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mmu_circCyp20a1_682
Basic information of circular RNA
PanCircBase ID:
mmu_circCyp20a1_682
mm39_Chr. Position ID:
chr1|60393672|60415346|+
Gene name:
Cyp20a1
Transcript:
ENSMUST00000060608.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
4,5,6,7,8,9
Exon/intron offsets:
0,8676,12135,16707,18076,21553
Genomic length:
21674
Exon/intron sizes in nt:
1,43,16,87,91,16,55,120
Flanking exon/introns:
chr1:60392234-60393672|chr1:60415346-60418532
Splice length:
682
Other database IDs:
circBase: hsa_circ_0118809
Human Ortholog IDs:
Mature spliced Sequence:
CGGACCCATTTGAAACCATGTTGAAGTCATTATTAGGGTATCAGTCTGGCGGAGGGAGTGCGGGTGAGGACCACGTGAGGAGGAAACTGTATGGAGATGCCGTGACAGCTTCTCTGCATAGTAACTTCCCTCTCCTGCTACAGCTTTCAGAAGAATTGTTAGATAAATGGCTGTCCTATCCAGAGACCCAGCACATACCTCTGAGCCAGCATATGCTCGGTTTTGCTTTGAAGTTTGTCACAAGGATGGTACTGGGTAGCACCTTTGAAGATGAACAGGAGGTCATCCGATTCCAAAAGATTCATGGCACAGTGTGGTCTGAGATTGGAAAAGGCTTTCTAGATGGGTCACTCGATAAAAACACCACTCGGAAAAAACAGTATCAAGAGGCTCTCATGCAATTGGAATCCACTTTAAAGAAAATCATAAAGGAACGAAAAGGAGGGAACTTCAGGCAACACACCTTCATCGACTCCTTAACACAGGGAAAACTTAATGAGCAACAGATCCTAGAGGACTGTGTGGTGTTCTCTCTGGCCAGCTGCATAATAACTGCAAGGTTGTGTACCTGGACGATCCATTTCCTTACGACGACTGGAGAAGTTCAGAAGAAGCTATGCAAGGAGATAGACCAAGTTTTAGGGGAGGGTCCTATCACTTCAGAGAAAATTGAGCAGCTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCAAGTTTTAGGGGAGGGTCC
59.99
CAGTTTCCTCCTCACGTGGT
59.61
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCAAGTTTTAGGGGAGGGTCC
59.99
ACAGTTTCCTCCTCACGTGG
59.61
141
PCR template sequence:
TCCTTACGACGACTGGAGAAGTTCAGAAGAAGCTATGCAAGGAGATAGACCAAGTTTTAGGGGAGGGTCCTATCACTTCAGAGAAAATTGAGCAGCTCAGCGGACCCATTTGAAACCATGTTGAAGTCATTATTAGGGTATCAGTCTGGCGGAGGGAGTGCGGGTGAGGACCACGTGAGGAGGAAACTGTATGGAGATGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-18a-5p(1), mmu-miR-216a-5p(1), mmu-miR-320-3p(1), mmu-miR-680(1), mmu-miR-29b-2-5p(1), mmu-miR-202-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTGAGCAGCTCAGCGGACCCATTTGA
siRNA sets
AATGGGTCCGCTGAGCTGC, AAATGGGTCCGCTGAGCTG, TCAAATGGGTCCGCTGAGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCYP20A1_682_ORF_1
0.8761
0.118474356
0.849577607
678
ORF sequence:
ATGTTGAAGTCATTATTAGGGTATCAGTCTGGCGGAGGGAGTGCGGGTGAGGACCACGTGAGGAGGAAACTGTATGGAGATGCCGTGACAGCTTCTCTGCATAGTAACTTCCCTCTCCTGCTACAGCTTTCAGAAGAATTGTTAGATAAATGGCTGTCCTATCCAGAGACCCAGCACATACCTCTGAGCCAGCATATGCTCGGTTTTGCTTTGAAGTTTGTCACAAGGATGGTACTGGGTAGCACCTTTGAAGATGAACAGGAGGTCATCCGATTCCAAAAGATTCATGGCACAGTGTGGTCTGAGATTGGAAAAGGCTTTCTAGATGGGTCACTCGATAAAAACACCACTCGGAAAAAACAGTATCAAGAGGCTCTCATGCAATTGGAATCCACTTTAAAGAAAATCATAAAGGAACGAAAAGGAGGGAACTTCAGGCAACACACCTTCATCGACTCCTTAACACAGGGAAAACTTAATGAGCAACAGATCCTAGAGGACTGTGTGGTGTTCTCTCTGGCCAGCTGCATAATAACTGCAAGGTTGTGTACCTGGACGATCCATTTCCTTACGACGACTGGAGAAGTTCAGAAGAAGCTATGCAAGGAGATAGACCAAGTTTTAGGGGAGGGTCCTATCACTTCAGAGAAAATTGAGCAGCTCAGCGGACCCATTTGA
Peptide sequence:
MLKSLLGYQSGGGSAGEDHVRRKLYGDAVTASLHSNFPLLLQLSEELLDKWLSYPETQHIPLSQHMLGFALKFVTRMVLGSTFEDEQEVIRFQKIHGTVWSEIGKGFLDGSLDKNTTRKKQYQEALMQLESTLKKIIKERKGGNFRQHTFIDSLTQGKLNEQQILEDCVVFSLASCIITARLCTWTIHFLTTTGEVQKKLCKEIDQVLGEGPITSEKIEQLSGPI
IRESfinder result
IRESfinder score
0.577037298
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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