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O60663 (LMX1B_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 142. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·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
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length402 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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

Subcellular location

Nucleus Potential.

Tissue specificity

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

Involvement in disease

Nail-patella syndrome (NPS) [MIM:161200]: Disease that cause abnormal skeletal patterning and renal dysplasia.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.1 Ref.5 Ref.6 Ref.7 Ref.8

Sequence similarities

Contains 1 homeobox DNA-binding domain.

Contains 2 LIM zinc-binding domains.

Sequence caution

The sequence AAC27294.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence AAC39738.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence AAH69601.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence AAI12121.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence AAI13492.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence CAH70295.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence CAI40918.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence EAW87642.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   DiseaseDisease mutation
   DomainHomeobox
LIM domain
Repeat
   LigandDNA-binding
Metal-binding
Zinc
   Molecular functionActivator
Developmental protein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcell death

Inferred from electronic annotation. Source: Ensembl

cell proliferation

Inferred from electronic annotation. Source: Ensembl

central nervous system neuron development

Inferred from electronic annotation. Source: Ensembl

cerebellum morphogenesis

Inferred from electronic annotation. Source: Ensembl

collagen fibril organization

Inferred from electronic annotation. Source: Ensembl

dopaminergic neuron differentiation

Inferred from electronic annotation. Source: Ensembl

dorsal/ventral pattern formation

Inferred from sequence or structural similarity. Source: UniProtKB

in utero embryonic development

Non-traceable author statement PubMed 12792813. Source: UniProtKB

limb morphogenesis

Inferred from electronic annotation. Source: Ensembl

midbrain development

Inferred from electronic annotation. Source: Ensembl

multicellular organismal development

Non-traceable author statement Ref.5Ref.1Ref.6. Source: UniProtKB

neuron differentiation

Inferred from sequence or structural similarity. Source: UniProtKB

neuron migration

Inferred from electronic annotation. Source: Ensembl

organ growth

Inferred from electronic annotation. Source: Ensembl

positive regulation of transcription from RNA polymerase II promoter

Inferred from electronic annotation. Source: Ensembl

regulation of transcription, DNA-templated

Inferred from direct assay PubMed 10767331. Source: UniProtKB

trabecular meshwork development

Inferred from electronic annotation. Source: Ensembl

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleus

Inferred from direct assay PubMed 10767331. Source: UniProtKB

   Molecular_functionprotein binding

Inferred from physical interaction PubMed 12792813. Source: UniProtKB

sequence-specific DNA binding

Inferred from electronic annotation. Source: InterPro

sequence-specific DNA binding transcription factor activity

Inferred from direct assay PubMed 10767331. Source: UniProtKB

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: O60663-1)

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.
Isoform 2 (identifier: O60663-2)

Also known as: Short;

The sequence of this isoform differs from the canonical sequence as follows:
     345-351: Missing.
Isoform 3 (identifier: O60663-3)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 402402LIM homeobox transcription factor 1-beta
PRO_0000075828

Regions

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

Natural variations

Alternative sequence2931L → LGQGEPGPGQGL in isoform 3.
VSP_046472
Alternative sequence345 – 3517Missing in isoform 2 and isoform 3.
VSP_003113
Natural variant591C → R in NPS. Ref.7
VAR_015201
Natural variant591C → S in NPS. Ref.7
VAR_015202
Natural variant751S → F.
Corresponds to variant rs2235058 [ dbSNP | Ensembl ].
VAR_047755
Natural variant771H → N in NPS. Ref.8
VAR_015190
Natural variant771H → Q in NPS. Ref.7
VAR_015203
Natural variant771H → Y in NPS. Ref.7
VAR_015204
Natural variant801C → R in NPS. Ref.7
VAR_015205
Natural variant811L → W in NPS. Ref.8
VAR_015191
Natural variant831C → F in NPS. Ref.8
VAR_015192
Natural variant831C → G in NPS. Ref.7
VAR_015206
Natural variant831C → W in NPS. Ref.8
VAR_015193
Natural variant831C → Y in NPS. Ref.7
VAR_015207
Natural variant861C → R in NPS. Ref.7
VAR_015208
Natural variant1031C → W in NPS. Ref.8
VAR_015194
Natural variant1061D → G in NPS. Ref.7
VAR_015209
Natural variant1181C → F in NPS. Ref.1
VAR_004198
Natural variant1181C → Y in NPS. Ref.7 Ref.8
VAR_015195
Natural variant1371H → Y in NPS. Ref.8
VAR_015196
Natural variant1401C → Y in NPS. Ref.8
VAR_015197
Natural variant1431C → S in NPS. Ref.7
VAR_015210
Natural variant1461C → F in NPS. Ref.7
VAR_015211
Natural variant1461C → Y in NPS. Ref.7
VAR_015212
Natural variant1651C → W in NPS. Ref.6
VAR_004199
Natural variant2231R → Q in NPS. Ref.6 Ref.8
Corresponds to variant rs28939692 [ dbSNP | Ensembl ].
VAR_004200
Natural variant2361A → P in NPS. Ref.6 Ref.8
VAR_004201
Natural variant2411S → P in NPS. Ref.6
VAR_004202
Natural variant2491R → P in NPS. Ref.6
VAR_004203
Natural variant2521L → P in NPS. Ref.7
VAR_015213
Natural variant2531A → V in NPS. Ref.6
VAR_004204
Natural variant2661W → C in NPS. Ref.8
VAR_015198
Natural variant2691N → K in NPS. Ref.5 Ref.6 Ref.8
VAR_004205

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (Long) [UniParc].

Last modified May 1, 2013. Version 3.
Checksum: E59FC36C39C7C9A3

FASTA40244,917
        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 QMPGDHMNPY GNDSIFHDID 

       370        380        390        400 
SDTSLTSLSD CFLGSSDVGS LQARVGNPID RLYSMQSSYF AS 

« Hide

Isoform 2 (Short) [UniParc].

Checksum: 9FFBF8A68E7AC676
Show »

FASTA39544,102
Isoform 3 [UniParc].

Checksum: 5FF15E73B7FD552E
Show »

FASTA40645,080

References

« Hide 'large scale' references
[1]"Loss-of-function mutations in the LIM-homeodomain gene, LMX1B, in nail-patella syndrome."
Vollrath D., Jaramillo-Babb V.L., Clough M.V., McIntosh I., Scott K.M., Lichter P.R., Richards J.E.
Hum. Mol. Genet. 7:1091-1098(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 1), VARIANT NPS PHE-118.
[2]"DNA sequence and analysis of human chromosome 9."
Humphray S.J., Oliver K., Hunt A.R., Plumb R.W., Loveland J.E., Howe K.L., Andrews T.D., Searle S., Hunt S.E., Scott C.E., Jones M.C., Ainscough R., Almeida J.P., Ambrose K.D., Ashwell R.I.S., Babbage A.K., Babbage S., Bagguley C.L. expand/collapse author list , Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beasley H., Beasley O., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burford D., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Chen Y., Clarke G., Clark S.Y., Clee C.M., Clegg S., Collier R.E., Corby N., Crosier M., Cummings A.T., Davies J., Dhami P., Dunn M., Dutta I., Dyer L.W., Earthrowl M.E., Faulkner L., Fleming C.J., Frankish A., Frankland J.A., French L., Fricker D.G., Garner P., Garnett J., Ghori J., Gilbert J.G.R., Glison C., Grafham D.V., Gribble S., Griffiths C., Griffiths-Jones S., Grocock R., Guy J., Hall R.E., Hammond S., Harley J.L., Harrison E.S.I., Hart E.A., Heath P.D., Henderson C.D., Hopkins B.L., Howard P.J., Howden P.J., Huckle E., Johnson C., Johnson D., Joy A.A., Kay M., Keenan S., Kershaw J.K., Kimberley A.M., King A., Knights A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C., Lloyd D.M., Lovell J., Martin S., Mashreghi-Mohammadi M., Matthews L., McLaren S., McLay K.E., McMurray A., Milne S., Nickerson T., Nisbett J., Nordsiek G., Pearce A.V., Peck A.I., Porter K.M., Pandian R., Pelan S., Phillimore B., Povey S., Ramsey Y., Rand V., Scharfe M., Sehra H.K., Shownkeen R., Sims S.K., Skuce C.D., Smith M., Steward C.A., Swarbreck D., Sycamore N., Tester J., Thorpe A., Tracey A., Tromans A., Thomas D.W., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Williams S.A., Wilming L., Wray P.W., Young L., Ashurst J.L., Coulson A., Blocker H., Durbin R.M., Sulston J.E., Hubbard T., Jackson M.J., Bentley D.R., Beck S., Rogers J., Dunham I.
Nature 429:369-374(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]"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] OF 8-402 (ISOFORM 2).
[5]"Mutations in LMX1B cause abnormal skeletal patterning and renal dysplasia in nail patella syndrome."
Dreyer S.D., Zhou G., Baldini A., Winterpacht A., Zabel B., Cole W., Johnson R.L., Lee B.
Nat. Genet. 19:47-50(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 24-402 (ISOFORM 2), VARIANT NPS LYS-269.
[6]"Mutation analysis of LMX1B gene in nail-patella syndrome patients."
McIntosh I., Dreyer S.D., Clough M.V., Dunston J.A., Eyaid W., Roig C.M., Montgomery T., Ala-Mello S., Kaitila I., Winterpacht A., Zabel B., Frydman M., Cole W.G., Francomano C.A., Lee B.
Am. J. Hum. Genet. 63:1651-1658(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS NPS TRP-165; GLN-223; PRO-236; PRO-241; PRO-249; VAL-253 AND LYS-269.
[7]"Restricted distribution of loss-of-function mutations within the LMX1B genes of nail-patella syndrome patients."
Clough M.V., Hamlington J.D., McIntosh I.
Hum. Mutat. 14:459-465(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS NPS ARG-59; SER-59; GLN-77; TYR-77; ARG-80; GLY-83; TYR-83; ARG-86; GLY-106; TYR-118; SER-143; PHE-146; TYR-146 AND PRO-252.
[8]"Twenty-two novel LMX1B mutations identified in nail patella syndrome (NPS) patients."
Hamlington J.D., Jones C., McIntosh I.
Hum. Mutat. 18:458-458(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS NPS ASN-77; TRP-81; PHE-83; TRP-83; TRP-103; TYR-118; TYR-137; TYR-140; GLN-223; PRO-236; CYS-266 AND LYS-269.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF059575 expand/collapse EMBL AC list , 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.
CCDSCCDS55342.1. [O60663-1]
CCDS55343.1. [O60663-3]
CCDS6866.2. [O60663-2]
RefSeqNP_001167618.1. NM_001174147.1. [O60663-1]
NP_002307.2. NM_002316.3. [O60663-2]
UniGeneHs.129133.

3D structure databases

ProteinModelPortalO60663.
SMRO60663. Positions 4-173, 214-276.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid110195. 2 interactions.
IntActO60663. 2 interactions.
STRING9606.ENSP00000347684.

PTM databases

PhosphoSiteO60663.

Proteomic databases

PaxDbO60663.
PRIDEO60663.

Protocols and materials databases

DNASU4010.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000355497; ENSP00000347684; ENSG00000136944. [O60663-3]
ENST00000373474; ENSP00000362573; ENSG00000136944. [O60663-1]
ENST00000425646; ENSP00000390923; ENSG00000136944.
ENST00000526117; ENSP00000436930; ENSG00000136944. [O60663-2]
GeneID4010.
KEGGhsa:4010.
UCSCuc004bqj.3. human. [O60663-1]

Organism-specific databases

CTD4010.
GeneCardsGC09P129376.
GeneReviewsLMX1B.
HGNCHGNC:6654. LMX1B.
MIM161200. phenotype.
602575. gene.
neXtProtNX_O60663.
Orphanet2614. Nail-patella syndrome.
PharmGKBPA30417.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG243427.
HOGENOMHOG000231629.
HOVERGENHBG052335.
InParanoidO60663.
KOK09371.
OMANRMEGMM.
OrthoDBEOG7BZVTB.
TreeFamTF315442.

Gene expression databases

ArrayExpressO60663.
BgeeO60663.
CleanExHS_LMX1B.
GenevestigatorO60663.

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

GeneWikiLMX1B.
GenomeRNAi4010.
NextBio15732.
PROO60663.
SOURCESearch...

Entry information

Entry nameLMX1B_HUMAN
AccessionPrimary (citable) accession number: O60663
Secondary accession number(s): F8W7W6 expand/collapse secondary AC list , O75463, Q5JU95, Q6ISC9
Entry history
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: May 1, 2013
Last modified: July 9, 2014
This is version 142 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 9

Human chromosome 9: entries, gene names and cross-references to MIM