Super Enhancer Details

General details

Super-Enhancer ID:	SE_00562
Genomic locus:	chr3:53255457-53305543
Size/Length:	50086 bp
Genome:	Mouse -
Cell/Tissue:	Adipose Nuclei
Factor(s) Used:	- (Used to define enhancers) - (Used to rank SEs)
Input/WCE:	GSM621401
Reference:	Hnisz D. et al., 2013 Cell - 24119843

Associated gene details

RefSeq ID:	NM_006254
Gene Symbol:	PRKCD
Chromosome:	chr3
TSS:	53195222 (Transcription start site)
TES:	53226733 (Transcription end site)
Strand:	+
Number of Exons:	19
External Links:

Software and parameters used

Stitching Distance:	12.5 kb
Read Mapping:	Bowtie (version 0.12.9) with parameters -k 2, -m 2, -n 2, -best.
Peak Calling:	MACS (version 1.4.1) with parameters -p 1e-9,-keep-dup = auto, -w -S -space = 50
TSS Exclusive Zone:	+/- 2 kb
Enhancer-gene Assignment:	Genes were assigned to SEs within a 50 kb window. In cases where experimentally verified enhancer-gene assignments were available, genes were assigned to enhancers based on those studies.

FASTA sequence

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Wiggle files

Download Wiggle (WIG) files, generated by original data source.

Constituents of Super-enhancer - SE_00562

Constituent ID	SE ID	Chrom	Start	End	Constituent Size	MACS score
C004129	SE_00562	chr3	53255457	53259501	4044	1318.6
C004130	SE_00562	chr3	53265339	53279305	13966	3100
C004131	SE_00562	chr3	53283316	53290526	7210	2051.18
C004132	SE_00562	chr3	53293601	53295193	1592	266.16
C004133	SE_00562	chr3	53295304	53296449	1145	134.36
C004134	SE_00562	chr3	53298563	53299769	1206	96.87
C004135	SE_00562	chr3	53303302	53305543	2241	1858.14