RNF40

ring finger protein 40 | BRE1B, KIAA0661, RBP95, STARING

The protein encoded by this gene contains a RING finger, a motif known to be involved in protein-protein and protein-DNA interactions. This protein was reported to interact with the tumor suppressor protein RB1. Studies of the rat counterpart suggested that this protein may function as an E3 ubiquitin-protein ligase, and facilitate the ubiquitination and degradation of syntaxin 1, which is an essential component of the neurotransmitter release machinery. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2011]

Biological processes 25 terms

HULC complex (GO:0033503)HULC complex (GO:0033503)HULC complex (GO:0033503)mRNA 3'-UTR binding (GO:0003730)mRNA 3'-UTR binding (GO:0003730)membrane (GO:0016020)metal ion binding (GO:0046872)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of transcription by RNA polymerase II (GO:0045944)protein binding (GO:0005515)protein homodimerization activity (GO:0042803)protein ubiquitination (GO:0016567)regulation of DNA-templated transcription (GO:0006355)regulation of mitotic cell cycle (GO:0007346)ubiquitin ligase complex (GO:0000151)ubiquitin protein ligase activity (GO:0061630)ubiquitin protein ligase activity (GO:0061630)ubiquitin protein ligase binding (GO:0031625)ubiquitin-dependent protein catabolic process (GO:0006511)ubiquitin-protein transferase activity (GO:0004842)ubiquitin-protein transferase activity (GO:0004842)

Expression (TPM)

TFs regulating RNF40 0 TFs

Transcription factors with Perturb-seq knockdown data for RNF40. 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 = RNF40 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 RNF40

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of RNF40, 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
chr16:30,526,068–30,527,896	234.9 kb	Distal (>10kb) Multiome	1004
chr16:30,534,370–30,535,460	227.4 kb	Distal (>10kb) Multiome	957
chr16:30,557,913–30,558,847	203.8 kb	Distal (>10kb) Multiome	1025
chr16:30,571,001–30,572,505	190.3 kb	Distal (>10kb) Multiome	950
chr16:30,585,243–30,586,223	176.5 kb	Distal (>10kb) Multiome	588
chr16:30,609,586–30,610,748	151.9 kb	Distal (>10kb) Multiome	1030
chr16:30,634,070–30,634,986	127.9 kb	Distal (>10kb) Multiome	907
chr16:30,650,029–30,651,831	111.6 kb	Distal (>10kb) Multiome	992
chr16:30,657,638–30,659,894	104.0 kb	Distal (>10kb) Multiome	1053
chr16:30,677,814–30,678,622	84.1 kb	Distal (>10kb) Multiome	177
chr16:30,697,755–30,699,614	63.2 kb	Distal (>10kb) Multiome	1153
chr16:30,747,864–30,748,943	14.0 kb	Distal (>10kb) Multiome	824
chr16:30,761,380–30,762,606	95 bp	At TSS Multiome	885
chr16:30,774,965–30,776,186	13.2 kb	Distal (>10kb) Multiome	1025
chr16:30,786,385–30,788,019	24.8 kb	Distal (>10kb) Multiome	885
chr16:30,805,468–30,806,187	43.4 kb	Distal (>10kb) Multiome	969
chr16:30,814,045–30,814,733	52.1 kb	Distal (>10kb) Multiome	995
chr16:30,841,062–30,841,882	79.2 kb	Distal (>10kb) Multiome	49
chr16:30,874,866–30,875,643	113.0 kb	Distal (>10kb) Multiome HiCAR	1108
chr16:30,893,485–30,894,587	131.9 kb	Distal (>10kb) Multiome HiCAR	950
chr16:30,895,854–30,897,426	134.7 kb	Distal (>10kb) Multiome HiCAR	822
chr16:30,901,969–30,902,794	140.0 kb	Distal (>10kb) Multiome HiCAR	579
chr16:30,921,611–30,925,097	161.1 kb	Distal (>10kb) Multiome HiCAR	1132
chr16:30,927,705–30,928,596	165.8 kb	Distal (>10kb) Multiome HiCAR	274
chr16:30,941,803–30,942,254	179.8 kb	Distal (>10kb) Multiome	507
chr16:30,947,471–30,950,635	187.9 kb	Distal (>10kb) Multiome	1066
chr16:30,953,370–30,954,135	191.5 kb	Distal (>10kb) Multiome	499
chr16:30,956,960–30,958,498	195.4 kb	Distal (>10kb) Multiome	1022
chr16:30,984,837–30,985,709	222.9 kb	Distal (>10kb) Multiome	787
chr16:30,996,877–30,998,001	235.1 kb	Distal (>10kb) Multiome	759
chr16:31,010,379–31,011,032	248.4 kb	Distal (>10kb) Multiome	117
chr16:31,032,789–31,034,448	271.2 kb	Distal (>10kb) Multiome	1047
chr16:31,041,996–31,042,665	280.0 kb	Distal (>10kb) Multiome	213

Genome Browser

Genomic view of the RNF40 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.