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O88609 (LMX1B_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 124. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:Lmx1b
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length395 AA.
Sequence statusComplete.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

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

Subcellular location

Nucleus Potential.

Sequence similarities

Contains 1 homeobox DNA-binding domain.

Contains 2 LIM zinc-binding domains.

Sequence caution

The sequence AAC27793.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence AAI19170.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence AAI25470.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence CAM26554.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence EDL08602.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   DomainHomeobox
LIM domain
Repeat
   LigandDNA-binding
Metal-binding
Zinc
   Molecular functionActivator
Developmental protein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcamera-type eye development

Inferred from mutant phenotype PubMed 10660670PubMed 20568247. Source: MGI

cell death

Inferred from mutant phenotype. Source: MGI

cell proliferation

Inferred from mutant phenotype PubMed 17166916. Source: MGI

central nervous system neuron development

Inferred from mutant phenotype PubMed 17151281. Source: MGI

cerebellum morphogenesis

Inferred from mutant phenotype PubMed 17166916. Source: MGI

collagen fibril organization

Inferred from mutant phenotype PubMed 10660670. Source: MGI

dopaminergic neuron differentiation

Inferred from mutant phenotype PubMed 21752929. Source: MGI

dorsal/ventral pattern formation

Inferred from expression pattern PubMed 10767331. Source: UniProtKB

embryonic limb morphogenesis

Non-traceable author statement PubMed 10767331. Source: UniProtKB

limb morphogenesis

Inferred from mutant phenotype PubMed 20589901. Source: MGI

midbrain development

Inferred from mutant phenotype PubMed 21752929. Source: MGI

neuron differentiation

Inferred from mutant phenotype PubMed 12897786PubMed 15229182. Source: MGI

neuron migration

Inferred from mutant phenotype PubMed 15229182. Source: MGI

organ growth

Inferred from mutant phenotype PubMed 17166916. Source: MGI

positive regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 17166916. Source: MGI

regulation of gene expression

Inferred from mutant phenotype PubMed 20589901. Source: MGI

regulation of transcription from RNA polymerase II promoter

Inferred from direct assay PubMed 21752929. Source: MGI

trabecular meshwork development

Inferred from mutant phenotype PubMed 20568247. Source: MGI

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleus

Inferred from sequence or structural similarity. Source: UniProtKB

   Molecular_functionsequence-specific DNA binding

Inferred from electronic annotation. Source: InterPro

sequence-specific DNA binding transcription factor activity

Inferred from electronic annotation. Source: InterPro

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 395395LIM homeobox transcription factor 1-beta
PRO_0000075830

Regions

Domain56 – 10651LIM zinc-binding 1
Domain115 – 16854LIM zinc-binding 2
DNA binding219 – 27860Homeobox
Compositional bias282 – 2887Poly-Gln

Experimental info

Sequence conflict3111P → A in AAC27793. Ref.4

Sequences

Sequence LengthMass (Da)Tools
O88609 [UniParc].

Last modified May 1, 2013. Version 3.
Checksum: 9FFBF8A68E7AC676

FASTA39544,102
        10         20         30         40         50         60 
MDIATGPESL ERCFPRGQTD CAKMLDGIKM EEHALRPGPA TLGVLLGSDC PHPAVCEGCQ 

        70         80         90        100        110        120 
RPISDRFLMR VNESSWHEEC LQCAACQQAL TTSCYFRDRK LYCKQDYQQL FAAKCSGCME 

       130        140        150        160        170        180 
KIAPTEFVMR ALECVYHLGC FCCCVCERQL RKGDEFVLKE GQLLCKGDYE KEKDLLSSVS 

       190        200        210        220        230        240 
PDESDSVKSE DEDGDMKPAK GQGSQSKGSG DDGKDPRRPK RPRTILTTQQ RRAFKASFEV 

       250        260        270        280        290        300 
SSKPCRKVRE TLAAETGLSV RVVQVWFQNQ RAKMKKLARR HQQQQEQQNS QRLGQEVLSS 

       310        320        330        340        350        360 
RMEGMMASYT PLAPPQQQIV AMEQSPYGSS DPFQQGLTPP QMPGNDSIFH DIDSDTSLTS 

       370        380        390 
LSDCFLGSSD VGSLQARVGN PIDRLYSMQS SYFAS 

« Hide

References

« Hide 'large scale' references
[1]"Lineage-specific biology revealed by a finished genome assembly of the mouse."
Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S. expand/collapse author list , Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K., Eichler E.E., Ponting C.P.
PLoS Biol. 7:E1000112-E1000112(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: C57BL/6J.
[2]Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Brain.
[4]"Limb and kidney defects in Lmx1b mutant mice suggest an involvement of LMX1B in human nail patella syndrome."
Chen H., Lun Y., Ovchinnikov D., Kokubo H., Oberg K.C., Pepicelli C.V., Gan L., Lee B., Johnson R.L.
Nat. Genet. 19:51-55(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 24-395.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AL929212 Genomic DNA. Translation: CAM26554.1. Different initiation.
CH466542 Genomic DNA. Translation: EDL08602.1. Different initiation.
BC119169 mRNA. Translation: AAI19170.1. Different initiation.
BC125469 mRNA. Translation: AAI25470.1. Different initiation.
AF078166 mRNA. Translation: AAC27793.1. Different initiation.
RefSeqNP_034855.2. NM_010725.2.
UniGeneMm.39825.

3D structure databases

ProteinModelPortalO88609.
SMRO88609. Positions 4-173, 214-276.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid201183. 7 interactions.
STRING10090.ENSMUSP00000043616.

PTM databases

PhosphoSiteO88609.

Proteomic databases

PRIDEO88609.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000041730; ENSMUSP00000043616; ENSMUSG00000038765.
GeneID16917.
KEGGmmu:16917.
UCSCuc008jhy.2. mouse.

Organism-specific databases

CTD4010.
MGIMGI:1100513. Lmx1b.

Phylogenomic databases

eggNOGNOG243427.
GeneTreeENSGT00750000117665.
HOGENOMHOG000231629.
HOVERGENHBG052335.
InParanoidQ0VEN6.
KOK09371.
OrthoDBEOG7BZVTB.
TreeFamTF315442.

Gene expression databases

BgeeO88609.
CleanExMM_LMX1B.
GenevestigatorO88609.

Family and domain databases

Gene3D1.10.10.60. 1 hit.
2.10.110.10. 2 hits.
InterProIPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR001781. Znf_LIM.
[Graphical view]
PfamPF00046. Homeobox. 1 hit.
PF00412. LIM. 2 hits.
[Graphical view]
SMARTSM00389. HOX. 1 hit.
SM00132. LIM. 2 hits.
[Graphical view]
SUPFAMSSF46689. SSF46689. 1 hit.
PROSITEPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
PS00478. LIM_DOMAIN_1. 2 hits.
PS50023. LIM_DOMAIN_2. 2 hits.
[Graphical view]
ProtoNetSearch...

Other

NextBio290964.
PROO88609.
SOURCESearch...

Entry information

Entry nameLMX1B_MOUSE
AccessionPrimary (citable) accession number: O88609
Secondary accession number(s): Q0VEN6
Entry history
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 1, 2013
Last modified: June 11, 2014
This is version 124 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot