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Protein

LIM/homeobox protein Lhx3

Gene

LHX3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Acts as a transcriptional activator. Binds to and activates the promoter of the alpha-glycoprotein gene, and synergistically enhances transcription from the prolactin promoter in cooperation with POU1F1/Pit-1 (By similarity). Required for the establishment of the specialized cells of the pituitary gland and the nervous system. Involved in the development of interneurons and motor neurons in cooperation with LDB1 and ISL1.By similarity1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi157 – 216HomeoboxPROSITE-ProRule annotationAdd BLAST60

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionActivator, DNA-binding
Biological processTranscription, Transcription regulation
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-9010553 Regulation of expression of SLITs and ROBOs
SignaLinkiQ9UBR4
SIGNORiQ9UBR4

Names & Taxonomyi

Protein namesi
Recommended name:
LIM/homeobox protein Lhx3
Short name:
LIM homeobox protein 3
Gene namesi
Name:LHX3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 9

Organism-specific databases

EuPathDBiHostDB:ENSG00000107187.15
HGNCiHGNC:6595 LHX3
MIMi600577 gene
neXtProtiNX_Q9UBR4

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

Involvement in diseasei

Pituitary hormone deficiency, combined, 3 (CPHD3)3 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionCombined pituitary hormone deficiency is defined as the impaired production of growth hormone and one or more of the other five anterior pituitary hormones. CPHD3 is characterized by a complete deficit in all but one (adrenocorticotropin) anterior pituitary hormone and a rigid cervical spine leading to limited head rotation.
See also OMIM:221750
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_010713111Y → C in CPHD3. 1 PublicationCorresponds to variant dbSNP:rs104894117EnsemblClinVar.1
Natural variantiVAR_079378141C → F in CPHD3; unknown pathological significance. 1 Publication1
Natural variantiVAR_079379151 – 397Missing in CPHD3. 1 PublicationAdd BLAST247
Natural variantiVAR_063240210A → V in CPHD3; associated with diminished DNA binding and pituitary gene activation. 1 PublicationCorresponds to variant dbSNP:rs137854503EnsemblClinVar.1

Keywords - Diseasei

Disease mutation, Dwarfism

Organism-specific databases

DisGeNETi8022
MalaCardsiLHX3
MIMi221750 phenotype
OpenTargetsiENSG00000107187
Orphaneti226307 Hypothyroidism due to deficient transcription factors involved in pituitary development or function
231720 Non-acquired combined pituitary hormone deficiency with spine abnormalities
PharmGKBiPA30366

Polymorphism and mutation databases

BioMutaiLHX3
DMDMi12643415

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000757811 – 397LIM/homeobox protein Lhx3Add BLAST397

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei63Phosphothreonine1 Publication1
Modified residuei71Phosphoserine1 Publication1
Modified residuei227Phosphotyrosine1 Publication1
Modified residuei234Phosphoserine1 Publication1
Modified residuei238Phosphoserine1 Publication1

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ9UBR4
PeptideAtlasiQ9UBR4
PRIDEiQ9UBR4
ProteomicsDBi84037
84038 [Q9UBR4-2]

PTM databases

iPTMnetiQ9UBR4
PhosphoSitePlusiQ9UBR4

Expressioni

Gene expression databases

BgeeiENSG00000107187
CleanExiHS_LHX3
ExpressionAtlasiQ9UBR4 baseline and differential
GenevisibleiQ9UBR4 HS

Interactioni

Subunit structurei

Interacts with POU1F1 (PubMed:26612202). At neuronal promoters, interacts with LDB1, in motor neurons LDB1 is displaced by ISL1 and a ternary complex is formed in which ISL1 contacts both LHX3 and LDB1 (By similarity).By similarity1 Publication

Binary interactionsi

Show more details

GO - Molecular functioni

  • RNA polymerase II transcription factor binding Source: UniProtKB

Protein-protein interaction databases

BioGridi113718, 7 interactors
IntActiQ9UBR4, 69 interactors
STRINGi9606.ENSP00000360811

Structurei

3D structure databases

ProteinModelPortaliQ9UBR4
SMRiQ9UBR4
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini31 – 81LIM zinc-binding 1PROSITE-ProRule annotationAdd BLAST51
Domaini90 – 144LIM zinc-binding 2PROSITE-ProRule annotationAdd BLAST55

Domaini

The LIM domain specifically interacts with the Pit-1 POU domain and is required for synergistic interactions with Pit-1, but not for basal transcriptional activation events.By similarity

Keywords - Domaini

Homeobox, LIM domain, Repeat

Phylogenomic databases

eggNOGiKOG4577 Eukaryota
ENOG410XPDC LUCA
GeneTreeiENSGT00760000118921
HOGENOMiHOG000231629
HOVERGENiHBG006263
InParanoidiQ9UBR4
KOiK09374
OMAiSFPLEHG
PhylomeDBiQ9UBR4
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 (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Note: Additional isoforms seem to exist.
Isoform A (identifier: Q9UBR4-1) [UniParc]FASTAAdd to basket

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
MLLETGLERD RARPGAAAVC TLGGTREIPL CAGCDQHILD RFILKALDRH
60 70 80 90 100
WHSKCLKCSD CHTPLAERCF SRGESVYCKD DFFKRFGTKC AACQLGIPPT
110 120 130 140 150
QVVRRAQDFV YHLHCFACVV CKRQLATGDE FYLMEDSRLV CKADYETAKQ
160 170 180 190 200
REAEATAKRP RTTITAKQLE TLKSAYNTSP KPARHVREQL SSETGLDMRV
210 220 230 240 250
VQVWFQNRRA KEKRLKKDAG RQRWGQYFRN MKRSRGGSKS DKDSVQEGQD
260 270 280 290 300
SDAEVSFPDE PSLAEMGPAN GLYGSLGEPT QALGRPSGAL GNFSLEHGGL
310 320 330 340 350
AGPEQYRELR PGSPYGVPPS PAAPQSLPGP QPLLSSLVYP DTSLGLVPSG
360 370 380 390
APGGPPPMRV LAGNGPSSDL STGSSGGYPD FPASPASWLD EVDHAQF
Length:397
Mass (Da):43,358
Last modified:January 24, 2001 - v2
Checksum:iFB4A2E48C015C249
GO
Isoform B (identifier: Q9UBR4-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-25: MLLETGLERDRARPGAAAVCTLGGT → MEARGELGPARESAGGDLLLALLARRADLR

Show »
Length:402
Mass (Da):43,978
Checksum:i23B71558AC877672
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti34C → R in AAF17291 (Ref. 2) Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_010713111Y → C in CPHD3. 1 PublicationCorresponds to variant dbSNP:rs104894117EnsemblClinVar.1
Natural variantiVAR_079378141C → F in CPHD3; unknown pathological significance. 1 Publication1
Natural variantiVAR_079379151 – 397Missing in CPHD3. 1 PublicationAdd BLAST247
Natural variantiVAR_063240210A → V in CPHD3; associated with diminished DNA binding and pituitary gene activation. 1 PublicationCorresponds to variant dbSNP:rs137854503EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0031071 – 25MLLET…TLGGT → MEARGELGPARESAGGDLLL ALLARRADLR in isoform B. CuratedAdd BLAST25

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF156888 mRNA Translation: AAF36808.1
AF156889 mRNA Translation: AAF36809.1
AH008761 Genomic DNA Translation: AAF17291.1
AF096169 mRNA Translation: AAF17292.1
AF214637 Genomic DNA Translation: AAF26412.1
AF367089
, AF367085, AF367086, AF367087, AF367088 Genomic DNA Translation: AAL26314.1
AL138781 Genomic DNA No translation available.
CH471090 Genomic DNA Translation: EAW88205.1
CH471090 Genomic DNA Translation: EAW88206.1
CCDSiCCDS6994.1 [Q9UBR4-1]
CCDS6995.1 [Q9UBR4-2]
RefSeqiNP_055379.1, NM_014564.4 [Q9UBR4-2]
NP_835258.1, NM_178138.5 [Q9UBR4-1]
UniGeneiHs.148427

Genome annotation databases

EnsembliENST00000371746; ENSP00000360811; ENSG00000107187 [Q9UBR4-2]
ENST00000371748; ENSP00000360813; ENSG00000107187 [Q9UBR4-1]
GeneIDi8022
KEGGihsa:8022
UCSCiuc004cgz.3 human [Q9UBR4-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiLHX3_HUMAN
AccessioniPrimary (citable) accession number: Q9UBR4
Secondary accession number(s): Q5TB39
, Q5TB40, Q9NZB5, Q9P0I8, Q9P0I9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: January 24, 2001
Last modified: June 20, 2018
This is version 169 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

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