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Protein

LIM homeobox transcription factor 1-beta

Gene

Lmx1b

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

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

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi219 – 27860HomeoboxPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. sequence-specific DNA binding Source: InterPro
  2. sequence-specific DNA binding transcription factor activity Source: MGI
  3. zinc ion binding Source: InterPro

GO - Biological processi

  1. camera-type eye development Source: MGI
  2. cell proliferation Source: MGI
  3. central nervous system neuron development Source: MGI
  4. cerebellum morphogenesis Source: MGI
  5. collagen fibril organization Source: MGI
  6. dopaminergic neuron differentiation Source: MGI
  7. dorsal/ventral pattern formation Source: UniProtKB
  8. embryonic limb morphogenesis Source: UniProtKB
  9. limb morphogenesis Source: MGI
  10. midbrain development Source: MGI
  11. neuron differentiation Source: MGI
  12. neuron migration Source: MGI
  13. organ growth Source: MGI
  14. positive regulation of transcription from RNA polymerase II promoter Source: MGI
  15. regulation of gene expression Source: MGI
  16. regulation of transcription, DNA-templated Source: MGI
  17. regulation of transcription from RNA polymerase II promoter Source: MGI
  18. trabecular meshwork development Source: MGI
  19. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Activator, Developmental protein

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

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
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 2

Organism-specific databases

MGIiMGI:1100513. Lmx1b.

Subcellular locationi

Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

  1. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 395395LIM homeobox transcription factor 1-betaPRO_0000075830Add
BLAST

Proteomic databases

PRIDEiO88609.

PTM databases

PhosphoSiteiO88609.

Expressioni

Gene expression databases

BgeeiO88609.
CleanExiMM_LMX1B.
GenevestigatoriO88609.

Interactioni

Protein-protein interaction databases

BioGridi201183. 7 interactions.
STRINGi10090.ENSMUSP00000043616.

Structurei

3D structure databases

ProteinModelPortaliO88609.
SMRiO88609. Positions 56-173, 214-276.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini56 – 10651LIM zinc-binding 1PROSITE-ProRule annotationAdd
BLAST
Domaini115 – 16854LIM zinc-binding 2PROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi282 – 2887Poly-Gln

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

eggNOGiNOG243427.
HOGENOMiHOG000231629.
HOVERGENiHBG052335.
InParanoidiO88609.
KOiK09371.
OrthoDBiEOG7BZVTB.
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]

Sequencei

Sequence statusi: Complete.

O88609-1 [UniParc]FASTAAdd to basket

« 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 QMPGNDSIFH
360 370 380 390
DIDSDTSLTS LSDCFLGSSD VGSLQARVGN PIDRLYSMQS SYFAS
Length:395
Mass (Da):44,102
Last modified:May 1, 2013 - v3
Checksum:i9FFBF8A68E7AC676
GO

Sequence cautioni

The sequence AAC27793.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAI19170.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAI25470.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence CAM26554.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence EDL08602.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti311 – 3111P → A in AAC27793 (PubMed:9590288).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
RefSeqiNP_034855.2. NM_010725.2.
UniGeneiMm.39825.

Genome annotation databases

GeneIDi16917.
KEGGimmu:16917.
UCSCiuc008jhy.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
RefSeqiNP_034855.2. NM_010725.2.
UniGeneiMm.39825.

3D structure databases

ProteinModelPortaliO88609.
SMRiO88609. Positions 56-173, 214-276.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi201183. 7 interactions.
STRINGi10090.ENSMUSP00000043616.

PTM databases

PhosphoSiteiO88609.

Proteomic databases

PRIDEiO88609.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi16917.
KEGGimmu:16917.
UCSCiuc008jhy.2. mouse.

Organism-specific databases

CTDi4010.
MGIiMGI:1100513. Lmx1b.

Phylogenomic databases

eggNOGiNOG243427.
HOGENOMiHOG000231629.
HOVERGENiHBG052335.
InParanoidiO88609.
KOiK09371.
OrthoDBiEOG7BZVTB.
TreeFamiTF315442.

Miscellaneous databases

ChiTaRSiLmx1b. mouse.
NextBioi290964.
PROiO88609.
SOURCEiSearch...

Gene expression databases

BgeeiO88609.
CleanExiMM_LMX1B.
GenevestigatoriO88609.

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...

Publicationsi

« Hide 'large scale' publications
  1. 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 (JUN-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(2003) [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(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 24-395.

Entry informationi

Entry nameiLMX1B_MOUSE
AccessioniPrimary (citable) accession number: O88609
Secondary accession number(s): Q0VEN6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 1, 2013
Last modified: March 4, 2015
This is version 131 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.