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Protein

LIM homeobox transcription factor 1-beta

Gene

LMX1B

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

Complete GO annotation...

Keywords - Molecular functioni

Activator, Developmental protein

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000136944-MONOMER.
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

HGNCiHGNC:6654. LMX1B.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

  • nucleus Source: UniProtKB
Complete GO annotation...

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 rs121909488dbSNPEnsembl.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 rs28939692dbSNPEnsembl.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 rs121909486dbSNPEnsembl.1

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi4010.
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.

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.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
LDB1Q86U703EBI-10258690,EBI-677177

Protein-protein interaction databases

BioGridi110195. 17 interactors.
IntActiO60663. 2 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

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.
HOGENOMiHOG000231629.
HOVERGENiHBG052335.
InParanoidiO60663.
KOiK09371.
OMAiNRMEGMM.
OrthoDBiEOG091G09Z3.
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 (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 rs2235058dbSNPEnsembl.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 rs121909488dbSNPEnsembl.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 rs28939692dbSNPEnsembl.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 rs121909486dbSNPEnsembl.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

Cross-referencesi

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.

3D structure databases

ProteinModelPortaliO60663.
SMRiO60663.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi110195. 17 interactors.
IntActiO60663. 2 interactors.
STRINGi9606.ENSP00000347684.

PTM databases

iPTMnetiO60663.
PhosphoSitePlusiO60663.

Polymorphism and mutation databases

BioMutaiLMX1B.

Proteomic databases

PaxDbiO60663.
PeptideAtlasiO60663.
PRIDEiO60663.

Protocols and materials databases

DNASUi4010.
Structural Biology KnowledgebaseSearch...

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]

Organism-specific databases

CTDi4010.
DisGeNETi4010.
GeneCardsiLMX1B.
GeneReviewsiLMX1B.
HGNCiHGNC:6654. LMX1B.
MalaCardsiLMX1B.
MIMi161200. phenotype.
602575. gene.
neXtProtiNX_O60663.
OpenTargetsiENSG00000136944.
Orphaneti2614. Nail-patella syndrome.
PharmGKBiPA30417.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0490. Eukaryota.
ENOG410YIJ3. LUCA.
GeneTreeiENSGT00760000118921.
HOGENOMiHOG000231629.
HOVERGENiHBG052335.
InParanoidiO60663.
KOiK09371.
OMAiNRMEGMM.
OrthoDBiEOG091G09Z3.
TreeFamiTF315442.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000136944-MONOMER.
SIGNORiO60663.

Miscellaneous databases

GeneWikiiLMX1B.
GenomeRNAii4010.
PROiO60663.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000136944.
CleanExiHS_LMX1B.
ExpressionAtlasiO60663. baseline and differential.
GenevisibleiO60663. 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 nameiLMX1B_HUMAN
AccessioniPrimary (citable) accession number: O60663
Secondary accession number(s): F8W7W6
, O75463, Q5JU95, Q6ISC9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: May 1, 2013
Last modified: November 2, 2016
This is version 161 of the entry and version 3 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. 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
  5. 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.