CRS M2544002

Location human (hg38)	Pscore	FDR
chrX:15570563-15570615 (reverse)	54.27	18.19 %

[Covariance model (INFERNAL 1.1.1)]

100 species tree

Sequence identity	Number species	G+C content	Alignment length	Log Odds SI stem / loop
60.85 %	50	50.42 %	97	0.55

Energy	Compensatory base pair changes	Mutual information	Structure conservation SCI	Structure conservation SECI
-10.02 kcal/mol	15	0.21	0.83	0.63

17 species tree

Sequence identity	Number species	Alignment length	Structure conservation SCI	Re-alignment
60.67 %	10	73	0.00	34.37 %

+ 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 M2544002 is not included in RNAcentral.

+ Annotation

Strand	Genomic context	Gene identifier	Distance (0 if overlap)
Forward	Intergenic	exon\|ENSG00000102010\|BMX	-14034
Reverse	MRNA_Intron	mrna_intron\|ENSG00000130234\|ACE2	0

Biotype	Rfam	PhyloCSF
intronic	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	0.0643	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
18	0.9 +/- 0.9	2

Significant covarying base pairs (E-value<0.05)

Left pos	Right pos	Score	E-value	Substitutions	Power
1	97	23.13	3.7576e-2	5	0.01
5	92	30.46	9.0909e-3	10	0.08

+ 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
	R	R	R	R	R	R

+ Protein binding sites

Transcription factor (ChIP)
GATA3, GATA2

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	0	Skin of body	0.106072
Colon	0	Stomach	0
Heart	0.483589	Heart	7.55823
Liver	0	Liver	0.51733
Lung	0	Lung	0.353362
Ovary	0	Uterus	1.43818
Prostate	0	Urinary bladder	0
Muscle	0	Skeletal muscle	0
Thyroid	0	Thyroid gland	0.223309
Brain	0	Frontal cortex	0
Lymph	0	Temporal lobe	0
Testes	0	Cerebellum	0
Blood	0	Spinal cord	0.0830789
Kidney	0	Diencephalon	0.349188
Breast	0	Parietal lobe	0.0704761
Adrenalin	0	Occipital	0.191624
		Metanephros	0
		Tongue	0
		Camera type eye	0.156201

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
1184	-	8.9929	9.4907	0.9777

Closest downstream poly-A site (3'-end sequencing)
Distance	Strand	Number of libraries
6532	-	2

Transcript stability (CAGE signal)
Distance	Strand	Expression in control cells	Expression after exosom depletion	Exosome sensitivity
83233	-	1.4375	3.0818	0.5336