LMX1A

LIM homeobox transcription factor 1 alpha | LMX1.1, LMX1

This gene encodes a homeodomain and LIM-domain containing protein. The encoded protein is a transcription factor that acts as a positive regulator of insulin gene transcription. This gene also plays a role in the development of dopamine producing neurons during embryogenesis. Mutations in this gene are associated with an increased risk of developing Parkinson's disease. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2012]

Developmental clusters: GC7

Biological processes 26 terms

DNA binding (GO:0003677)DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228)DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977)RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977)RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977)chromatin (GO:0000785)dopaminergic neuron differentiation (GO:0071542)dopaminergic neuron differentiation (GO:0071542)midbrain dopaminergic neuron differentiation (GO:1904948)midbrain dopaminergic neuron differentiation (GO:1904948)midbrain dopaminergic neuron differentiation (GO:1904948)neuron differentiation (GO:0030182)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)protein binding (GO:0005515)regulation of DNA-templated transcription (GO:0006355)regulation of transcription by RNA polymerase II (GO:0006357)sequence-specific double-stranded DNA binding (GO:1990837)sequence-specific double-stranded DNA binding (GO:1990837)synapse organization (GO:0050808)

Expression (TPM)

TFs regulating LMX1A 0 TFs

Transcription factors with Perturb-seq knockdown data for LMX1A. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = LMX1A upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

TF	Mean coef	Binding	Outlier	TF→Gene link

Rows:

Elements linked to LMX1A

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of LMX1A, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Element	Dist. to TSS	Link type	TFs
chr1:165,185,733–165,186,757	169.6 kb	Distal (>10kb) Multiome	116
chr1:165,235,066–165,236,469	120.2 kb	Distal (>10kb) Multiome	448
chr1:165,258,008–165,258,694	97.4 kb	Distal (>10kb) Multiome	239
chr1:165,323,635–165,324,626	31.5 kb	Distal (>10kb) Multiome	142
chr1:165,350,948–165,351,178	4.6 kb	Proximal (<10kb)	45
chr1:165,352,314–165,353,360	2.4 kb	Proximal (<10kb)	112
chr1:165,354,185–165,354,555	1.2 kb	Proximal (<10kb)	52
chr1:165,354,810–165,355,111	634 bp	At TSS	29
chr1:165,355,237–165,357,320	at TSS	At TSS	163
chr1:165,365,159–165,365,914	9.8 kb	Proximal (<10kb) Multiome	151
chr1:165,375,930–165,377,162	20.8 kb	Distal (>10kb) Multiome	364
chr1:165,443,654–165,446,226	89.5 kb	Distal (>10kb) Multiome	304
chr1:165,597,953–165,599,004	242.6 kb	Distal (>10kb) Multiome	625
chr1:165,630,162–165,632,376	275.3 kb	Distal (>10kb) Multiome	964

Genome Browser

Genomic view of the LMX1A locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.