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LMX1B LIM homeobox transcription factor 1, beta [ Homo sapiens (human) ]

Gene ID: 4010, updated on 19-Jul-2014
Official Symbol
LMX1Bprovided by HGNC
Official Full Name
LIM homeobox transcription factor 1, betaprovided by HGNC
Primary source
HGNC:6654
Locus tag
RP11-489N22.3
See related
Ensembl:ENSG00000136944; HPRD:03986; MIM:602575
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NPS1; LMX1.2
Summary
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]
See LMX1B in Epigenomics, MapViewer
Location:
9q33.3
Exon count:
8
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 9 NC_000009.12 (126614443..126701032)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (129376722..129463311)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101929116 Neighboring gene multivesicular body subunit 12B Neighboring gene non-protein coding RNA, repressor of NFAT Neighboring gene zinc finger and BTB domain containing 43 Neighboring gene zinc finger and BTB domain containing 34

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Nail-patella syndrome
MedGen: C0027341 OMIM: 161200 GeneReviews: Nail-Patella Syndrome
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-04-19)

ISCA Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-19)

ISCA Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.
NHGRI GWA Catalog
  • SIDS Susceptibility Pathways, organism-specific biosystem (from WikiPathways)
    SIDS Susceptibility Pathways, organism-specific biosystemIn this model, we provide an integrated view of Sudden Infant Death Syndrome (SIDS) at the level of implicated tissues, signaling networks and genetics. The purpose of this model is to serve as an ov...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • MGC138325, MGC142051

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
sequence-specific DNA binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cell death IEA
Inferred from Electronic Annotation
more info
 
cell proliferation IEA
Inferred from Electronic Annotation
more info
 
central nervous system neuron development IEA
Inferred from Electronic Annotation
more info
 
cerebellum morphogenesis IEA
Inferred from Electronic Annotation
more info
 
collagen fibril organization IEA
Inferred from Electronic Annotation
more info
 
dopaminergic neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
dorsal/ventral pattern formation ISS
Inferred from Sequence or Structural Similarity
more info
 
in utero embryonic development NAS
Non-traceable Author Statement
more info
PubMed 
limb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
midbrain development IEA
Inferred from Electronic Annotation
more info
 
multicellular organismal development NAS
Non-traceable Author Statement
more info
PubMed 
neuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
neuron migration IEA
Inferred from Electronic Annotation
more info
 
organ growth IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription from RNA polymerase II promoter IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
trabecular meshwork development IEA
Inferred from Electronic Annotation
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
LIM homeobox transcription factor 1-beta
Names
LIM homeobox transcription factor 1-beta
LMX-1.2
LIM/homeobox protein 1.2
LIM/homeobox protein LMX1B

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_017039.1 

    Range
    5001..91590
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001174146.1NP_001167617.1  LIM homeobox transcription factor 1-beta isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate donor splice site at an internal coding exon compared to variant 1, resulting in a longer isoform (3) containing an additional 11 aa protein segment compared to isoform 1.
    Source sequence(s)
    AL161731, AL161908, BC143801, EL952935
    Consensus CDS
    CCDS55343.1
    UniProtKB/TrEMBL
    B7ZLH2
    Related
    ENSP00000347684, ENST00000355497
    Conserved Domains (3) summary
    cd09371
    Location:56108
    Blast Score: 283
    LIM1_Lmx1b; The first LIM domain of Lmx1b
    cd09378
    Location:115169
    Blast Score: 273
    LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
    cd00086
    Location:220276
    Blast Score: 195
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
  2. NM_001174147.1NP_001167618.1  LIM homeobox transcription factor 1-beta isoform 2

    See proteins identical to NP_001167618.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate donor splice site at the penultimate coding exon compared to variant 1, resulting in a longer isoform (2) containing an additional 7 aa protein segment compared to isoform 1.
    Source sequence(s)
    AL161731, AL161908, BC069588, BC113491, EL952935
    Consensus CDS
    CCDS55342.1
    UniProtKB/Swiss-Prot
    O60663
    UniProtKB/TrEMBL
    Q6ISE0
    Conserved Domains (3) summary
    cd09371
    Location:56108
    Blast Score: 284
    LIM1_Lmx1b; The first LIM domain of Lmx1b
    cd09378
    Location:115169
    Blast Score: 274
    LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
    cd00086
    Location:220276
    Blast Score: 196
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
  3. NM_002316.3NP_002307.2  LIM homeobox transcription factor 1-beta isoform 1

    See proteins identical to NP_002307.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript and encodes isoform 1.
    Source sequence(s)
    AL161731, AL161908, BC113491, EL952935
    Consensus CDS
    CCDS6866.2
    UniProtKB/Swiss-Prot
    O60663
    Related
    ENSP00000390923, ENST00000425646
    Conserved Domains (3) summary
    cd09371
    Location:56108
    Blast Score: 283
    LIM1_Lmx1b; The first LIM domain of Lmx1b
    cd09378
    Location:115169
    Blast Score: 273
    LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
    cd00086
    Location:220276
    Blast Score: 195
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000009.12 

    Range
    126614443..126701032
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

  1. AC_000141.1 

    Range
    98989870..99079726
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018920.2 

    Range
    129527362..129614009
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)