TRIM39

tripartite motif containing 39 | RNF23

The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The function of this protein has not been identified. This gene lies within the major histocompatibility complex class I region on chromosome 6. Alternate splicing results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

Developmental clusters: GC7

Biological processes 27 terms

cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytosol (GO:0005829)cytosol (GO:0005829)cytosol (GO:0005829)identical protein binding (GO:0042802)innate immune response (GO:0045087)mitochondrion (GO:0005739)mitochondrion (GO:0005739)mitotic G2 DNA damage checkpoint signaling (GO:0007095)negative regulation of canonical NF-kappaB signal transduction (GO:0043124)negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)negative regulation of ubiquitin-dependent protein catabolic process (GO:2000059)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of apoptotic signaling pathway (GO:2001235)positive regulation of apoptotic signaling pathway (GO:2001235)protein binding (GO:0005515)protein stabilization (GO:0050821)protein stabilization (GO:0050821)protein ubiquitination (GO:0016567)regulation of cell cycle G1/S phase transition (GO:1902806)regulation of gene expression (GO:0010468)ubiquitin protein ligase activity (GO:0061630)ubiquitin protein ligase activity (GO:0061630)zinc ion binding (GO:0008270)

Expression (TPM)

TFs regulating TRIM39 0 TFs

Transcription factors with Perturb-seq knockdown data for TRIM39. 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 = TRIM39 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 TRIM39

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of TRIM39, 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
chr6:30,060,737–30,061,999	265.2 kb	Distal (>10kb) Multiome	973
chr6:30,066,588–30,067,716	259.3 kb	Distal (>10kb) Multiome	952
chr6:30,101,800–30,102,573	224.4 kb	Distal (>10kb) Multiome	644
chr6:30,103,094–30,103,626	223.1 kb	Distal (>10kb) Multiome	616
chr6:30,171,597–30,172,574	154.5 kb	Distal (>10kb) Multiome	185
chr6:30,207,044–30,207,811	119.1 kb	Distal (>10kb) Multiome	514
chr6:30,212,953–30,213,888	113.0 kb	Distal (>10kb) Multiome	826
chr6:30,213,977–30,214,728	111.9 kb	Distal (>10kb) Multiome	758
chr6:30,259,131–30,260,199	66.9 kb	Distal (>10kb) Multiome	475
chr6:30,325,606–30,327,611	499 bp	At TSS Multiome	1043
chr6:30,344,843–30,345,715	18.8 kb	Distal (>10kb) Multiome	892
chr6:30,357,696–30,358,238	31.4 kb	Distal (>10kb) Multiome	207
chr6:30,466,230–30,466,713	140.1 kb	Distal (>10kb) Multiome	369
chr6:30,489,117–30,490,512	163.8 kb	Distal (>10kb) Multiome	750
chr6:30,516,006–30,516,707	189.9 kb	Distal (>10kb) Multiome	739
chr6:30,555,407–30,557,765	230.2 kb	Distal (>10kb) Multiome	1161
chr6:30,570,822–30,571,949	244.9 kb	Distal (>10kb) Multiome	1000
chr6:30,614,393–30,615,939	288.7 kb	Distal (>10kb) Multiome	837
chr6:30,616,770–30,618,155	291.1 kb	Distal (>10kb) Multiome	1072
chr6:30,626,560–30,627,206	300.4 kb	Distal (>10kb) Multiome	802

Genome Browser

Genomic view of the TRIM39 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.