CCNT1

cyclin T1 | CCNT, CYCT1, HIVE1

This gene encodes a member of the highly conserved cyclin C subfamily. The encoded protein tightly associates with cyclin-dependent kinase 9, and is a major subunit of positive transcription elongation factor b (p-TEFb). In humans, there are multiple forms of positive transcription elongation factor b, which may include one of several different cyclins along with cyclin-dependent kinase 9. The complex containing the encoded cyclin and cyclin-dependent kinase 9 acts as a cofactor of human immunodeficiency virus type 1 (HIV-1) Tat protein, and is both necessary and sufficient for full activation of viral transcription. This cyclin and its kinase partner are also involved in triggering transcript elongation through phosphorylation of the carboxy-terminal domain of the largest RNA polymerase II subunit. Overexpression of this gene is implicated in tumor growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2013]

Member of: DE-5

Biological processes 37 terms

7SK snRNA binding (GO:0097322)7SK snRNA binding (GO:0097322)DNA binding (GO:0003677)DNA-binding transcription factor binding (GO:0140297)P-TEFb complex (GO:0070691)RNA polymerase binding (GO:0070063)RNA polymerase binding (GO:0070063)chromatin binding (GO:0003682)cyclin-dependent protein serine/threonine kinase activator activity (GO:0061575)cyclin-dependent protein serine/threonine kinase activator activity (GO:0061575)cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)cyclin/CDK positive transcription elongation factor complex (GO:0008024)cyclin/CDK positive transcription elongation factor complex (GO:0008024)cyclin/CDK positive transcription elongation factor complex (GO:0008024)host-mediated activation of viral transcription (GO:0043923)host-mediated activation of viral transcription (GO:0043923)molecular condensate scaffold activity (GO:0140693)nucleolus (GO:0005730)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of DNA-templated transcription, elongation (GO:0032786)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription elongation by RNA polymerase II (GO:0032968)positive regulation of transcription elongation by RNA polymerase II (GO:0032968)protein binding (GO:0005515)protein kinase binding (GO:0019901)regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)regulation of transcription by RNA polymerase II (GO:0006357)snRNA binding (GO:0017069)transcription by RNA polymerase II (GO:0006366)transcription by RNA polymerase II (GO:0006366)transcription cis-regulatory region binding (GO:0000976)

Expression (TPM)

TFs regulating CCNT1 0 TFs

Transcription factors with Perturb-seq knockdown data for CCNT1. 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 = CCNT1 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 CCNT1

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of CCNT1, 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
chr12:48,681,532–48,682,844	34.4 kb	Distal (>10kb) Multiome	933
chr12:48,716,299–48,717,435	168 bp	At TSS Multiome	1077
chr12:48,788,600–48,789,901	72.6 kb	Distal (>10kb) Multiome	478
chr12:48,795,703–48,796,330	79.3 kb	Distal (>10kb) Multiome HiCAR	333
chr12:48,814,087–48,815,981	98.1 kb	Distal (>10kb) Multiome	815
chr12:48,817,927–48,819,273	101.8 kb	Distal (>10kb) Multiome	459
chr12:48,851,862–48,852,825	135.5 kb	Distal (>10kb) Multiome	900
chr12:48,864,974–48,866,292	149.2 kb	Distal (>10kb) Multiome	649
chr12:48,883,231–48,884,168	167.1 kb	Distal (>10kb) Multiome	433
chr12:48,890,671–48,891,380	174.2 kb	Distal (>10kb) Multiome	517
chr12:48,924,659–48,925,688	208.2 kb	Distal (>10kb) Multiome	413
chr12:48,956,252–48,957,974	239.8 kb	Distal (>10kb) Multiome	831
chr12:48,978,055–48,978,819	261.6 kb	Distal (>10kb) Multiome	360
chr12:48,980,647–48,981,153	264.2 kb	Distal (>10kb) Multiome	259
chr12:48,997,612–48,998,829	281.6 kb	Distal (>10kb) Multiome	620

Genome Browser

Genomic view of the CCNT1 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.