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mmu_circSycp2_486
Basic information of circular RNA
PanCircBase ID:
mmu_circSycp2_486
mm39_Chr. Position ID:
chr2|177999887|178005264|-
Gene name:
Sycp2
Transcript:
ENSMUST00000081134.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
32,31,30,29,28
Exon/intron offsets:
0,614,2211,4845,5321
Genomic length:
5377
Exon/intron sizes in nt:
177,38,163,52,56
Flanking exon/introns:
chr2:177998431-177999887|chr2:178005264-178006490
Splice length:
486
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATCCAAGAATTTCAAGCTACAACTAGAGAAGCCAGTATGGATAATTCATTAAAATTGGTAAAGAATCATGATGAACATGACCCTTTTCTCAAAACAAAAGATAAAAGAATGTTAAGTTATGAGAAGAAAACTCTCTTAAGTGACACTGAAACCGAATGTGGATGTGATGACAGCAAGACTGACATTAGCTGGCTAAAAGAACCAAAAACAAAAAGACTAATGGATTATAGTAGAAATAAAAACACAACAAAATATAAAAGTAGAAAATCAAGATCATCCATGGAAAAAGGACAACCAAGACCCACAATGGTACTCAATAAAAACAGTATGAAAAATGATTATGAAGTAGTTGTAGATGGGAGAACCAGACTTCCACGAAGAGCAACAAAAACAAAAAAAAATTATAAAGATCTTTCAACTTCAGAATCAGAATCAGAGAGTGAAAAAGAATGTTCATATTTGTTTAAAGATAAACTGCCAACAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTTCAGAATCAGAATCAGAGAGTGA
59.56
TGAGAAAAGGGTCATGTTCATCA
58.02
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCAGAATCAGAATCAGAGAGTGA
56.49
TGAGAAAAGGGTCATGTTCATCA
58.02
157
PCR template sequence:
AAAAACAAAAAAAAATTATAAAGATCTTTCAACTTCAGAATCAGAATCAGAGAGTGAAAAAGAATGTTCATATTTGTTTAAAGATAAACTGCCAACAAAGATCCAAGAATTTCAAGCTACAACTAGAGAAGCCAGTATGGATAATTCATTAAAATTGGTAAAGAATCATGATGAACATGACCCTTTTCTCAAAACAAAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-431-5p(1), mmu-miR-325-3p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTGCCAACAAAGATCCAAGAATTTC
siRNA sets
AATTCTTGGATCTTTGTTG, ATTCTTGGATCTTTGTTGG, TCTTGGATCTTTGTTGGCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSYCP2_486_ORF_1
0.9049
-0.130147546
0.933350394
936
ORF sequence:
ATGGATAATTCATTAAAATTGGTAAAGAATCATGATGAACATGACCCTTTTCTCAAAACAAAAGATAAAAGAATGTTAAGTTATGAGAAGAAAACTCTCTTAAGTGACACTGAAACCGAATGTGGATGTGATGACAGCAAGACTGACATTAGCTGGCTAAAAGAACCAAAAACAAAAAGACTAATGGATTATAGTAGAAATAAAAACACAACAAAATATAAAAGTAGAAAATCAAGATCATCCATGGAAAAAGGACAACCAAGACCCACAATGGTACTCAATAAAAACAGTATGAAAAATGATTATGAAGTAGTTGTAGATGGGAGAACCAGACTTCCACGAAGAGCAACAAAAACAAAAAAAAATTATAAAGATCTTTCAACTTCAGAATCAGAATCAGAGAGTGAAAAAGAATGTTCATATTTGTTTAAAGATAAACTGCCAACAAAGATCCAAGAATTTCAAGCTACAACTAGAGAAGCCAGTATGGATAATTCATTAAAATTGGTAAAGAATCATGATGAACATGACCCTTTTCTCAAAACAAAAGATAAAAGAATGTTAAGTTATGAGAAGAAAACTCTCTTAAGTGACACTGAAACCGAATGTGGATGTGATGACAGCAAGACTGACATTAGCTGGCTAAAAGAACCAAAAACAAAAAGACTAATGGATTATAGTAGAAATAAAAACACAACAAAATATAAAAGTAGAAAATCAAGATCATCCATGGAAAAAGGACAACCAAGACCCACAATGGTACTCAATAAAAACAGTATGAAAAATGATTATGAAGTAGTTGTAGATGGGAGAACCAGACTTCCACGAAGAGCAACAAAAACAAAAAAAAATTATAAAGATCTTTCAACTTCAGAATCAGAATCAGAGAGTGAAAAAGAATGTTCATATTTGTTTAAAGATAAACTGCCAACAAAG
Peptide sequence:
MDNSLKLVKNHDEHDPFLKTKDKRMLSYEKKTLLSDTETECGCDDSKTDISWLKEPKTKRLMDYSRNKNTTKYKSRKSRSSMEKGQPRPTMVLNKNSMKNDYEVVVDGRTRLPRRATKTKKNYKDLSTSESESESEKECSYLFKDKLPTKIQEFQATTREASMDNSLKLVKNHDEHDPFLKTKDKRMLSYEKKTLLSDTETECGCDDSKTDISWLKEPKTKRLMDYSRNKNTTKYKSRKSRSSMEKGQPRPTMVLNKNSMKNDYEVVVDGRTRLPRRATKTKKNYKDLSTSESESESEKECSYLFKDKLPTK
IRESfinder result
IRESfinder score
0.617501695
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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