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mmu_circCarmil1_1170
Basic information of circular RNA
PanCircBase ID:
mmu_circCarmil1_1170
mm39_Chr. Position ID:
chr13|24206478|24228353|-
Gene name:
Carmil1
Transcript:
ENSMUST00000125901.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
23,22,21,20,19,18
Exon/intron offsets:
0,1827,3358,13689,19177,21678
Genomic length:
21875
Exon/intron sizes in nt:
141,213,82,424,113,197
Flanking exon/introns:
chr13:24204054-24206478|chr13:24228353-24228998
Splice length:
1170
Other database IDs:
CIRCpedia: MMU_CIRCpedia_14017, circAtlas: mmu-Lrrc16a_0034
Human Ortholog IDs:
Mature spliced Sequence:
AAATGGAGTTTGATCTTGATAAAGCCCTGGAAGAGGTGCCGATTCACATCGAAGACCCACCTTTCCCATCAGTCCGGCAAGAGAAGCGAAGCTCGGGGTTAATCTCTGAGCTGCCCTCGGAGGAAGGCAGGAGACTGGAACACTTCACCAAGTTAAGGCCCAAGCGGAACAAGAAGCAGCAACCTACGCAAGCAGCGGTCTGTACCATCAGCATCTTGCCCCAGGATGGAGAACAGAATGGCCTCATGGGCAGAGTGGATGAAGGGGTAGATGAGTTTTTCACCAAGAAGGTGACTAAAATGGATTGCAAGAGGTCATCCTCGCGCTCCTCAGATGCCCACGAACTCGGGGAAGGAGATGAGAAGAAAAAACGGGACTCTCGGAGGAGTGGCTTCCTCAACCTGATTAAATCCAGGTCCAGATCTGAGCGGCCACCCACAGTCCTGATGACGGAAGAGCTCTCCTCCCCGAAAGGGGCAATGCGGAGCCCACCAGTGGATACCACCAGGAAGGAGATAAAGGCAGCGGAGCACAATGGTGCTCCAGACCGCACAGAAGAGATTAAGACACCGGAACCCCTGGAGGAGGGTCCAGCAGAGGAAGCTGGCAGGGCTGAGCGCAGTGACAGCAGGGGCAGCCCGCAGGGTGGCCGGCGCTATGTGCAGGTGATGGGCAGCGGCCTGCTGGCCGAGATGAAGGCCAAGCAGGAGCGGAGGGCAGCATGTGCACAGAAGAAGCTCGGCAATGATGTCATCTCCCAGGATCCTTCCAGCCCAGTCTCGTGCAACACAGAGCGTTTAGAAGGAGGGGCGACAGTGCCTAAACTGCAACCAGGTCTTCCAGAGGCCCGCTTTGGTTCGGGAACACCAGAAAAGAATGCCAAAGCTGAACCCAGAGTGGATGGAGGCTGCAGGTCCCGGAGCTCCTCCAGCATGCCCACCAGCCCAAAGCCCCTCCTTCAGTCCCCTAAGCCCAGCCCTTCAGCCCGGCCTTCTATCCCTCAGAAGCCAAGAACTGCCTCCCGACCTGAAGACACCCCAGACTCTCCATCTGGTCCTAGTTCCCCTAAAGTTGCCCTCCTTCCACCCATCCTCAAAAAAGTCTCCTCGGACAAGGAGCGTGACGGCCAGAACAGCTCACAGTCCAGTCCTAGGAGCTTCTCCCAGGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTCCTTCCACCCATCCTCA
60.62
GGACTGATGGGAAAGGTGGG
60.03
170
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTCCTTCCACCCATCCTCA
60.62
GTGAATCGGCACCTCTTCCA
60.04
142
PCR template sequence:
GTTGCCCTCCTTCCACCCATCCTCAAAAAAGTCTCCTCGGACAAGGAGCGTGACGGCCAGAACAGCTCACAGTCCAGTCCTAGGAGCTTCTCCCAGGAAGAAATGGAGTTTGATCTTGATAAAGCCCTGGAAGAGGTGCCGATTCACATCGAAGACCCACCTTTCCCATCAGTCCGGCAAGAGAAGCGAAGCTCGGGGTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-205-5p(2), mmu-miR-7b-5p(1), mmu-miR-31-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-7a-5p(1), mmu-miR-143-3p(1), mmu-miR-383-5p(1), mmu-miR-27a-5p(1), mmu-miR-680(1), mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
TTCTCCCAGGAAGAAATGGAGTTTGA
siRNA sets
CAAACTCCATTTCTTCCTG, AAACTCCATTTCTTCCTGG, TCAAACTCCATTTCTTCCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCARMIL1_1170_ORF_1
0.758
0.367227924
0.999999484
2337
ORF sequence:
ATGGAGTTTGATCTTGATAAAGCCCTGGAAGAGGTGCCGATTCACATCGAAGACCCACCTTTCCCATCAGTCCGGCAAGAGAAGCGAAGCTCGGGGTTAATCTCTGAGCTGCCCTCGGAGGAAGGCAGGAGACTGGAACACTTCACCAAGTTAAGGCCCAAGCGGAACAAGAAGCAGCAACCTACGCAAGCAGCGGTCTGTACCATCAGCATCTTGCCCCAGGATGGAGAACAGAATGGCCTCATGGGCAGAGTGGATGAAGGGGTAGATGAGTTTTTCACCAAGAAGGTGACTAAAATGGATTGCAAGAGGTCATCCTCGCGCTCCTCAGATGCCCACGAACTCGGGGAAGGAGATGAGAAGAAAAAACGGGACTCTCGGAGGAGTGGCTTCCTCAACCTGATTAAATCCAGGTCCAGATCTGAGCGGCCACCCACAGTCCTGATGACGGAAGAGCTCTCCTCCCCGAAAGGGGCAATGCGGAGCCCACCAGTGGATACCACCAGGAAGGAGATAAAGGCAGCGGAGCACAATGGTGCTCCAGACCGCACAGAAGAGATTAAGACACCGGAACCCCTGGAGGAGGGTCCAGCAGAGGAAGCTGGCAGGGCTGAGCGCAGTGACAGCAGGGGCAGCCCGCAGGGTGGCCGGCGCTATGTGCAGGTGATGGGCAGCGGCCTGCTGGCCGAGATGAAGGCCAAGCAGGAGCGGAGGGCAGCATGTGCACAGAAGAAGCTCGGCAATGATGTCATCTCCCAGGATCCTTCCAGCCCAGTCTCGTGCAACACAGAGCGTTTAGAAGGAGGGGCGACAGTGCCTAAACTGCAACCAGGTCTTCCAGAGGCCCGCTTTGGTTCGGGAACACCAGAAAAGAATGCCAAAGCTGAACCCAGAGTGGATGGAGGCTGCAGGTCCCGGAGCTCCTCCAGCATGCCCACCAGCCCAAAGCCCCTCCTTCAGTCCCCTAAGCCCAGCCCTTCAGCCCGGCCTTCTATCCCTCAGAAGCCAAGAACTGCCTCCCGACCTGAAGACACCCCAGACTCTCCATCTGGTCCTAGTTCCCCTAAAGTTGCCCTCCTTCCACCCATCCTCAAAAAAGTCTCCTCGGACAAGGAGCGTGACGGCCAGAACAGCTCACAGTCCAGTCCTAGGAGCTTCTCCCAGGAAGAAATGGAGTTTGATCTTGATAAAGCCCTGGAAGAGGTGCCGATTCACATCGAAGACCCACCTTTCCCATCAGTCCGGCAAGAGAAGCGAAGCTCGGGGTTAATCTCTGAGCTGCCCTCGGAGGAAGGCAGGAGACTGGAACACTTCACCAAGTTAAGGCCCAAGCGGAACAAGAAGCAGCAACCTACGCAAGCAGCGGTCTGTACCATCAGCATCTTGCCCCAGGATGGAGAACAGAATGGCCTCATGGGCAGAGTGGATGAAGGGGTAGATGAGTTTTTCACCAAGAAGGTGACTAAAATGGATTGCAAGAGGTCATCCTCGCGCTCCTCAGATGCCCACGAACTCGGGGAAGGAGATGAGAAGAAAAAACGGGACTCTCGGAGGAGTGGCTTCCTCAACCTGATTAAATCCAGGTCCAGATCTGAGCGGCCACCCACAGTCCTGATGACGGAAGAGCTCTCCTCCCCGAAAGGGGCAATGCGGAGCCCACCAGTGGATACCACCAGGAAGGAGATAAAGGCAGCGGAGCACAATGGTGCTCCAGACCGCACAGAAGAGATTAAGACACCGGAACCCCTGGAGGAGGGTCCAGCAGAGGAAGCTGGCAGGGCTGAGCGCAGTGACAGCAGGGGCAGCCCGCAGGGTGGCCGGCGCTATGTGCAGGTGATGGGCAGCGGCCTGCTGGCCGAGATGAAGGCCAAGCAGGAGCGGAGGGCAGCATGTGCACAGAAGAAGCTCGGCAATGATGTCATCTCCCAGGATCCTTCCAGCCCAGTCTCGTGCAACACAGAGCGTTTAGAAGGAGGGGCGACAGTGCCTAAACTGCAACCAGGTCTTCCAGAGGCCCGCTTTGGTTCGGGAACACCAGAAAAGAATGCCAAAGCTGAACCCAGAGTGGATGGAGGCTGCAGGTCCCGGAGCTCCTCCAGCATGCCCACCAGCCCAAAGCCCCTCCTTCAGTCCCCTAAGCCCAGCCCTTCAGCCCGGCCTTCTATCCCTCAGAAGCCAAGAACTGCCTCCCGACCTGAAGACACCCCAGACTCTCCATCTGGTCCTAGTTCCCCTAAAGTTGCCCTCCTTCCACCCATCCTCAAAAAAGTCTCCTCGGACAAGGAGCGTGACGGCCAGAACAGCTCACAGTCCAGTCCTAGGAGCTTCTCCCAGGAA
Peptide sequence:
MEFDLDKALEEVPIHIEDPPFPSVRQEKRSSGLISELPSEEGRRLEHFTKLRPKRNKKQQPTQAAVCTISILPQDGEQNGLMGRVDEGVDEFFTKKVTKMDCKRSSSRSSDAHELGEGDEKKKRDSRRSGFLNLIKSRSRSERPPTVLMTEELSSPKGAMRSPPVDTTRKEIKAAEHNGAPDRTEEIKTPEPLEEGPAEEAGRAERSDSRGSPQGGRRYVQVMGSGLLAEMKAKQERRAACAQKKLGNDVISQDPSSPVSCNTERLEGGATVPKLQPGLPEARFGSGTPEKNAKAEPRVDGGCRSRSSSSMPTSPKPLLQSPKPSPSARPSIPQKPRTASRPEDTPDSPSGPSSPKVALLPPILKKVSSDKERDGQNSSQSSPRSFSQEEMEFDLDKALEEVPIHIEDPPFPSVRQEKRSSGLISELPSEEGRRLEHFTKLRPKRNKKQQPTQAAVCTISILPQDGEQNGLMGRVDEGVDEFFTKKVTKMDCKRSSSRSSDAHELGEGDEKKKRDSRRSGFLNLIKSRSRSERPPTVLMTEELSSPKGAMRSPPVDTTRKEIKAAEHNGAPDRTEEIKTPEPLEEGPAEEAGRAERSDSRGSPQGGRRYVQVMGSGLLAEMKAKQERRAACAQKKLGNDVISQDPSSPVSCNTERLEGGATVPKLQPGLPEARFGSGTPEKNAKAEPRVDGGCRSRSSSSMPTSPKPLLQSPKPSPSARPSIPQKPRTASRPEDTPDSPSGPSSPKVALLPPILKKVSSDKERDGQNSSQSSPRSFSQE
IRESfinder result
IRESfinder score
0.306344132
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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