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Protein

LIM/homeobox protein Lhx6

Gene

LHX6

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

Keywordsi

Molecular functionDevelopmental protein, DNA-binding
Biological processDifferentiation, Neurogenesis, Transcription, Transcription regulation
LigandMetal-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
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 9

Organism-specific databases

EuPathDBiHostDB:ENSG00000106852.15
HGNCiHGNC:21735 LHX6
MIMi608215 gene
neXtProtiNX_Q9UPM6

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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
PeptideAtlasiQ9UPM6
PRIDEiQ9UPM6
ProteomicsDBi85374
85375 [Q9UPM6-2]
85376 [Q9UPM6-3]
85377 [Q9UPM6-4]
85378 [Q9UPM6-5]

PTM databases

iPTMnetiQ9UPM6
PhosphoSitePlusiQ9UPM6

Expressioni

Gene expression databases

BgeeiENSG00000106852 Expressed in 152 organ(s), highest expression level in anterior cingulate cortex
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, 9 interactors
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

Keywords - Domaini

Homeobox, LIM domain, Repeat

Phylogenomic databases

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

Family and domain databases

CDDicd00086 homeodomain, 1 hit
InterProiView protein in InterPro
IPR009057 Homeobox-like_sf
IPR017970 Homeobox_CS
IPR001356 Homeobox_dom
IPR001781 Znf_LIM
PfamiView protein in Pfam
PF00046 Homeobox, 1 hit
PF00412 LIM, 2 hits
SMARTiView protein in SMART
SM00389 HOX, 1 hit
SM00132 LIM, 2 hits
SUPFAMiSSF46689 SSF46689, 1 hit
PROSITEiView protein in PROSITE
PS00027 HOMEOBOX_1, 1 hit
PS50071 HOMEOBOX_2, 1 hit
PS00478 LIM_DOMAIN_1, 2 hits
PS50023 LIM_DOMAIN_2, 2 hits

Sequences (6+)i

Sequence statusi: Complete.

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

This entry has 6 described isoforms and 3 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 3 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
H0YMH3H0YMH3_HUMAN
LIM/homeobox protein Lhx6
LHX6
33Annotation score:
H0YMY8H0YMY8_HUMAN
LIM/homeobox protein Lhx6
LHX6
50Annotation score:
H0YKH7H0YKH7_HUMAN
LIM/homeobox protein Lhx6
LHX6
35Annotation score:

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 No translation available.
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]
CCDS87683.1 [Q9UPM6-2]
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_001335119.1, NM_001348190.1 [Q9UPM6-2]
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

Similar proteinsi

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 No translation available.
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]
CCDS87683.1 [Q9UPM6-2]
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_001335119.1, NM_001348190.1 [Q9UPM6-2]
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, 9 interactors
STRINGi9606.ENSP00000377854

PTM databases

iPTMnetiQ9UPM6
PhosphoSitePlusiQ9UPM6

Polymorphism and mutation databases

BioMutaiLHX6
DMDMi90185239

Proteomic databases

PaxDbiQ9UPM6
PeptideAtlasiQ9UPM6
PRIDEiQ9UPM6
ProteomicsDBi85374
85375 [Q9UPM6-2]
85376 [Q9UPM6-3]
85377 [Q9UPM6-4]
85378 [Q9UPM6-5]

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
EuPathDBiHostDB:ENSG00000106852.15
GeneCardsiLHX6
HGNCiHGNC:21735 LHX6
HPAiHPA047854
HPA058319
MIMi608215 gene
neXtProtiNX_Q9UPM6
OpenTargetsiENSG00000106852
PharmGKBiPA134949308
GenAtlasiSearch...

Phylogenomic databases

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

Miscellaneous databases

ChiTaRSiLHX6 human
GeneWikiiLHX6
GenomeRNAii26468
PROiPR:Q9UPM6
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000106852 Expressed in 152 organ(s), highest expression level in anterior cingulate cortex
CleanExiHS_LHX6
ExpressionAtlasiQ9UPM6 baseline and differential
GenevisibleiQ9UPM6 HS

Family and domain databases

CDDicd00086 homeodomain, 1 hit
InterProiView protein in InterPro
IPR009057 Homeobox-like_sf
IPR017970 Homeobox_CS
IPR001356 Homeobox_dom
IPR001781 Znf_LIM
PfamiView protein in Pfam
PF00046 Homeobox, 1 hit
PF00412 LIM, 2 hits
SMARTiView protein in SMART
SM00389 HOX, 1 hit
SM00132 LIM, 2 hits
SUPFAMiSSF46689 SSF46689, 1 hit
PROSITEiView protein in PROSITE
PS00027 HOMEOBOX_1, 1 hit
PS50071 HOMEOBOX_2, 1 hit
PS00478 LIM_DOMAIN_1, 2 hits
PS50023 LIM_DOMAIN_2, 2 hits
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 historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: March 7, 2006
Last modified: November 7, 2018
This is version 174 of the entry and version 2 of the sequence. See 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. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  2. Human chromosome 9
    Human chromosome 9: entries, gene names and cross-references to MIM
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