Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

Q9UPM6 (LHX6_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 141. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
LIM/homeobox protein Lhx6

Short name=LIM homeobox protein 6
Alternative name(s):
LIM/homeobox protein Lhx6.1
Gene names
Name:LHX6
Synonyms:LHX6.1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length363 AA.
Sequence statusComplete.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

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 By similarity.

Subunit structure

Interacts with LDB1 (via the LIM zinc-binding domains) By similarity.

Subcellular location

Nucleus Probable.

Sequence similarities

Contains 1 homeobox DNA-binding domain.

Contains 2 LIM zinc-binding domains.

Sequence caution

The sequence AAI03937.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence AAI03938.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence CAB66505.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Alternative products

This entry describes 6 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9UPM6-1)

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.
Isoform 2 (identifier: Q9UPM6-2)

Also known as: Lhx6.1b;

The sequence of this isoform differs from the canonical sequence as follows:
     324-363: QVQCGQVHCRLPYTAPPVHLKADMDGPLSNRGEKVILFQY → HPFSVLTLPALPHLPVGAPQLPLSR
Isoform 3 (identifier: Q9UPM6-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MYWKHENAAPALPEGCRLPAEGGPATDQVM
Isoform 4 (identifier: Q9UPM6-4)

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MYWKHENAAPALPEGCRLPAEGGPATDQVM
     324-363: QVQCGQVHCRLPYTAPPVHLKADMDGPLSNRGEKVILFQY → HPFSVLTLPALPHLPVGAPQLPLSR
Isoform 5 (identifier: Q9UPM6-5)

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MRRGLCRRSAENPDAGPVM
     324-363: QVQCGQVHCRLPYTAPPVHLKADMDGPLSNRGEKVILFQY → HPFSVLTLPALPHLPVGAPQLPLSR
Isoform 6 (identifier: Q9UPM6-6)

The sequence of this isoform differs from the canonical sequence as follows:
     1-187: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 363363LIM/homeobox protein Lhx6
PRO_0000075794

Regions

Domain70 – 12253LIM zinc-binding 1
Domain131 – 18454LIM zinc-binding 2
DNA binding219 – 27860Homeobox
Region55 – 194140Required for interaction with LDB1 By similarity

Natural variations

Alternative sequence1 – 187187Missing in isoform 6.
VSP_046043
Alternative sequence11M → MYWKHENAAPALPEGCRLPA EGGPATDQVM in isoform 3 and isoform 4.
VSP_037745
Alternative sequence11M → MRRGLCRRSAENPDAGPVM in isoform 5.
VSP_042073
Alternative sequence324 – 36340QVQCG…ILFQY → HPFSVLTLPALPHLPVGAPQ LPLSR in isoform 2, isoform 4 and isoform 5.
VSP_003109

Experimental info

Sequence conflict161E → K in BAA83422. Ref.1
Sequence conflict161E → K in BAA83423. Ref.1
Isoform 2:
Sequence conflict3461L → F in BAA83423. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (Lhx6.1a) [UniParc].

Last modified March 7, 2006. Version 2.
Checksum: 3633B5112D548532

FASTA36340,045
        10         20         30         40         50         60 
MAQPGSGCKA TTRCLEGTAP PAMAQSDAEA LAGALDKDEG QASPCTPSTP SVCSPPSAAS 

        70         80         90        100        110        120 
SVPSAGKNIC SSCGLEILDR YLLKVNNLIW HVRCLECSVC RTSLRQQNSC YIKNKEIFCK 

       130        140        150        160        170        180 
MDYFSRFGTK CARCGRQIYA SDWVRRARGN AYHLACFACF SCKRQLSTGE EFGLVEEKVL 

       190        200        210        220        230        240 
CRIHYDTMIE NLKRAAENGN GLTLEGAVPS EQDSQPKPAK RARTSFTAEQ LQVMQAQFAQ 

       250        260        270        280        290        300 
DNNPDAQTLQ KLADMTGLSR RVIQVWFQNC RARHKKHTPQ HPVPPSGAPP SRLPSALSDD 

       310        320        330        340        350        360 
IHYTPFSSPE RARMVTLHGY IESQVQCGQV HCRLPYTAPP VHLKADMDGP LSNRGEKVIL 


FQY 

« Hide

Isoform 2 (Lhx6.1b) [UniParc].

Checksum: DC0A3056BC56EF37
Show »

FASTA34838,193
Isoform 3 [UniParc].

Checksum: D2A915F07BFC73C0
Show »

FASTA39243,136
Isoform 4 [UniParc].

Checksum: 132637341D6A94B4
Show »

FASTA37741,284
Isoform 5 [UniParc].

Checksum: F78470DB966B0E28
Show »

FASTA36640,160
Isoform 6 [UniParc].

Checksum: 58A580E0C2AEE8FD
Show »

FASTA17619,618

References

« Hide 'large scale' references
[1]"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).
[2]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 3; 5 AND 6).
Tissue: Brain and Hippocampus.
[3]"DNA sequence and analysis of human chromosome 9."
Humphray S.J., Oliver K., Hunt A.R., Plumb R.W., Loveland J.E., Howe K.L., Andrews T.D., Searle S., Hunt S.E., Scott C.E., Jones M.C., Ainscough R., Almeida J.P., Ambrose K.D., Ashwell R.I.S., Babbage A.K., Babbage S., Bagguley C.L. expand/collapse author list , Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beasley H., Beasley O., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burford D., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Chen Y., Clarke G., Clark S.Y., Clee C.M., Clegg S., Collier R.E., Corby N., Crosier M., Cummings A.T., Davies J., Dhami P., Dunn M., Dutta I., Dyer L.W., Earthrowl M.E., Faulkner L., Fleming C.J., Frankish A., Frankland J.A., French L., Fricker D.G., Garner P., Garnett J., Ghori J., Gilbert J.G.R., Glison C., Grafham D.V., Gribble S., Griffiths C., Griffiths-Jones S., Grocock R., Guy J., Hall R.E., Hammond S., Harley J.L., Harrison E.S.I., Hart E.A., Heath P.D., Henderson C.D., Hopkins B.L., Howard P.J., Howden P.J., Huckle E., Johnson C., Johnson D., Joy A.A., Kay M., Keenan S., Kershaw J.K., Kimberley A.M., King A., Knights A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C., Lloyd D.M., Lovell J., Martin S., Mashreghi-Mohammadi M., Matthews L., McLaren S., McLay K.E., McMurray A., Milne S., Nickerson T., Nisbett J., Nordsiek G., Pearce A.V., Peck A.I., Porter K.M., Pandian R., Pelan S., Phillimore B., Povey S., Ramsey Y., Rand V., Scharfe M., Sehra H.K., Shownkeen R., Sims S.K., Skuce C.D., Smith M., Steward C.A., Swarbreck D., Sycamore N., Tester J., Thorpe A., Tracey A., Tromans A., Thomas D.W., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Williams S.A., Wilming L., Wray P.W., Young L., Ashurst J.L., Coulson A., Blocker H., Durbin R.M., Sulston J.E., Hubbard T., Jackson M.J., Bentley D.R., Beck S., Rogers J., Dunham I.
Nature 429:369-374(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs."
Wiemann S., Weil B., Wellenreuther R., Gassenhuber J., Glassl S., Ansorge W., Boecher M., Bloecker H., Bauersachs S., Blum H., Lauber J., Duesterhoeft A., Beyer A., Koehrer K., Strack N., Mewes H.-W., Ottenwaelder B., Obermaier B. expand/collapse author list , Tampe J., Heubner D., Wambutt R., Korn B., Klein M., Poustka A.
Genome Res. 11:422-435(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: PARTIAL NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
Tissue: Amygdala.
[6]"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: PARTIAL NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 3 AND 4).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB031041 mRNA. Translation: BAA83422.1.
AB031042 mRNA. Translation: BAA83423.1.
AK126982 mRNA. No translation available.
AK289827 mRNA. Translation: BAF82516.1.
AK297175 mRNA. Translation: BAH12516.1.
AK299709 mRNA. Translation: BAH13108.1.
AK313808 mRNA. Translation: BAG36544.1.
AL162424 Genomic DNA. Translation: CAO03566.1.
AL162424 Genomic DNA. Translation: CAI14703.1.
AL162424 Genomic DNA. Translation: CAI14704.1.
AL162424 Genomic DNA. Translation: CAO03565.1.
CH471090 Genomic DNA. Translation: EAW87515.1.
CH471090 Genomic DNA. Translation: EAW87516.1.
AL136570 mRNA. Translation: CAB66505.1. Different initiation.
BC103936 mRNA. Translation: AAI03937.1. Different initiation.
BC103937 mRNA. Translation: AAI03938.1. Different initiation.
CCDSCCDS56583.1. [Q9UPM6-1]
CCDS56584.1. [Q9UPM6-5]
CCDS59144.1. [Q9UPM6-6]
CCDS6837.2. [Q9UPM6-4]
CCDS6838.2. [Q9UPM6-3]
PIRT46907.
RefSeqNP_001229262.1. NM_001242333.1. [Q9UPM6-5]
NP_001229263.1. NM_001242334.1. [Q9UPM6-1]
NP_001229264.1. NM_001242335.1. [Q9UPM6-6]
NP_055183.2. NM_014368.4. [Q9UPM6-3]
NP_954629.2. NM_199160.3. [Q9UPM6-4]
UniGeneHs.103137.

3D structure databases

ProteinModelPortalQ9UPM6.
SMRQ9UPM6. Positions 69-187, 214-277.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

MINTMINT-4718974.
STRING9606.ENSP00000377854.

Polymorphism databases

DMDM90185239.

Proteomic databases

PaxDbQ9UPM6.
PRIDEQ9UPM6.

Protocols and materials databases

DNASU26468.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000340587; ENSP00000340137; ENSG00000106852. [Q9UPM6-4]
ENST00000373754; ENSP00000362859; ENSG00000106852. [Q9UPM6-2]
ENST00000373755; ENSP00000362860; ENSG00000106852. [Q9UPM6-1]
ENST00000394319; ENSP00000377854; ENSG00000106852. [Q9UPM6-3]
ENST00000541397; ENSP00000441464; ENSG00000106852. [Q9UPM6-5]
ENST00000559895; ENSP00000475927; ENSG00000106852. [Q9UPM6-6]
GeneID26468.
KEGGhsa:26468.
UCSCuc004blx.4. human. [Q9UPM6-3]
uc004bly.4. human. [Q9UPM6-4]
uc010mvw.3. human. [Q9UPM6-1]
uc022bmx.1. human. [Q9UPM6-5]

Organism-specific databases

CTD26468.
GeneCardsGC09M124964.
HGNCHGNC:21735. LHX6.
HPAHPA047854.
MIM608215. gene.
neXtProtNX_Q9UPM6.
PharmGKBPA134949308.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG264882.
HOGENOMHOG000038965.
HOVERGENHBG006261.
InParanoidQ9UPM6.
KOK09375.
OMALSEDIHY.
OrthoDBEOG744T9J.
PhylomeDBQ9UPM6.
TreeFamTF315442.

Gene expression databases

ArrayExpressQ9UPM6.
BgeeQ9UPM6.
CleanExHS_LHX6.
GenevestigatorQ9UPM6.

Family and domain databases

Gene3D1.10.10.60. 1 hit.
2.10.110.10. 2 hits.
InterProIPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR001781. Znf_LIM.
[Graphical view]
PfamPF00046. Homeobox. 1 hit.
PF00412. LIM. 2 hits.
[Graphical view]
SMARTSM00389. HOX. 1 hit.
SM00132. LIM. 2 hits.
[Graphical view]
SUPFAMSSF46689. SSF46689. 1 hit.
PROSITEPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
PS00478. LIM_DOMAIN_1. 2 hits.
PS50023. LIM_DOMAIN_2. 2 hits.
[Graphical view]
ProtoNetSearch...

Other

GeneWikiLHX6.
GenomeRNAi26468.
NextBio48705.
PROQ9UPM6.
SOURCESearch...

Entry information

Entry nameLHX6_HUMAN
AccessionPrimary (citable) accession number: Q9UPM6
Secondary accession number(s): A6PVQ1 expand/collapse secondary AC list , A6PVQ2, A8K1B2, B7Z4D0, H0YN76, Q5T7S7, Q5T7S8, Q9NTK3, Q9UPM5
Entry history
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: March 7, 2006
Last modified: July 9, 2014
This is version 141 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 9

Human chromosome 9: entries, gene names and cross-references to MIM