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mmu_circCcnl2_412
Basic information of circular RNA
PanCircBase ID:
mmu_circCcnl2_412
mm39_Chr. Position ID:
chr4|155902379|155905571|+
Gene name:
Ccnl2
Transcript:
ENSMUST00000030944.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,6,7,8
Exon/intron offsets:
0,2406,2861,3050
Genomic length:
3192
Exon/intron sizes in nt:
65,10,01,05,142
Flanking exon/introns:
chr4:155899820-155902379|chr4:155905571-155906268
Splice length:
412
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATAATCGTTATGTACCTTCAGGTGTTAGAATGTGAGCGTAATCAACACCTGGTCCAGACTGCATGGAACTACATGAATGACAGCCTTCGCACAGATGTCTTTGTCCGGTTCCAGCCTGAAAGCATTGCTTGTGCCTGTATCTACCTTGCTGCCCGGACACTGGAGATCCCTTTACCCAATCGTCCACATTGGTTTCTTTTGTTTGGAGCAACTGAAGAAGAAATTCAAGAAATTTGCTTTAAAATCTTGCAGCTTTATACACGGAAAAAGGTTGATTTGACGCATCTGGAGAGTGAAGTGGAGAAGAGAAAGCACGCCATTGAAGAAGCAAAGGCCCGAGCAAAGGGCCTGCTCCCAGGGACTGCGCCAGGCCTGGACAGTGCTGCGGGGTTCTCGCCTGCTCCCAAGCTGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGAAGAAGCAAAGGCCCGA
60.18
GTTCCATGCAGTCTGGACCA
59.96
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGAAGAAGCAAAGGCCCGA
60.18
TTCCATGCAGTCTGGACCAG
59.67
161
PCR template sequence:
CACGCCATTGAAGAAGCAAAGGCCCGAGCAAAGGGCCTGCTCCCAGGGACTGCGCCAGGCCTGGACAGTGCTGCGGGGTTCTCGCCTGCTCCCAAGCTGGATAATCGTTATGTACCTTCAGGTGTTAGAATGTGAGCGTAATCAACACCTGGTCCAGACTGCATGGAACTACATGAATGACAGCCTTCGCACAGATGTCT
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-199a-5p(1), mmu-miR-103-3p(1), mmu-miR-214-3p(1), mmu-miR-340-5p(1), mmu-miR-107-3p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
GCTCCCAAGCTGGATAATCGTTATGT
siRNA sets
TAACGATTATCCAGCTTGG,AACGATTATCCAGCTTGGG,ATAACGATTATCCAGCTTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCCNL2_412_ORF_1
1.0003
0.171317327
0.612781061
438
ORF sequence:
ATGTACCTTCAGGTGTTAGAATGTGAGCGTAATCAACACCTGGTCCAGACTGCATGGAACTACATGAATGACAGCCTTCGCACAGATGTCTTTGTCCGGTTCCAGCCTGAAAGCATTGCTTGTGCCTGTATCTACCTTGCTGCCCGGACACTGGAGATCCCTTTACCCAATCGTCCACATTGGTTTCTTTTGTTTGGAGCAACTGAAGAAGAAATTCAAGAAATTTGCTTTAAAATCTTGCAGCTTTATACACGGAAAAAGGTTGATTTGACGCATCTGGAGAGTGAAGTGGAGAAGAGAAAGCACGCCATTGAAGAAGCAAAGGCCCGAGCAAAGGGCCTGCTCCCAGGGACTGCGCCAGGCCTGGACAGTGCTGCGGGGTTCTCGCCTGCTCCCAAGCTGGATAATCGTTATGTACCTTCAGGTGTTAGAATGTGA
Peptide sequence:
MYLQVLECERNQHLVQTAWNYMNDSLRTDVFVRFQPESIACACIYLAARTLEIPLPNRPHWFLLFGATEEEIQEICFKILQLYTRKKVDLTHLESEVEKRKHAIEEAKARAKGLLPGTAPGLDSAAGFSPAPKLDNRYVPSGVRM
IRESfinder result
IRESfinder score
0.626596081
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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