NELFE

negative elongation factor complex member E | D6S45, NELF-E, RD, RDP, RDBP

The protein encoded by this gene is part of a complex termed negative elongation factor (NELF) which represses RNA polymerase II transcript elongation. This protein bears similarity to nuclear RNA-binding proteins; however, it has not been demonstrated that this protein binds RNA. The protein contains a tract of alternating basic and acidic residues, largely arginine (R) and aspartic acid (D). The gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. [provided by RefSeq, Jul 2008]

Member of: DE-1 DE-1.38

Biological processes 31 terms

NELF complex (GO:0032021)NELF complex (GO:0032021)NELF complex (GO:0032021)RNA binding (GO:0003723)RNA binding (GO:0003723)RNA binding (GO:0003723)RNA binding (GO:0003723)RNA polymerase inhibitor activity (GO:0140870)chromatin (GO:0000785)chromatin (GO:0000785)chromatin binding (GO:0003682)chromatin binding (GO:0003682)chromosome (GO:0005694)mRNA binding (GO:0003729)negative regulation of transcription by RNA polymerase II (GO:0000122)negative regulation of transcription elongation by RNA polymerase II (GO:0034244)negative regulation of transcription elongation by RNA polymerase II (GO:0034244)negative regulation of transcription elongation by RNA polymerase II (GO:0034244)nuclear body (GO:0016604)nucleic acid binding (GO:0003676)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of ERK1 and ERK2 cascade (GO:0070374)positive regulation of transcription by RNA polymerase II (GO:0045944)protein binding (GO:0005515)regulation of DNA-templated transcription (GO:0006355)transcription pausing by RNA polymerase II (GO:0160239)

Expression (TPM)

TFs regulating NELFE 0 TFs

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

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of NELFE, 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
chr6:31,660,325–31,660,941	298.2 kb	Distal (>10kb) Multiome	892
chr6:31,664,725–31,666,373	294.1 kb	Distal (>10kb) Multiome	1039
chr6:31,682,887–31,683,880	275.6 kb	Distal (>10kb) Multiome HiCAR	248
chr6:31,702,816–31,703,520	255.7 kb	Distal (>10kb) Multiome	875
chr6:31,713,576–31,714,641	244.8 kb	Distal (>10kb) Multiome	171
chr6:31,728,852–31,730,814	228.7 kb	Distal (>10kb) Multiome	979
chr6:31,739,236–31,740,741	219.1 kb	Distal (>10kb) Multiome	1043
chr6:31,766,045–31,766,778	192.5 kb	Distal (>10kb) Multiome	351
chr6:31,795,097–31,796,366	163.0 kb	Distal (>10kb) Multiome	979
chr6:31,806,162–31,807,183	152.0 kb	Distal (>10kb) Multiome	947
chr6:31,814,125–31,815,936	144.4 kb	Distal (>10kb) Multiome	822
chr6:31,818,020–31,818,663	140.6 kb	Distal (>10kb) Multiome	280
chr6:31,821,306–31,822,544	137.0 kb	Distal (>10kb) Multiome	714
chr6:31,826,770–31,828,135	131.5 kb	Distal (>10kb) Multiome	1000
chr6:31,834,277–31,835,371	124.2 kb	Distal (>10kb) Multiome	1085
chr6:31,862,148–31,864,173	96.0 kb	Distal (>10kb) Multiome	1118
chr6:31,896,965–31,898,037	61.4 kb	Distal (>10kb) Multiome	654
chr6:31,901,114–31,902,643	56.7 kb	Distal (>10kb) Multiome	826
chr6:31,958,527–31,959,598	95 bp	At TSS Multiome	953
chr6:31,971,421–31,972,872	13.3 kb	Distal (>10kb) Multiome	1059
chr6:32,048,217–32,048,679	89.4 kb	Distal (>10kb) Multiome	611
chr6:32,087,265–32,088,160	128.8 kb	Distal (>10kb) Multiome	473
chr6:32,127,621–32,128,720	169.3 kb	Distal (>10kb) Multiome	683
chr6:32,129,973–32,130,800	171.4 kb	Distal (>10kb) Multiome	717
chr6:32,144,531–32,145,041	185.8 kb	Distal (>10kb) Multiome	44
chr6:32,148,431–32,149,344	189.9 kb	Distal (>10kb) Multiome	145
chr6:32,153,307–32,155,059	195.0 kb	Distal (>10kb) Multiome	908
chr6:32,167,399–32,168,187	209.1 kb	Distal (>10kb) Multiome	411
chr6:32,175,673–32,176,347	217.2 kb	Distal (>10kb) Multiome	654
chr6:32,177,078–32,178,952	219.0 kb	Distal (>10kb) Multiome	820
chr6:32,190,108–32,191,167	231.4 kb	Distal (>10kb) Multiome	661
chr6:32,195,084–32,196,878	236.8 kb	Distal (>10kb) Multiome	1063
chr6:32,255,200–32,255,686	296.4 kb	Distal (>10kb) Multiome	364

Genome Browser

Genomic view of the NELFE 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.