THRA

thyroid hormone receptor alpha | AR7, EAR-7.1/EAR-7.2, ERBA, NR1A1, THRA3, THRalpha, THRalpha1, THRalpha2, TRalpha, TRalpha1, TRalpha2, c-ERBA-1, c-erbA, ERBA1, THRA1, THRA2

The protein encoded by this gene is a nuclear hormone receptor for triiodothyronine. It is one of the several receptors for thyroid hormone, and has been shown to mediate the biological activities of thyroid hormone. Knockout studies in mice suggest that the different receptors, while having certain extent of redundancy, may mediate different functions of thyroid hormone. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

Biological processes 49 terms

DNA binding (GO:0003677)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)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II transcription regulator complex (GO:0090575)TBP-class protein binding (GO:0017025)cell differentiation (GO:0030154)chromatin (GO:0000785)chromatin DNA binding (GO:0031490)cytoplasm (GO:0005737)cytosol (GO:0005829)general transcription initiation factor binding (GO:0140296)hormone-mediated signaling pathway (GO:0009755)mRNA transcription by RNA polymerase II (GO:0042789)mRNA transcription by RNA polymerase II (GO:0042789)negative regulation of DNA-templated transcription (GO:0045892)negative regulation of DNA-templated transcription initiation (GO:2000143)negative regulation of RNA polymerase II transcription preinitiation complex assembly (GO:0017055)negative regulation of transcription by RNA polymerase II (GO:0000122)nuclear receptor activity (GO:0004879)nuclear receptor activity (GO:0004879)nuclear receptor activity (GO:0004879)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of cold-induced thermogenesis (GO:0120162)positive regulation of cold-induced thermogenesis (GO:0120162)positive regulation of thyroid hormone receptor signaling pathway (GO:0002157)positive regulation of thyroid hormone receptor signaling pathway (GO:0002157)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)protein binding (GO:0005515)protein domain specific binding (GO:0019904)protein-containing complex binding (GO:0044877)regulation of DNA-templated transcription (GO:0006355)regulation of transcription by RNA polymerase II (GO:0006357)retinoic acid receptor signaling pathway (GO:0048384)sequence-specific DNA binding (GO:0043565)thyroid hormone binding (GO:0070324)thyroid hormone binding (GO:0070324)thyroid hormone receptor signaling pathway (GO:0002154)transcription by RNA polymerase II (GO:0006366)transcription cis-regulatory region binding (GO:0000976)transcription cis-regulatory region binding (GO:0000976)zinc ion binding (GO:0008270)

Expression (TPM)

TFs regulating THRA 0 TFs

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

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of THRA, 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
chr17:39,926,716–39,928,343	135.3 kb	Distal (>10kb) Multiome	942
chr17:39,952,356–39,953,923	109.8 kb	Distal (>10kb) Multiome	598
chr17:39,979,964–39,981,234	82.3 kb	Distal (>10kb) Multiome	1148
chr17:40,054,311–40,054,810	8.4 kb	Proximal (<10kb) Multiome	694
chr17:40,062,700–40,063,624	42 bp	At TSS Multiome	609
chr17:40,075,390–40,075,997	12.7 kb	Distal (>10kb) Multiome	556
chr17:40,098,950–40,099,858	36.3 kb	Distal (>10kb) Multiome	997
chr17:40,100,155–40,101,301	37.8 kb	Distal (>10kb) Multiome	954
chr17:40,111,702–40,112,164	48.9 kb	Distal (>10kb) Multiome	678
chr17:40,113,185–40,113,691	50.5 kb	Distal (>10kb) Multiome	864
chr17:40,121,452–40,123,602	59.0 kb	Distal (>10kb) Multiome	799
chr17:40,139,909–40,141,108	77.4 kb	Distal (>10kb) Multiome	1121
chr17:40,177,152–40,178,398	114.5 kb	Distal (>10kb) Multiome	329
chr17:40,191,326–40,192,022	128.8 kb	Distal (>10kb) Multiome	588
chr17:40,218,712–40,219,963	156.4 kb	Distal (>10kb) Multiome	901
chr17:40,287,308–40,288,608	224.8 kb	Distal (>10kb) Multiome	870
chr17:40,316,576–40,317,119	253.8 kb	Distal (>10kb) Multiome	557
chr17:40,317,794–40,318,727	255.2 kb	Distal (>10kb) Multiome	799
chr17:40,341,205–40,342,644	278.9 kb	Distal (>10kb) Multiome	835
chr17:40,344,939–40,346,042	282.5 kb	Distal (>10kb) Multiome	730
chr17:40,362,469–40,363,831	299.9 kb	Distal (>10kb) Multiome	846

Genome Browser

Genomic view of the THRA 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.