YLLKVNNLIW HVRCLECSVC
110 120 130 140 150
RTSLRQQNSC YIKNKEIYCK MDYFSRFGTK CARCGRQIYA SDWVRRARGN
160 170 180 190 200
AYHLACFACF SCKRQLSTGE EFGLVEEKVL CRIHYDTMIE NLKRAAENGN
210 220 230 240 250
GLTLEGAVPS EQDSQPKPAK RARTSFTAEQ LQVMQAQFAQ DNNPDAQTLQ
260 270 280 290 300
KLADMTGLSR RVIQVWFQNC RARHKKHTPQ HPVPPSGAPP TRLPSALSDD
310 320 330 340 350
IHYSPFSSPE RARMVTLHGY IESQVQCGQV HCRLPYTAPP VHLKADLDGP
360
LSSRGEKVIL FQY
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]
ENSMUST00000148852; ENSMUSP00000135693; 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 ]
ENSMUST00000148852 ; ENSMUSP00000135693 ; 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 ENSGT00760000118921.
HOGENOMi HOG000038965.
HOVERGENi HBG006261.
InParanoidi Q9R1R0.
KOi K09375.
OrthoDBi EOG744T9J.

Miscellaneous databases

NextBioi 290850.
PROi Q9R1R0.
SOURCEi Search...

Gene expression databases

Bgeei Q9R1R0.
ExpressionAtlasi Q9R1R0. baseline and differential.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 120 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