CRS M2543994

Location human (hg38)	Pscore	FDR
chrX:15566304-15566360 (reverse)	61.86	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
61.43 %	79	43.43 %	85	0.27

Energy	Compensatory base pair changes	Mutual information	Structure conservation SCI	Structure conservation SECI
-10.03 kcal/mol	12	0.22	0.20	0.64

17 species tree

Sequence identity	Number species	Alignment length	Structure conservation SCI	Re-alignment
64.12 %	15	75	0.00	25.37 %

+ 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 M2543994 is not included in RNAcentral.

+ Annotation

Strand	Genomic context	Gene identifier	Distance (0 if overlap)
Forward	Intergenic	exon\|ENSG00000102010\|BMX	-9775
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)
NA	0.5883	NA

+ Covarying base pairs

100 species tree

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

Number base pairs (bps)	Expected covarying bps	Observed covarying bps
15	1.2 +/- 1.0	1

Significant covarying base pairs (E-value<0.05)

Left pos	Right pos	Score	E-value	Substitutions	Power
6	81	45.64	2.5982e-3	16	0.16

+ Chromatin signatures

DNase hypersensitive sites (95 cell types from ENCODE)	score	cell types
	237	16

Genome Segmentations from ENCODE	GM12878	H1hESC	HeLaS3	HepG2	HUVEC	K562
	CTCF	CTCF	CTCF	CTCF	NULL	CTCF

+ Protein binding sites

Transcription factor (ChIP)
CTCF, RAD21

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	6.12578	Skin of body	0
Colon	8.36863	Stomach	0
Heart	8.49735	Heart	1.89539
Liver	0.490839	Liver	0.0893923
Lung	0	Lung	0
Ovary	0	Uterus	0.945247
Prostate	0.293375	Urinary bladder	0
Muscle	3.61733	Skeletal muscle	0
Thyroid	2.18299	Thyroid gland	0
Brain	0	Frontal cortex	0
Lymph	0.662624	Temporal lobe	0
Testes	0	Cerebellum	0
Blood	0	Spinal cord	0
Kidney	0.923055	Diencephalon	0.272931
Breast	0	Parietal lobe	0
Adrenalin	0	Occipital	0.0478313
		Metanephros	0
		Tongue	0
		Camera type eye	0

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
5439	-	8.9929	9.4907	0.9777

Closest downstream poly-A site (3'-end sequencing)
Distance	Strand	Number of libraries
2273	-	2

Transcript stability (CAGE signal)
Distance	Strand	Expression in control cells	Expression after exosom depletion	Exosome sensitivity
87488	-	1.4375	3.0818	0.5336