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mmu_circC2cd5_456
Basic information of circular RNA
PanCircBase ID:
mmu_circC2cd5_456
mm39_Chr. Position ID:
chr6|142963608|142975937|-
Gene name:
C2cd5
Transcript:
ENSMUST00000087485.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
23,22,21,20
Exon/intron offsets:
0,11277,11690,12239
Genomic length:
12329
Exon/intron sizes in nt:
191,87,88,90
Flanking exon/introns:
chr6:142959074-142963608|chr6:142975937-142976503
Splice length:
456
Other database IDs:
CIRCpedia: MMU_CIRCpedia_39561, circAtlas: mmu-C2cd5_0033
Human Ortholog IDs:
Mature spliced Sequence:
AGCCTGTATTTCAAACTTCGGTCCATGACCCCCTGCTGCCTCTGCCATGTGAACTTTACAGTGTCTCTGCCTGAAGATGAGTTAATCCAGGTCACAGTCACAGCAGTTGCAATAACTTTTGATAAAAACCAGGCCTTACAGACCACAAAACCCCACGTTGAAAAGTCACTACAAAGAGCCTCCACAGATAACGAAGAACTGCTGCAGTTCCCACTGGAGCTCTGCTCAGACTCACTGCCTCCTCATCCTTTCCCAGCAGCTAAAGCTGTGACTGTTGAAAAAGCAAGTGCCATGGGTGATGGAAATTTCCGGAATCGCTCTGCTCCACCTTGTGCAAGTCCCACAGTTGGGGTTGTTAAGATGACGCCGCTTTCTTTCATCCCTGGAGCAAAGATAACCAAGTACCTCGGCATCATTAACATGTTTTTCATTCGGGAAACCACTTCTCTCCGCGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GACGCCGCTTTCTTTCATCC
59.9
AAGTTCACATGGCAGAGGCA
59.89
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GACGCCGCTTTCTTTCATCC
59.9
AGTTCACATGGCAGAGGCAG
60.32
149
PCR template sequence:
TAAGATGACGCCGCTTTCTTTCATCCCTGGAGCAAAGATAACCAAGTACCTCGGCATCATTAACATGTTTTTCATTCGGGAAACCACTTCTCTCCGCGAGAGCCTGTATTTCAAACTTCGGTCCATGACCCCCTGCTGCCTCTGCCATGTGAACTTTACAGTGTCTCTGCCTGAAGATGAGTTAATCCAGGTCACAGTCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-140-5p(1), mmu-miR-134-5p(1), mmu-let-7b-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-let-7c-5p(1), mmu-miR-132-3p(1), mmu-miR-185-5p(1), mmu-miR-183-5p(1), mmu-miR-34b-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTCTCTCCGCGAGAGCCTGTATTTCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCC2CD5_456_ORF_1
0.9742
0.148332896
0.97239591
888
ORF sequence:
ATGACCCCCTGCTGCCTCTGCCATGTGAACTTTACAGTGTCTCTGCCTGAAGATGAGTTAATCCAGGTCACAGTCACAGCAGTTGCAATAACTTTTGATAAAAACCAGGCCTTACAGACCACAAAACCCCACGTTGAAAAGTCACTACAAAGAGCCTCCACAGATAACGAAGAACTGCTGCAGTTCCCACTGGAGCTCTGCTCAGACTCACTGCCTCCTCATCCTTTCCCAGCAGCTAAAGCTGTGACTGTTGAAAAAGCAAGTGCCATGGGTGATGGAAATTTCCGGAATCGCTCTGCTCCACCTTGTGCAAGTCCCACAGTTGGGGTTGTTAAGATGACGCCGCTTTCTTTCATCCCTGGAGCAAAGATAACCAAGTACCTCGGCATCATTAACATGTTTTTCATTCGGGAAACCACTTCTCTCCGCGAGAGCCTGTATTTCAAACTTCGGTCCATGACCCCCTGCTGCCTCTGCCATGTGAACTTTACAGTGTCTCTGCCTGAAGATGAGTTAATCCAGGTCACAGTCACAGCAGTTGCAATAACTTTTGATAAAAACCAGGCCTTACAGACCACAAAACCCCACGTTGAAAAGTCACTACAAAGAGCCTCCACAGATAACGAAGAACTGCTGCAGTTCCCACTGGAGCTCTGCTCAGACTCACTGCCTCCTCATCCTTTCCCAGCAGCTAAAGCTGTGACTGTTGAAAAAGCAAGTGCCATGGGTGATGGAAATTTCCGGAATCGCTCTGCTCCACCTTGTGCAAGTCCCACAGTTGGGGTTGTTAAGATGACGCCGCTTTCTTTCATCCCTGGAGCAAAGATAACCAAGTACCTCGGCATCATTAACATGTTTTTCATTCGGGAAACCACTTCTCTCCGCGAG
Peptide sequence:
MTPCCLCHVNFTVSLPEDELIQVTVTAVAITFDKNQALQTTKPHVEKSLQRASTDNEELLQFPLELCSDSLPPHPFPAAKAVTVEKASAMGDGNFRNRSAPPCASPTVGVVKMTPLSFIPGAKITKYLGIINMFFIRETTSLRESLYFKLRSMTPCCLCHVNFTVSLPEDELIQVTVTAVAITFDKNQALQTTKPHVEKSLQRASTDNEELLQFPLELCSDSLPPHPFPAAKAVTVEKASAMGDGNFRNRSAPPCASPTVGVVKMTPLSFIPGAKITKYLGIINMFFIRETTSLRE
IRESfinder result
IRESfinder score
0.634111482
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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