CRS M2544008

Location human (hg38)	Pscore	FDR
chrX:15594802-15595013 (reverse)	62.01	11.66 %

[Covariance model (INFERNAL 1.1.1)]

100 species tree

Sequence identity	Number species	G+C content	Alignment length	Log Odds SI stem / loop
67.22 %	76	44.33 %	302	0.00

Energy	Compensatory base pair changes	Mutual information	Structure conservation SCI	Structure conservation SECI
-36.86 kcal/mol	24	0.13	0.14	0.72

17 species tree

Sequence identity	Number species	Alignment length	Structure conservation SCI	Re-alignment
68.84 %	13	235	0.00	0.90 %

+ Consensus structure

100 species tree

Structure as dot-bracket notation:

.............................((.(((.(((.......)))......)))...))....................................................................(((((...........))))).(((((((...................................((((..(((.....................................................)))))))...........)))))))....................

Structure as forna illustration (bases are named as consensus sequence and colored by relative entropy):
Color scheme relative entropy

17 species tree

Structure with human sequence and color coding of conservation: [PNG]

+ Alignment

100 species tree

[PNG] [STOCKHOLM 1.0]

17 species tree

[PNG] [STOCKHOLM 1.0]

[View 17 species tree alignment]

+ Overlap with RNAcentral

CRS M2544008 is not included in RNAcentral.

+ Annotation

Strand	Genomic context	Gene identifier	Distance (0 if overlap)
Forward	Intergenic	antisense\|ENSG00000225833\|GS1-594A7.3	7868
Reverse	CDS	CDS\|ENSG00000130234\|ACE2	0

Biotype	Rfam	PhyloCSF
CDS	NULL	NULL

Repeat Masker	Tandem Repeats
NULL	NULL

CpG island	Exon-Intron Junction
NULL	1

Common SNP (dbSNP 147)	Flagged SNP (dbSNP 147)
NULL	NULL

Disease association from GWAS
NULL

+ Evolutionary selection

Selection ratio (SR) (FDR(SR))	PhastCons score	Minor Allele Frequency (p-value)
0.3834 (0.0484)	0.4938	NA

+ Covarying base pairs

100 species tree

Consensus structure with covarying base pairs (estimated by R-scape with E-value<0.05) depicted in green (R2R drawing): [PDF]

Number base pairs (bps)	Expected covarying bps	Observed covarying bps
27	3.2 +/- 1.6	0

+ Chromatin signatures

DNase hypersensitive sites (95 cell types from ENCODE)	score	cell types
	NULL	NULL

Genome Segmentations from ENCODE	GM12878	H1hESC	HeLaS3	HepG2	HUVEC	K562
	CTCF,R	R	CTCF,R	CTCF,R	CTCF,R	CTCF,R

+ Protein binding sites

Transcription factor (ChIP)
NULL

RNA binding protein (CLIP)	P-value
NULL

+ Expression

Poly-A selected RNA (Human Body Map 2.0)		Total RNA (Human ENCODE phase 3)
Tissue	Expression level (CPM/RLE)	Tissue	Expression level (CPM/RLE)
Adipose	7.97324	Skin of body	0
Colon	6.22666	Stomach	0
Heart	15.1294	Heart	1.0592
Liver	0.785343	Liver	0.338545
Lung	0	Lung	0
Ovary	0	Uterus	0.177429
Prostate	0.749735	Urinary bladder	0.146586
Muscle	0	Skeletal muscle	0
Thyroid	3.29363	Thyroid gland	0
Brain	0.412773	Frontal cortex	0
Lymph	0.14725	Temporal lobe	0.0850524
Testes	0	Cerebellum	0
Blood	0	Spinal cord	0
Kidney	0	Diencephalon	0
Breast	0	Parietal lobe	0
Adrenalin	0	Occipital	0
		Metanephros	0
		Tongue	0
		Camera type eye	0.0793836

Targeted CRS expression in human fetal brain (CaptureSeq)
Read island identifier	Hybridization temperature	Strand	P-value	Max. Read Count
NULL	NULL	NULL	NULL	NULL

+ Transcript boundaries and stability

Closest upstream 5' site (CAGE signal)
Distance	Strand	Maximal expression	Aggregated sum of expression	Cell type-specific score
5925	-	175.5710	652.0250	0.7371

Closest downstream poly-A site (3'-end sequencing)
Distance	Strand	Number of libraries
26468	+	3

Transcript stability (CAGE signal)
Distance	Strand	Expression in control cells	Expression after exosom depletion	Exosome sensitivity
58835	-	1.4375	3.0818	0.5336