NFIX

nuclear factor I X | NF1A

The protein encoded by this gene is a transcription factor that binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3 in viral and cellular promoters. The encoded protein can also stimulate adenovirus replication in vitro. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2012]

Biological processes 18 terms

DNA-binding transcription factor activity (GO:0003700)DNA-binding transcription factor activity (GO:0003700)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 cis-regulatory region sequence-specific DNA binding (GO:0000978)chromatin (GO:0000785)negative regulation of transcription by RNA polymerase II (GO:0000122)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of DNA-templated transcription (GO:0045893)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)transcription by RNA polymerase II (GO:0006366)

Expression (TPM)

TFs regulating NFIX 0 TFs

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

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of NFIX, 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
chr19:12,774,659–12,776,025	294.5 kb	Distal (>10kb) Multiome	803
chr19:12,777,481–12,778,589	292.2 kb	Distal (>10kb) Multiome	661
chr19:12,789,543–12,790,654	280.0 kb	Distal (>10kb) Multiome	717
chr19:12,790,960–12,793,231	278.5 kb	Distal (>10kb) Multiome	1015
chr19:12,793,340–12,794,240	276.3 kb	Distal (>10kb) Multiome	808
chr19:12,801,120–12,802,290	268.1 kb	Distal (>10kb) Multiome	901
chr19:12,806,212–12,806,984	263.4 kb	Distal (>10kb) Multiome	827
chr19:12,825,565–12,826,186	244.2 kb	Distal (>10kb) Multiome	436
chr19:12,832,484–12,833,101	237.3 kb	Distal (>10kb) Multiome	970
chr19:12,833,638–12,834,477	236.1 kb	Distal (>10kb) Multiome	310
chr19:12,838,114–12,838,869	231.5 kb	Distal (>10kb) Multiome	377
chr19:12,840,071–12,841,485	229.2 kb	Distal (>10kb) Multiome	391
chr19:12,847,633–12,848,090	222.2 kb	Distal (>10kb) Multiome	535
chr19:12,867,327–12,868,022	202.3 kb	Distal (>10kb) Multiome	315
chr19:12,872,968–12,873,990	196.8 kb	Distal (>10kb) Multiome	263
chr19:12,880,834–12,881,875	188.5 kb	Distal (>10kb) Multiome	656
chr19:12,884,836–12,886,381	184.7 kb	Distal (>10kb) Multiome	717
chr19:12,890,614–12,891,603	179.0 kb	Distal (>10kb) Multiome	841
chr19:12,913,054–12,913,584	156.7 kb	Distal (>10kb) Multiome	373
chr19:12,919,018–12,919,719	150.6 kb	Distal (>10kb) Multiome	732
chr19:12,933,441–12,934,086	136.2 kb	Distal (>10kb) Multiome	789
chr19:12,937,426–12,939,166	131.5 kb	Distal (>10kb) Multiome	943
chr19:12,945,275–12,946,647	124.0 kb	Distal (>10kb) Multiome	1015
chr19:12,956,801–12,957,360	112.8 kb	Distal (>10kb) Multiome	747
chr19:12,964,998–12,965,862	104.5 kb	Distal (>10kb) Multiome	733
chr19:12,983,506–12,983,997	86.3 kb	Distal (>10kb) Multiome HiCAR	688
chr19:13,051,485–13,052,169	18.2 kb	Distal (>10kb) Multiome	649
chr19:13,061,195–13,061,672	8.5 kb	Proximal (<10kb) Multiome	544
chr19:13,069,469–13,070,306	at TSS	At TSS	334
chr19:13,093,620–13,094,260	23.9 kb	Distal (>10kb) Multiome	411
chr19:13,095,079–13,096,870	25.5 kb	Distal (>10kb) Multiome	501
chr19:13,116,411–13,117,080	46.7 kb	Distal (>10kb) Multiome	812
chr19:13,117,979–13,119,416	48.2 kb	Distal (>10kb) Multiome	699
chr19:13,149,468–13,156,577	83.1 kb	Distal (>10kb) Multiome	1333
chr19:13,162,579–13,165,523	94.7 kb	Distal (>10kb) Multiome	1112
chr19:13,167,359–13,168,023	97.7 kb	Distal (>10kb) Multiome	764

Genome Browser

Genomic view of the NFIX 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.