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Protein

LIM homeobox transcription factor 1-beta

Gene

LMX1B

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

Functioni

Essential for the specification of dorsal limb fate at both the zeugopodal and autopodal levels.

Regions

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

GO - Molecular functioni

GO - Biological processi

Keywordsi

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

Enzyme and pathway databases

SIGNORiO60663

Names & Taxonomyi

Protein namesi
Recommended name:
LIM homeobox transcription factor 1-beta
Alternative name(s):
LIM/homeobox protein 1.2
Short name:
LMX-1.2
LIM/homeobox protein LMX1B
Gene namesi
Name:LMX1B
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 9

Organism-specific databases

EuPathDBiHostDB:ENSG00000136944.17
HGNCiHGNC:6654 LMX1B
MIMi602575 gene
neXtProtiNX_O60663

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

Nail-patella syndrome (NPS)5 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionDisease that cause abnormal skeletal patterning and renal dysplasia.
See also OMIM:161200
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_01520159C → R in NPS. 1 Publication1
Natural variantiVAR_01520259C → S in NPS. 1 Publication1
Natural variantiVAR_01519077H → N in NPS. 1 Publication1
Natural variantiVAR_01520377H → Q in NPS. 1 Publication1
Natural variantiVAR_01520477H → Y in NPS. 1 Publication1
Natural variantiVAR_01520580C → R in NPS. 1 Publication1
Natural variantiVAR_01519181L → W in NPS. 1 Publication1
Natural variantiVAR_01519283C → F in NPS. 1 Publication1
Natural variantiVAR_01520683C → G in NPS. 1 Publication1
Natural variantiVAR_01519383C → W in NPS. 1 Publication1
Natural variantiVAR_01520783C → Y in NPS. 1 Publication1
Natural variantiVAR_01520886C → R in NPS. 1 Publication1
Natural variantiVAR_015194103C → W in NPS. 1 Publication1
Natural variantiVAR_015209106D → G in NPS. 1 Publication1
Natural variantiVAR_004198118C → F in NPS. 1 PublicationCorresponds to variant dbSNP:rs121909488EnsemblClinVar.1
Natural variantiVAR_015195118C → Y in NPS. 2 Publications1
Natural variantiVAR_015196137H → Y in NPS. 1 Publication1
Natural variantiVAR_015197140C → Y in NPS. 1 Publication1
Natural variantiVAR_015210143C → S in NPS. 1 Publication1
Natural variantiVAR_015211146C → F in NPS. 1 Publication1
Natural variantiVAR_015212146C → Y in NPS. 1 Publication1
Natural variantiVAR_004199165C → W in NPS. 1 Publication1
Natural variantiVAR_004200223R → Q in NPS. 2 PublicationsCorresponds to variant dbSNP:rs121909491EnsemblClinVar.1
Natural variantiVAR_004201236A → P in NPS. 2 Publications1
Natural variantiVAR_004202241S → P in NPS. 1 Publication1
Natural variantiVAR_004203249R → P in NPS. 1 Publication1
Natural variantiVAR_015213252L → P in NPS. 1 Publication1
Natural variantiVAR_004204253A → V in NPS. 1 Publication1
Natural variantiVAR_015198266W → C in NPS. 1 Publication1
Natural variantiVAR_004205269N → K in NPS. 3 PublicationsCorresponds to variant dbSNP:rs121909486EnsemblClinVar.1

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi4010
GeneReviewsiLMX1B
MalaCardsiLMX1B
MIMi161200 phenotype
OpenTargetsiENSG00000136944
Orphaneti2614 Nail-patella syndrome
PharmGKBiPA30417

Polymorphism and mutation databases

BioMutaiLMX1B

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000758281 – 402LIM homeobox transcription factor 1-betaAdd BLAST402

Proteomic databases

PaxDbiO60663
PeptideAtlasiO60663
PRIDEiO60663
ProteomicsDBi49506
49507 [O60663-2]

PTM databases

iPTMnetiO60663
PhosphoSitePlusiO60663

Expressioni

Tissue specificityi

Expressed in most tissues. Highest levels in testis, thyroid, duodenum, skeletal muscle, and pancreatic islets.

Gene expression databases

BgeeiENSG00000136944
CleanExiHS_LMX1B
ExpressionAtlasiO60663 baseline and differential
GenevisibleiO60663 HS

Organism-specific databases

HPAiHPA073716

Interactioni

Subunit structurei

Interacts with DHX9 (PubMed:23308148).1 Publication

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi110195, 18 interactors
IntActiO60663, 5 interactors
STRINGi9606.ENSP00000347684

Structurei

3D structure databases

ProteinModelPortaliO60663
SMRiO60663
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini56 – 106LIM zinc-binding 1PROSITE-ProRule annotationAdd BLAST51
Domaini115 – 168LIM zinc-binding 2PROSITE-ProRule annotationAdd BLAST54

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi282 – 288Poly-Gln7

Keywords - Domaini

Homeobox, LIM domain, Repeat

Phylogenomic databases

eggNOGiKOG0490 Eukaryota
ENOG410YIJ3 LUCA
GeneTreeiENSGT00760000118921
HOGENOMiHOG000231629
HOVERGENiHBG052335
InParanoidiO60663
KOiK09371
OMAiNRMEGMM
OrthoDBiEOG091G09Z3
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 (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: O60663-1) [UniParc]FASTAAdd to basket
Also known as: Long

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
MDIATGPESL ERCFPRGQTD CAKMLDGIKM EEHALRPGPA TLGVLLGSDC
60 70 80 90 100
PHPAVCEGCQ RPISDRFLMR VNESSWHEEC LQCAACQQAL TTSCYFRDRK
110 120 130 140 150
LYCKQDYQQL FAAKCSGCME KIAPTEFVMR ALECVYHLGC FCCCVCERQL
160 170 180 190 200
RKGDEFVLKE GQLLCKGDYE KEKDLLSSVS PDESDSVKSE DEDGDMKPAK
210 220 230 240 250
GQGSQSKGSG DDGKDPRRPK RPRTILTTQQ RRAFKASFEV SSKPCRKVRE
260 270 280 290 300
TLAAETGLSV RVVQVWFQNQ RAKMKKLARR HQQQQEQQNS QRLGQEVLSS
310 320 330 340 350
RMEGMMASYT PLAPPQQQIV AMEQSPYGSS DPFQQGLTPP QMPGDHMNPY
360 370 380 390 400
GNDSIFHDID SDTSLTSLSD CFLGSSDVGS LQARVGNPID RLYSMQSSYF

AS
Length:402
Mass (Da):44,917
Last modified:May 1, 2013 - v3
Checksum:iE59FC36C39C7C9A3
GO
Isoform 2 (identifier: O60663-2) [UniParc]FASTAAdd to basket
Also known as: Short

The sequence of this isoform differs from the canonical sequence as follows:
     345-351: Missing.

Show »
Length:395
Mass (Da):44,102
Checksum:i9FFBF8A68E7AC676
GO
Isoform 3 (identifier: O60663-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     293-293: L → LGQGEPGPGQGL
     345-351: Missing.

Show »
Length:406
Mass (Da):45,080
Checksum:i5FF15E73B7FD552E
GO

Sequence cautioni

The sequence AAC27294 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAC39738 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAH69601 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAI12121 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAI13492 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence CAH70295 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence CAI40918 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence EAW87642 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_01520159C → R in NPS. 1 Publication1
Natural variantiVAR_01520259C → S in NPS. 1 Publication1
Natural variantiVAR_04775575S → F. Corresponds to variant dbSNP:rs2235058Ensembl.1
Natural variantiVAR_01519077H → N in NPS. 1 Publication1
Natural variantiVAR_01520377H → Q in NPS. 1 Publication1
Natural variantiVAR_01520477H → Y in NPS. 1 Publication1
Natural variantiVAR_01520580C → R in NPS. 1 Publication1
Natural variantiVAR_01519181L → W in NPS. 1 Publication1
Natural variantiVAR_01519283C → F in NPS. 1 Publication1
Natural variantiVAR_01520683C → G in NPS. 1 Publication1
Natural variantiVAR_01519383C → W in NPS. 1 Publication1
Natural variantiVAR_01520783C → Y in NPS. 1 Publication1
Natural variantiVAR_01520886C → R in NPS. 1 Publication1
Natural variantiVAR_015194103C → W in NPS. 1 Publication1
Natural variantiVAR_015209106D → G in NPS. 1 Publication1
Natural variantiVAR_004198118C → F in NPS. 1 PublicationCorresponds to variant dbSNP:rs121909488EnsemblClinVar.1
Natural variantiVAR_015195118C → Y in NPS. 2 Publications1
Natural variantiVAR_015196137H → Y in NPS. 1 Publication1
Natural variantiVAR_015197140C → Y in NPS. 1 Publication1
Natural variantiVAR_015210143C → S in NPS. 1 Publication1
Natural variantiVAR_015211146C → F in NPS. 1 Publication1
Natural variantiVAR_015212146C → Y in NPS. 1 Publication1
Natural variantiVAR_004199165C → W in NPS. 1 Publication1
Natural variantiVAR_004200223R → Q in NPS. 2 PublicationsCorresponds to variant dbSNP:rs121909491EnsemblClinVar.1
Natural variantiVAR_004201236A → P in NPS. 2 Publications1
Natural variantiVAR_004202241S → P in NPS. 1 Publication1
Natural variantiVAR_004203249R → P in NPS. 1 Publication1
Natural variantiVAR_015213252L → P in NPS. 1 Publication1
Natural variantiVAR_004204253A → V in NPS. 1 Publication1
Natural variantiVAR_015198266W → C in NPS. 1 Publication1
Natural variantiVAR_004205269N → K in NPS. 3 PublicationsCorresponds to variant dbSNP:rs121909486EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_046472293L → LGQGEPGPGQGL in isoform 3. Curated1
Alternative sequenceiVSP_003113345 – 351Missing in isoform 2 and isoform 3. 2 Publications7

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF059575
, AF059572, AF059573, AF059574 Genomic DNA Translation: AAC27294.1 Different initiation.
AL161908, AL161731 Genomic DNA Translation: CAH70294.1
AL161908, AL161731 Genomic DNA Translation: CAH70295.1 Different initiation.
AL161731, AL161908 Genomic DNA Translation: CAI40917.1
AL161731, AL161908 Genomic DNA Translation: CAI40918.1 Different initiation.
CH471090 Genomic DNA Translation: EAW87642.1 Different initiation.
BC069601 mRNA Translation: AAH69601.1 Different initiation.
BC112120 mRNA Translation: AAI12121.1 Different initiation.
BC113491 mRNA Translation: AAI13492.1 Different initiation.
AF057135 mRNA Translation: AAC39738.1 Different initiation.
CCDSiCCDS55342.1 [O60663-1]
CCDS55343.1 [O60663-3]
CCDS6866.2 [O60663-2]
RefSeqiNP_001167618.1, NM_001174147.1 [O60663-1]
NP_002307.2, NM_002316.3 [O60663-2]
UniGeneiHs.129133

Genome annotation databases

EnsembliENST00000355497; ENSP00000347684; ENSG00000136944 [O60663-3]
ENST00000373474; ENSP00000362573; ENSG00000136944 [O60663-1]
ENST00000526117; ENSP00000436930; ENSG00000136944 [O60663-2]
GeneIDi4010
KEGGihsa:4010
UCSCiuc004bqi.4 human [O60663-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiLMX1B_HUMAN
AccessioniPrimary (citable) accession number: O60663
Secondary accession number(s): F8W7W6
, O75463, Q5JU95, Q6ISC9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: May 1, 2013
Last modified: June 20, 2018
This is version 174 of the entry and version 3 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. Human chromosome 9
    Human chromosome 9: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

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