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Aliases for LMX1B Gene

Aliases for LMX1B Gene

  • LIM Homeobox Transcription Factor 1, Beta 2 3
  • LIM/Homeobox Protein LMX1B 3 4
  • LIM/Homeobox Protein 1.2 3 4
  • LMX-1.2 3 4
  • NPS1 3 6
  • LIM Homeobox Transcription Factor 1-Beta 3
  • LMX1.2 3

External Ids for LMX1B Gene

Previous Symbols for LMX1B Gene

  • NPS1

Summaries for LMX1B Gene

Entrez Gene Summary for LMX1B Gene

  • This gene encodes a member of LIM-homeodomain family of proteins containing two N-terminal zinc-binding LIM domains, 1 homeodomain, and a C-terminal glutamine-rich domain. It functions as a transcription factor, and is essential for the normal development of dorsal limb structures, the glomerular basement membrane, the anterior segment of the eye, and dopaminergic and serotonergic neurons. Mutations in this gene are associated with nail-patella syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]

GeneCards Summary for LMX1B Gene

LMX1B (LIM Homeobox Transcription Factor 1, Beta) is a Protein Coding gene. Diseases associated with LMX1B include nail-patella syndrome and genitopatellar syndrome. Among its related pathways are SIDS Susceptibility Pathways. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is LHX4.

UniProtKB/Swiss-Prot for LMX1B Gene

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

Gene Wiki entry for LMX1B Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LMX1B Gene

Genomics for LMX1B Gene

Genomic Location for LMX1B Gene

Start:
126,614,443 bp from pter
End:
126,701,032 bp from pter
Size:
86,590 bases
Orientation:
Plus strand

Genomic View for LMX1B Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for LMX1B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LMX1B Gene

Regulatory Elements for LMX1B Gene

Proteins for LMX1B Gene

  • Protein details for LMX1B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O60663-LMX1B_HUMAN
    Recommended name:
    LIM homeobox transcription factor 1-beta
    Protein Accession:
    O60663
    Secondary Accessions:
    • F8W7W6
    • O75463
    • Q5JU95
    • Q6ISC9

    Protein attributes for LMX1B Gene

    Size:
    402 amino acids
    Molecular mass:
    44917 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAC27294.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAC39738.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAH69601.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAI12121.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAI13492.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAH70295.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAI40918.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=EAW87642.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for LMX1B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LMX1B Gene

Proteomics data for LMX1B Gene at MOPED

Post-translational modifications for LMX1B Gene

No Post-translational modifications

Other Protein References for LMX1B Gene

No data available for DME Specific Peptides for LMX1B Gene

Domains for LMX1B Gene

Gene Families for LMX1B Gene

HGNC:
  • LIM :Homeoboxes / LIM class

Protein Domains for LMX1B Gene

Suggested Antigen Peptide Sequences for LMX1B Gene

Graphical View of Domain Structure for InterPro Entry

O60663

UniProtKB/Swiss-Prot:

LMX1B_HUMAN
Domain:
  • Contains 1 homeobox DNA-binding domain.:
    • O60663
  • Contains 2 LIM zinc-binding domains.:
    • O60663
genes like me logo Genes that share domains with LMX1B: view

Function for LMX1B Gene

Molecular function for LMX1B Gene

GENATLAS Biochemistry: transcriptional regulator of the LIM-homeo domain,LMX1A related gene,highly expressed in renal development and skeletal patterning,found in adult testis,thyroid,duodenum,skeletal muscle,pancreatic islets,involved in dorsal-ventral limb patterning and kidney development
UniProtKB/Swiss-Prot Function: Essential for the specification of dorsal limb fate at both the zeugopodal and autopodal levels

Gene Ontology (GO) - Molecular Function for LMX1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding --
GO:0003700 sequence-specific DNA binding transcription factor activity IDA 10767331
GO:0005515 protein binding IPI 12792813
GO:0008270 zinc ion binding IEA --
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with LMX1B: view
genes like me logo Genes that share phenotypes with LMX1B: view

Animal Models for LMX1B Gene

MGI Knock Outs for LMX1B:

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for LMX1B Gene

Localization for LMX1B Gene

Subcellular locations from UniProtKB/Swiss-Prot for LMX1B Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LMX1B Gene COMPARTMENTS Subcellular localization image for LMX1B gene
Compartment Confidence
nucleus 5
cytosol 2
extracellular 1
lysosome 1
vacuole 1

Gene Ontology (GO) - Cellular Components for LMX1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 10767331
genes like me logo Genes that share ontologies with LMX1B: view

Pathways for LMX1B Gene

SuperPathways for LMX1B Gene

genes like me logo Genes that share pathways with LMX1B: view

Pathways by source for LMX1B Gene

1 BioSystems pathway for LMX1B Gene

Gene Ontology (GO) - Biological Process for LMX1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001701 in utero embryonic development NAS 12792813
GO:0001764 neuron migration IEA --
GO:0002930 trabecular meshwork development IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IDA 10767331
genes like me logo Genes that share ontologies with LMX1B: view

Compounds for LMX1B Gene

(4) Novoseek inferred chemical compound relationships for LMX1B Gene

Compound -log(P) Hits PubMed IDs
dopamine 42.9 6
tyrosine 9.17 1
steroid 0 1
zinc 0 1
genes like me logo Genes that share compounds with LMX1B: view

Transcripts for LMX1B Gene

mRNA/cDNA for LMX1B Gene

(3) REFSEQ mRNAs :
(7) Additional mRNA sequences :
(8) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for LMX1B Gene

LIM homeobox transcription factor 1, beta:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for LMX1B Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10
SP1: - - -
SP2: - -
SP3:

Relevant External Links for LMX1B Gene

GeneLoc Exon Structure for
LMX1B
ECgene alternative splicing isoforms for
LMX1B

Expression for LMX1B Gene

mRNA expression in normal human tissues for LMX1B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LMX1B Gene

This gene is overexpressed in Breast - Mammary Tissue (9.6), Heart - Atrial Appendage (4.9), Skin - Sun Exposed (Lower leg) (4.8), and Brain - Spinal cord (cervical c-1) (4.3).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for LMX1B Gene

SOURCE GeneReport for Unigene cluster for LMX1B Gene Hs.129133

mRNA Expression by UniProt/SwissProt for LMX1B Gene

O60663-LMX1B_HUMAN
Tissue specificity: Expressed in most tissues. Highest levels in testis, thyroid, duodenum, skeletal muscle, and pancreatic islets
genes like me logo Genes that share expressions with LMX1B: view

Orthologs for LMX1B Gene

This gene was present in the common ancestor of animals.

Orthologs for LMX1B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LMX1B 35
  • 99.16 (n)
  • 100 (a)
LMX1B 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LMX1B 35
  • 94.16 (n)
  • 98.36 (a)
LMX1B 36
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LMX1B 35
  • 95.41 (n)
  • 100 (a)
LMX1B 36
  • 100 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lmx1b 35
  • 93.37 (n)
  • 100 (a)
Lmx1b 16
Lmx1b 36
  • 100 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LMX1B 36
  • 97 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LMX1B 36
  • 95 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lmx1b 35
  • 93.53 (n)
  • 99.75 (a)
chicken
(Gallus gallus)
Aves LMX1B 35
  • 80.11 (n)
  • 93.37 (a)
LMX1B 36
  • 90 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LMX1B 36
  • 89 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100495130 35
  • 78.67 (n)
  • 89.5 (a)
Str.18490 35
zebrafish
(Danio rerio)
Actinopterygii lmx1ba 36
  • 80 (a)
OneToMany
lmx1bb 35
  • 79.64 (n)
  • 87.47 (a)
lmx1bb 36
  • 85 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG32105 36
  • 24 (a)
ManyToMany
CG4328 36
  • 28 (a)
ManyToMany
CG4328 37
  • 41 (a)
worm
(Caenorhabditis elegans)
Secernentea lim-6 35
  • 49.11 (n)
  • 45.98 (a)
lim-6 36
  • 39 (a)
OneToMany
lim-6 37
  • 43 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.235 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 24 (a)
ManyToMany
-- 36
  • 32 (a)
ManyToMany
Species with no ortholog for LMX1B:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for LMX1B Gene

ENSEMBL:
Gene Tree for LMX1B (if available)
TreeFam:
Gene Tree for LMX1B (if available)

Paralogs for LMX1B Gene

Paralogs for LMX1B Gene

Selected SIMAP similar genes for LMX1B Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with LMX1B: view

Variants for LMX1B Gene

Sequence variations from dbSNP and Humsavar for LMX1B Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type MAF
rs870956 -- 126,640,438(+) TTGTG(A/T)CCTGT intron-variant
rs944102 -- 126,619,837(-) ATCCT(A/C)CCAGC intron-variant
rs944103 -- 126,651,211(-) TGCCC(A/G)GGATG intron-variant
rs944104 -- 126,644,647(+) GAAGA(G/T)AATGG intron-variant
rs944105 -- 126,644,710(+) GTGTC(A/C)CTGCC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LMX1B Gene

Variant ID Type Subtype PubMed ID
nsv893849 CNV Gain 21882294
nsv825080 CNV Gain 20364138
nsv831723 CNV Gain+Loss 17160897
dgv1234n67 CNV Gain 20364138
nsv517494 CNV Loss 19592680
nsv528719 CNV Loss 19592680
esv2659178 CNV Deletion 23128226
nsv6718 CNV Loss 18451855
dgv8283n71 CNV Loss 21882294
dgv8284n71 CNV Loss 21882294
nsv466568 CNV Loss 19166990
esv2739046 CNV Deletion 23290073
dgv8285n71 CNV Loss 21882294
nsv825083 CNV Gain 20364138

Relevant External Links for LMX1B Gene

HapMap Linkage Disequilibrium report
LMX1B
Human Gene Mutation Database (HGMD)
LMX1B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LMX1B Gene

Disorders for LMX1B Gene

(1) OMIM Diseases for LMX1B Gene (602575)

UniProtKB/Swiss-Prot

LMX1B_HUMAN
  • Nail-patella syndrome (NPS) [MIM:161200]: Disease that cause abnormal skeletal patterning and renal dysplasia. {ECO:0000269 PubMed:10571942, ECO:0000269 PubMed:11668639, ECO:0000269 PubMed:9590287, ECO:0000269 PubMed:9618165, ECO:0000269 PubMed:9837817}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(3) University of Copenhagen DISEASES for LMX1B Gene

(11) Novoseek inferred disease relationships for LMX1B Gene

Disease -log(P) Hits PubMed IDs
nail-patella syndrome 98.3 36
genitopatellar syndrome 88.3 4
renal disease 58.5 6
glaucoma 53.5 8
renal dysplasia 50.5 2

Relevant External Links for LMX1B

GeneTests
LMX1B
GeneReviews
LMX1B
Genetic Association Database (GAD)
LMX1B
Human Genome Epidemiology (HuGE) Navigator
LMX1B
genes like me logo Genes that share disorders with LMX1B: view

Publications for LMX1B Gene

  1. Mutations in LMX1B cause abnormal skeletal patterning and renal dysplasia in nail patella syndrome. (PMID: 9590287) Dreyer S.D. … Lee B. (Nat. Genet. 1998) 2 3 4 23
  2. Restricted distribution of loss-of-function mutations within the LMX1B genes of nail-patella syndrome patients. (PMID: 10571942) Clough M.V. … McIntosh I. (Hum. Mutat. 1999) 3 4 23
  3. Loss-of-function mutations in the LIM-homeodomain gene, LMX1B, in nail-patella syndrome. (PMID: 9618165) Vollrath D. … Richards J.E. (Hum. Mol. Genet. 1998) 3 4 23
  4. Mutation analysis of LMX1B gene in nail-patella syndrome patients. (PMID: 9837817) McIntosh I. … Lee B. (Am. J. Hum. Genet. 1998) 3 4 23
  5. Twenty-two novel LMX1B mutations identified in nail patella syndrome (NPS) patients. (PMID: 11668639) Hamlington J.D. … McIntosh I. (Hum. Mutat. 2001) 3 4 23

Products for LMX1B Gene

Sources for LMX1B Gene

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