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mmu_circShld2_438
Basic information of circular RNA
PanCircBase ID:
mmu_circShld2_438
mm39_Chr. Position ID:
chr14|33970840|33981689|-
Gene name:
Shld2
Transcript:
ENSMUST00000111917.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
7,6,5
Exon/intron offsets:
0,293,10741
Genomic length:
10849
Exon/intron sizes in nt:
13,51,95,108
Flanking exon/introns:
chr14:33967325-33970840|chr14:33981689-33989457
Splice length:
438
Other database IDs:
circAtlas: mmu-Fam35a_0004
Human Ortholog IDs:
Mature spliced Sequence:
ACGTTGTTCTTTATGAGGATCAGTGGATTGGTGAGACAGTACTCCAATCAACATTTACAAGTCAGTTACTAAATCTTGGAAGTTATTCATATGTCCAGCCTGAAAAATATTCCAATGTAATTGCCAATGTTATACTTCAGGACTTATTGACATATGTGTCTACAAAACATTCCTATCTCAAAGATCTGCCTCAGAGGCAGCCTCAGAAAATGAACACTGTAGAGTTTGTGGAGTTGGAGCAGTTGCAGCCTGATATATTAGTCCATGCAGTACTCAGAGTAGTGGATGTCACTGTATTGACAGAGGCATTATATAGTTATAGAGGACAGAAGCAAAGAAAAGTTGTGTTAACCGTGGAACAGGCTCAAGGTCAACACTATGTGCTTGTATTATGGGGTCCTGGAGCAGCCTGGTATACTCAGCTTCAAAGGAAAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGTTAACCGTGGAACAGGC
59.41
TGGAGTACTGTCTCACCAATCC
59.17
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTTAACCGTGGAACAGGCT
59.53
TTGGAGTACTGTCTCACCAATCC
59.74
140
PCR template sequence:
AAAGTTGTGTTAACCGTGGAACAGGCTCAAGGTCAACACTATGTGCTTGTATTATGGGGTCCTGGAGCAGCCTGGTATACTCAGCTTCAAAGGAAAAAAGACGTTGTTCTTTATGAGGATCAGTGGATTGGTGAGACAGTACTCCAATCAACATTTACAAGTCAGTTACTAAATCTTGGAAGTTATTCATATGTCCAGCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-139-5p(1), mmu-miR-181b-5p(1), mmu-miR-381-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CAAAGGAAAAAAGACGTTGTTCTTTA
siRNA sets
AGAACAACGTCTTTTTTCC,GAACAACGTCTTTTTTCCT,AACAACGTCTTTTTTCCTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSHLD2_438_ORF_1
1.0644
-0.087574244
0.762032318
666
ORF sequence:
ATGAACACTGTAGAGTTTGTGGAGTTGGAGCAGTTGCAGCCTGATATATTAGTCCATGCAGTACTCAGAGTAGTGGATGTCACTGTATTGACAGAGGCATTATATAGTTATAGAGGACAGAAGCAAAGAAAAGTTGTGTTAACCGTGGAACAGGCTCAAGGTCAACACTATGTGCTTGTATTATGGGGTCCTGGAGCAGCCTGGTATACTCAGCTTCAAAGGAAAAAAGACGTTGTTCTTTATGAGGATCAGTGGATTGGTGAGACAGTACTCCAATCAACATTTACAAGTCAGTTACTAAATCTTGGAAGTTATTCATATGTCCAGCCTGAAAAATATTCCAATGTAATTGCCAATGTTATACTTCAGGACTTATTGACATATGTGTCTACAAAACATTCCTATCTCAAAGATCTGCCTCAGAGGCAGCCTCAGAAAATGAACACTGTAGAGTTTGTGGAGTTGGAGCAGTTGCAGCCTGATATATTAGTCCATGCAGTACTCAGAGTAGTGGATGTCACTGTATTGACAGAGGCATTATATAGTTATAGAGGACAGAAGCAAAGAAAAGTTGTGTTAACCGTGGAACAGGCTCAAGGTCAACACTATGTGCTTGTATTATGGGGTCCTGGAGCAGCCTGGTATACTCAGCTTCAAAGGAAAAAA
Peptide sequence:
MNTVEFVELEQLQPDILVHAVLRVVDVTVLTEALYSYRGQKQRKVVLTVEQAQGQHYVLVLWGPGAAWYTQLQRKKDVVLYEDQWIGETVLQSTFTSQLLNLGSYSYVQPEKYSNVIANVILQDLLTYVSTKHSYLKDLPQRQPQKMNTVEFVELEQLQPDILVHAVLRVVDVTVLTEALYSYRGQKQRKVVLTVEQAQGQHYVLVLWGPGAAWYTQLQRKK
IRESfinder result
IRESfinder score
0.705195989
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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