LIM homeobox transcription factor 1-beta.1 - Xenopus laevis (African clawed frog)

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Q8UVR3 (LMX1B_XENLA) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 88. History...

Clusters with 100%, 90%, 50% identity |

Documents (1) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
LIM homeobox transcription factor 1-beta.1

Alternative name(s):
LIM homeobox protein 1b
Short name=Xlmx1b

Gene names

Name:	lmx1b.1
Synonyms:	lmx1b

Organism

Xenopus laevis (African clawed frog)

Taxonomic identifier

8355 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Amphibia › Batrachia › Anura › Pipoidea › Pipidae › Xenopodinae › Xenopus › Xenopus

Protein attributes

Sequence length	400 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	Required for early specification of the kidney glomus, lying upstream of wt1 in the pathway controlling glomus differentiation. The balance in levels and expression patterns of binding partners such as lhx1/lim-1 influences differentiation into glomus or tubule derivatives. Involved in specification of serotonergic neurons. Ref.1 Ref.2 Ref.3
Subcellular location	Nucleus Potential.
Tissue specificity	Shows a temporal expression pattern in three main areas: neural, kidney and limbs. From stage 13 onwards, expressed in regions of the nervous system including the placodes and otic vesicles, eye, specific sets of neurons, and in discreet regions of the neural tube. From stage 13, also expressed in the presumptive pronephros, and from stage 27 expression is predominant in the capsule of the pronephric glomus. Also expressed in the developing forelimbs and hindlimbs. In metamorphosing tadpoles, expressed in the eye, brain, muscle and mesonephric kidney. Ref.1 Ref.2
Developmental stage	Expressed zygotically from stage 10.5. Expression is elevated between stages 12.5 and 14, and continues throughout neurulae, tailbud and swimming tadpole stages. Ref.1
Induction	By activin; retinoic acid (RA) inhibits this up-regulation. Expression in neurons is regulated by calcium (Ca2+) activity: the lower the activity, the larger the number of neurons showing expression. Ref.1 Ref.3
Sequence similarities	Contains 1 homeobox DNA-binding domain. Contains 2 LIM zinc-binding domains.

Ontologies

Keywords
Biological process	Differentiation Neurogenesis Transcription Transcription regulation
Cellular component	Nucleus
Domain	Homeobox LIM domain Repeat
Ligand	DNA-binding Metal-binding Zinc
Molecular function	Developmental protein
Gene Ontology (GO)
Biological_process	glomus development Inferred from mutant phenotype Ref.2. Source: UniProtKB neuron differentiation Inferred from mutant phenotype Ref.3. Source: UniProtKB pronephric nephron tubule development Inferred from mutant phenotype Ref.2. Source: UniProtKB transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	nucleus Inferred from sequence or structural similarity. Source: UniProtKB
Molecular_function	sequence-specific DNA binding Inferred from electronic annotation. Source: InterPro sequence-specific DNA binding transcription factor activity Inferred from sequence or structural similarity. Source: UniProtKB zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 400

400

LIM homeobox transcription factor 1-beta.1

PRO_0000399037

Regions

Domain

54 – 113

LIM zinc-binding 1

Domain

114 – 175

LIM zinc-binding 2

DNA binding

218 – 277

Homeobox

Compositional bias

281 – 287

Poly-Gln

Sequences

Sequence

Length

Mass (Da)

Tools

Q8UVR3 [UniParc].

Last modified March 1, 2002. Version 1.
Checksum: 8F8AB0CC0E455EF9
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FASTA

400

45,106

        10         20         30         40         50         60 
MDIATGPESL DRCFTRGPSD CAKMLDTIKM EDHPLRTGTA TLGVLLGSEC QHQAVCEGCQ 

        70         80         90        100        110        120 
RPISDRFLMR VNEASWHEEC LQCTVCQQPL TTSCYFRDRK LFCKQDYQQL FAAKCSGCME 

       130        140        150        160        170        180 
KIAPTEFVMR ALECVYHLSC FCCCVCERQL RKGDEFVLKE GQLLCKSDYE KEKDLLSSGS 

       190        200        210        220        230        240 
PDDSDSVKSD DEEGDVKPGK GRVNQGKGSD DGKDPRRPKR PRTILTTQQR RAFKASFEVS 

       250        260        270        280        290        300 
SKPCRKVRET LAAETGLSVR VVQVWFQNQR AKIKKLARRH QQQQEQQNSQ RLGQEVMSSR 

       310        320        330        340        350        360 
MEGMMTSYAP LAPSQQQIVT MDQNSYSTDP FQQGLTPPQM PGDHMNPYGN DTIFHDIDSD 

       370        380        390        400 
TSLTSLSDCF LASSEVTSMQ ARVGNPIDRL YSMQSSYFAS

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References

[1]	"Isolation and growth factor inducibility of the Xenopus laevis Lmx1b gene." Haldin C.E., Nijjar S., Masse K., Barnett M.W., Jones E.A. Int. J. Dev. Biol. 47:253-262(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, INDUCTION. Tissue: Neurula.
[2]	"The lmx1b gene is pivotal in glomus development in Xenopus laevis." Haldin C.E., Masse K.L., Bhamra S., Simrick S., Kyuno J., Jones E.A. Dev. Biol. 322:74-85(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, TISSUE SPECIFICITY.
[3]	"Activity-dependent expression of Lmx1b regulates specification of serotonergic neurons modulating swimming behavior." Demarque M., Spitzer N.C. Neuron 67:321-334(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INDUCTION.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF414086 mRNA. Translation: AAL32444.1.
RefSeq	NP_001083902.1. NM_001090433.1.
UniGene	Xl.12464.
3D structure databases
HSSP	HSSP built from PDB template 1BW5 based on UniProtKB P50480.
ProteinModelPortal	Q8UVR3.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	399182.
KEGG	xla:399182.
Organism-specific databases
CTD	399182.
Xenbase	XB-GENE-494754. lmx1b.1.
Phylogenomic databases
HOVERGEN	HBG052335.
KO	K09371.
Family and domain databases
Gene3D	1.10.10.60. 1 hit. 2.10.110.10. 2 hits.
InterPro	IPR017970. Homeobox_CS. IPR001356. Homeodomain. IPR009057. Homeodomain-like. IPR001781. Znf_LIM. [Graphical view]
Pfam	PF00046. Homeobox. 1 hit. PF00412. LIM. 2 hits. [Graphical view]
SMART	SM00389. HOX. 1 hit. SM00132. LIM. 2 hits. [Graphical view]
SUPFAM	SSF46689. Homeodomain_like. 1 hit.
PROSITE	PS00027. HOMEOBOX_1. 1 hit. PS50071. HOMEOBOX_2. 1 hit. PS00478. LIM_DOMAIN_1. 2 hits. PS50023. LIM_DOMAIN_2. 2 hits. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

LMX1B_XENLA

Accession

Primary (citable) accession number: Q8UVR3

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 5, 2010
Last sequence update:	March 1, 2002
Last modified:	April 3, 2013
This is version 88 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Family and domain databases

Entry information

Relevant documents