IRX1

iroquois homeobox 1 | IRX-5

This gene encodes a member of the Iroquois homeobox protein family. Homeobox genes in this family are involved in pattern formation in the embryo. The gene product has been identified as a tumor suppressor in gastric (PMID: 21602894, 20440264) and head and neck cancers (PMID: 18559491). A pseudogene of this gene is located on chromosome 13. [provided by RefSeq, Dec 2011]

Member of: DE-7 DE-7.2

Biological processes 20 terms

DNA binding (GO:0003677)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)DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)cell development (GO:0048468)chromatin (GO:0000785)metanephros development (GO:0001656)negative regulation of transcription by RNA polymerase II (GO:0000122)neuron differentiation (GO:0030182)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of gene expression (GO:0010628)proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)regulation of DNA-templated transcription (GO:0006355)regulation of transcription by RNA polymerase II (GO:0006357)sequence-specific DNA binding (GO:0043565)sequence-specific double-stranded DNA binding (GO:1990837)specification of loop of Henle identity (GO:0072086)

Expression (TPM)

TFs regulating IRX1 0 TFs

Transcription factors with Perturb-seq knockdown data for IRX1. 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 = IRX1 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 IRX1

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of IRX1, 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
chr5:3,590,352–3,590,750	5.1 kb	Proximal (<10kb)	56
chr5:3,591,008–3,591,512	4.3 kb	Proximal (<10kb)	68
chr5:3,593,719–3,593,942	1.9 kb	Proximal (<10kb)	17
chr5:3,594,314–3,596,993	37 bp	At TSS Multiome	308
chr5:3,597,102–3,597,644	1.3 kb	Proximal (<10kb)	52
chr5:3,597,938–3,598,179	2.1 kb	Proximal (<10kb)	23
chr5:3,598,317–3,598,518	2.5 kb	Proximal (<10kb)	27
chr5:3,598,629–3,599,113	2.8 kb	Proximal (<10kb)	36
chr5:3,599,731–3,601,253	3.9 kb	Proximal (<10kb)	171
chr5:3,602,005–3,603,376	7.1 kb	Proximal (<10kb) Multiome	201

Genome Browser

Genomic view of the IRX1 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.