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Protein

LIM/homeobox protein Lhx6

Gene

LHX6

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 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 (By similarity).By similarity

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi219 – 278HomeoboxPROSITE-ProRule annotationAdd BLAST60

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Differentiation, Neurogenesis, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000106852-MONOMER.

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
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 9

Organism-specific databases

HGNCiHGNC:21735. LHX6.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi26468.
OpenTargetsiENSG00000106852.
PharmGKBiPA134949308.

Polymorphism and mutation databases

BioMutaiLHX6.
DMDMi90185239.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000757941 – 363LIM/homeobox protein Lhx6Add BLAST363

Proteomic databases

PaxDbiQ9UPM6.
PRIDEiQ9UPM6.

PTM databases

iPTMnetiQ9UPM6.
PhosphoSitePlusiQ9UPM6.

Expressioni

Gene expression databases

BgeeiENSG00000106852.
CleanExiHS_LHX6.
ExpressionAtlasiQ9UPM6. baseline and differential.
GenevisibleiQ9UPM6. HS.

Organism-specific databases

HPAiHPA047854.
HPA058319.

Interactioni

Subunit structurei

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

Binary interactionsi

WithEntry#Exp.IntActNotes
LDB1Q86U703EBI-10258746,EBI-677177

Protein-protein interaction databases

BioGridi117692. 22 interactors.
IntActiQ9UPM6. 2 interactors.
MINTiMINT-4718974.
STRINGi9606.ENSP00000377854.

Structurei

3D structure databases

ProteinModelPortaliQ9UPM6.
SMRiQ9UPM6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini70 – 122LIM zinc-binding 1PROSITE-ProRule annotationAdd BLAST53
Domaini131 – 184LIM zinc-binding 2PROSITE-ProRule annotationAdd BLAST54

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni55 – 194Required for interaction with LDB1By similarityAdd BLAST140

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

eggNOGiKOG0490. Eukaryota.
ENOG410YIJ3. LUCA.
GeneTreeiENSGT00760000118921.
HOGENOMiHOG000038965.
HOVERGENiHBG006261.
InParanoidiQ9UPM6.
KOiK09375.
OMAiKNVCASC.
OrthoDBiEOG091G0EXT.
PhylomeDBiQ9UPM6.
TreeFamiTF315442.

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 (6)i

Sequence statusi: Complete.

This entry describes 6 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9UPM6-1) [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 QASPCTPSTP
60 70 80 90 100
SVCSPPSAAS SVPSAGKNIC SSCGLEILDR YLLKVNNLIW HVRCLECSVC
110 120 130 140 150
RTSLRQQNSC YIKNKEIFCK 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 SRLPSALSDD
310 320 330 340 350
IHYTPFSSPE RARMVTLHGY IESQVQCGQV HCRLPYTAPP VHLKADMDGP
360
LSNRGEKVIL FQY
Length:363
Mass (Da):40,045
Last modified:March 7, 2006 - v2
Checksum:i3633B5112D548532
GO
Isoform 2 (identifier: Q9UPM6-2) [UniParc]FASTAAdd to basket
Also known as: Lhx6.1b

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

Show »
Length:348
Mass (Da):38,193
Checksum:iDC0A3056BC56EF37
GO
Isoform 3 (identifier: Q9UPM6-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MYWKHENAAPALPEGCRLPAEGGPATDQVM

Show »
Length:392
Mass (Da):43,136
Checksum:iD2A915F07BFC73C0
GO
Isoform 4 (identifier: Q9UPM6-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MYWKHENAAPALPEGCRLPAEGGPATDQVM
     324-363: QVQCGQVHCRLPYTAPPVHLKADMDGPLSNRGEKVILFQY → HPFSVLTLPALPHLPVGAPQLPLSR

Show »
Length:377
Mass (Da):41,284
Checksum:i132637341D6A94B4
GO
Isoform 5 (identifier: Q9UPM6-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MRRGLCRRSAENPDAGPVM
     324-363: QVQCGQVHCRLPYTAPPVHLKADMDGPLSNRGEKVILFQY → HPFSVLTLPALPHLPVGAPQLPLSR

Show »
Length:366
Mass (Da):40,160
Checksum:iF78470DB966B0E28
GO
Isoform 6 (identifier: Q9UPM6-6) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-187: Missing.

Note: No experimental confirmation available.
Show »
Length:176
Mass (Da):19,618
Checksum:i58A580E0C2AEE8FD
GO

Sequence cautioni

The sequence AAI03937 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAI03938 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence CAB66505 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti16E → K in BAA83422 (PubMed:10393337).Curated1
Sequence conflicti16E → K in BAA83423 (PubMed:10393337).Curated1
Isoform 2 (identifier: Q9UPM6-2)
Sequence conflicti346L → F in BAA83423 (PubMed:10393337).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0460431 – 187Missing in isoform 6. 1 PublicationAdd BLAST187
Alternative sequenceiVSP_0377451M → MYWKHENAAPALPEGCRLPA EGGPATDQVM in isoform 3 and isoform 4. 1 Publication1
Alternative sequenceiVSP_0420731M → MRRGLCRRSAENPDAGPVM in isoform 5. 1 Publication1
Alternative sequenceiVSP_003109324 – 363QVQCG…ILFQY → HPFSVLTLPALPHLPVGAPQ LPLSR in isoform 2, isoform 4 and isoform 5. 2 PublicationsAdd BLAST40

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS56583.1. [Q9UPM6-1]
CCDS56584.1. [Q9UPM6-5]
CCDS59144.1. [Q9UPM6-6]
CCDS6837.2. [Q9UPM6-4]
CCDS6838.2. [Q9UPM6-3]
PIRiT46907.
RefSeqiNP_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]
UniGeneiHs.103137.

Genome annotation databases

EnsembliENST00000340587; 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]
GeneIDi26468.
KEGGihsa:26468.
UCSCiuc004blx.5. human. [Q9UPM6-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS56583.1. [Q9UPM6-1]
CCDS56584.1. [Q9UPM6-5]
CCDS59144.1. [Q9UPM6-6]
CCDS6837.2. [Q9UPM6-4]
CCDS6838.2. [Q9UPM6-3]
PIRiT46907.
RefSeqiNP_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]
UniGeneiHs.103137.

3D structure databases

ProteinModelPortaliQ9UPM6.
SMRiQ9UPM6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi117692. 22 interactors.
IntActiQ9UPM6. 2 interactors.
MINTiMINT-4718974.
STRINGi9606.ENSP00000377854.

PTM databases

iPTMnetiQ9UPM6.
PhosphoSitePlusiQ9UPM6.

Polymorphism and mutation databases

BioMutaiLHX6.
DMDMi90185239.

Proteomic databases

PaxDbiQ9UPM6.
PRIDEiQ9UPM6.

Protocols and materials databases

DNASUi26468.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000340587; 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]
GeneIDi26468.
KEGGihsa:26468.
UCSCiuc004blx.5. human. [Q9UPM6-1]

Organism-specific databases

CTDi26468.
DisGeNETi26468.
GeneCardsiLHX6.
HGNCiHGNC:21735. LHX6.
HPAiHPA047854.
HPA058319.
MIMi608215. gene.
neXtProtiNX_Q9UPM6.
OpenTargetsiENSG00000106852.
PharmGKBiPA134949308.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0490. Eukaryota.
ENOG410YIJ3. LUCA.
GeneTreeiENSGT00760000118921.
HOGENOMiHOG000038965.
HOVERGENiHBG006261.
InParanoidiQ9UPM6.
KOiK09375.
OMAiKNVCASC.
OrthoDBiEOG091G0EXT.
PhylomeDBiQ9UPM6.
TreeFamiTF315442.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000106852-MONOMER.

Miscellaneous databases

ChiTaRSiLHX6. human.
GeneWikiiLHX6.
GenomeRNAii26468.
PROiQ9UPM6.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000106852.
CleanExiHS_LHX6.
ExpressionAtlasiQ9UPM6. baseline and differential.
GenevisibleiQ9UPM6. HS.

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]
ProtoNetiSearch...

Entry informationi

Entry nameiLHX6_HUMAN
AccessioniPrimary (citable) accession number: Q9UPM6
Secondary accession number(s): A6PVQ1
, A6PVQ2, A8K1B2, B7Z4D0, H0YN76, Q5T7S7, Q5T7S8, Q9NTK3, Q9UPM5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: March 7, 2006
Last modified: November 30, 2016
This is version 158 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (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.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 9
    Human chromosome 9: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.