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mmu_circCcdc18_1999
Basic information of circular RNA
PanCircBase ID:
mmu_circCcdc18_1999
mm39_Chr. Position ID:
chr5|108315874|108354604|+
Gene name:
Ccdc18
Transcript:
ENSMUST00000047677.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
14
Exon/intron indexes:
11,12,13,14,15,16,17,18,19,20,21,22,23,24
Exon/intron offsets:
0,3604,5742,6857,12389,12805,20923,23874,25692,27987,29748,33316,34056,38586
Genomic length:
38730
Exon/intron sizes in nt:
15,52,21,11,11,32,13,50,00,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr5:108311638-108315874|chr5:108354604-108359959
Splice length:
1999
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GATTAAGCTTGCAATAAGAGAGGCTGAAATTCAAAAGCTTCATGCAAATCTGACTGTGAACCAGCTCTCTCAAAATGTTGCTAATGATAGTCAAGAATGTGGTAAAGTAAACACGTTAGAAACAGAACCGGTAAAATTAGGAGGTAGTCAAGTCGAAAGTATAAAGGATGGAGATCAGCAGACTGTGAACAAGCAGTATGAAAGAGAGAAGCAGCGACTTGCTACCGGGATAGAAGAACTGCGTGCTAAGCTGACACAGATAGAAGCTGAGAACTCTGACTTGAAGGTTAACATGGCACACAGAACTAGTCAGTTTCAGCTAATTCAAGAGGAACTACTAGAGAAAGCTTCAAATGCTAGCAAACTAGAAAATGAAATGACAAAGAAGTGTTCTCAACTTTTAATTCTAGAGAAACAGCTAGAAGAAAAAATTATTGCATATTCTTCTATTGCTGCAAAAAATGCAGAACTTGAACAAGAACTTATGGAGAAAAATGAAAAAATAAGAAGCCTAGAATCAAATATCAACACAGAACATGAGAAAATTTGTTTTGCTTTTGAAAAAGCAAAGAAAATTCATCTTGAACAGCATAAGGAAATGGAAAAACAGATTGAGCAACTCGAAACTCAACTGGAGAAAAGAGACCAACAGTTTAAAGAACAAGAAAAGACTATGTCCATTTTGCAGCAAGATATACTGTGTAAACAGCATCACCTTGAATCACTAGATAGACTCTTGACAGAAAGTAAAGTGGAAATGGAAAAAGAAAATATGAAGAAAGATGAAGCTTTAAAAGCATTGCAGATTCATGTATCTGAAGAAACAATCAAGGTCAGACAACTGGATTCAGCGTTAGAAATCTGTAAGGAAGAGCTTGCTTTGCATTTGAATCAATTGGAAAGAAATAAGGAAAAATTTGAAAGACAGCTGAAGAAGAAATCTGAAGAGGTATATTGTTTGCAGAAAGAGCTAAAGATAAAGACTCATAATCTTGAAGAGACGAGTGAACAAAATGCCATCCTACAGCACACTCTTCAGCAGCAGCAGCAGATGTTACAGCAAGAGACCATGAGAAATGGAGAGCTAGAAGATACTCAGAGTAAACTTGAAAAACAGGTATCAAAGCAAGAACAAGAGCTTCAGAAACAAAGGGAAAGTTCAACAGAAAAGTTGAGAAAAATGGAAGAGAAATATGAAACAGCCATACGTGAAGTGGATTTGAAAAGGCAAAAAATTATCGAGCTAACTGGTACTGCCAGGCAAGCCAAACTTGAGATGGATCAGTACAAAGAGGAGCTGTCTAAAATGGAAAAAGAAATAATTCATTTGAAGCGAGATGGGGAAAATAAATCCATGCAGCTTTCTCAGTTAGATATGGTTTTAGATCAAACAAAAACAGAACTAGAAAAGACAACAAATTCAGTGAAGGAGTTAGAAAGGTTACAACACCACACAGAAACTGAATTAACAGAAACCATGCAGAAACGGGAAGCTCTCGAAAACGAACTACAGAATGCTCATGGAGAATTGAAAAGTACCTTAAGACAACTACAGGAATTGAGAGATGTATTACAAAAGGCTCAGTTATCATTAGAGGAAAAATACACTACAATAAAGGATCTCACTGCTGAACTGAGAGAATGTAAGATGGAGATTGAAGACAAAAAACAAGAACTTATTGAAATGGATCAGGCGCTTAAGGAGAGAAATTGGGAGCTAAAGCAAAGAGCAGCTCAGGTTACACATTTGGATATGACTATTCGTGAACACAGAGGAGAAATGGAGCAAAAAATAATCAAATTGGAGGGTACCCTGGAAAAATCAGAATTAGAACTTAAAGAATGCAACAAACAGGTAGAAAGCTTAAATGAAAAGTTGCAAAATGCCAAAGAACAGCTTCGAGAAAAGGAGTTTATAATGCTCCAAAATGAACAGGAGATATCACAACTGAAAAAGGAAATCGAAAGAACACAGCAAAGGATGAAAGAAATGGAAAGT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGCTCCAAAATGAACAGGA
55.21
GCAACATTTTGAGAGAGCTGGT
59.44
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AATGCTCCAAAATGAACAGGA
56.03
GCAACATTTTGAGAGAGCTGGT
59.44
163
PCR template sequence:
TCGAGAAAAGGAGTTTATAATGCTCCAAAATGAACAGGAGATATCACAACTGAAAAAGGAAATCGAAAGAACACAGCAAAGGATGAAAGAAATGGAAAGTGATTAAGCTTGCAATAAGAGAGGCTGAAATTCAAAAGCTTCATGCAAATCTGACTGTGAACCAGCTCTCTCAAAATGTTGCTAATGATAGTCAAGAATGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
17
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-375-3p(1), mmu-miR-103-3p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-335-5p(1), mmu-miR-320-3p(1), mmu-miR-136-5p(1), mmu-miR-34b-5p(1), mmu-miR-107-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-300-3p(1), mmu-miR-335-3p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAAATGGAAAGTGATTAAGCTTGCA
siRNA sets
TTAATCACTTTCCATTTCT, AAGCTTAATCACTTTCCAT, CTTAATCACTTTCCATTTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCCDC18_1999_ORF_1
1.1556
0.087225027
0.999927415
1713
ORF sequence:
ATGGCACACAGAACTAGTCAGTTTCAGCTAATTCAAGAGGAACTACTAGAGAAAGCTTCAAATGCTAGCAAACTAGAAAATGAAATGACAAAGAAGTGTTCTCAACTTTTAATTCTAGAGAAACAGCTAGAAGAAAAAATTATTGCATATTCTTCTATTGCTGCAAAAAATGCAGAACTTGAACAAGAACTTATGGAGAAAAATGAAAAAATAAGAAGCCTAGAATCAAATATCAACACAGAACATGAGAAAATTTGTTTTGCTTTTGAAAAAGCAAAGAAAATTCATCTTGAACAGCATAAGGAAATGGAAAAACAGATTGAGCAACTCGAAACTCAACTGGAGAAAAGAGACCAACAGTTTAAAGAACAAGAAAAGACTATGTCCATTTTGCAGCAAGATATACTGTGTAAACAGCATCACCTTGAATCACTAGATAGACTCTTGACAGAAAGTAAAGTGGAAATGGAAAAAGAAAATATGAAGAAAGATGAAGCTTTAAAAGCATTGCAGATTCATGTATCTGAAGAAACAATCAAGGTCAGACAACTGGATTCAGCGTTAGAAATCTGTAAGGAAGAGCTTGCTTTGCATTTGAATCAATTGGAAAGAAATAAGGAAAAATTTGAAAGACAGCTGAAGAAGAAATCTGAAGAGGTATATTGTTTGCAGAAAGAGCTAAAGATAAAGACTCATAATCTTGAAGAGACGAGTGAACAAAATGCCATCCTACAGCACACTCTTCAGCAGCAGCAGCAGATGTTACAGCAAGAGACCATGAGAAATGGAGAGCTAGAAGATACTCAGAGTAAACTTGAAAAACAGGTATCAAAGCAAGAACAAGAGCTTCAGAAACAAAGGGAAAGTTCAACAGAAAAGTTGAGAAAAATGGAAGAGAAATATGAAACAGCCATACGTGAAGTGGATTTGAAAAGGCAAAAAATTATCGAGCTAACTGGTACTGCCAGGCAAGCCAAACTTGAGATGGATCAGTACAAAGAGGAGCTGTCTAAAATGGAAAAAGAAATAATTCATTTGAAGCGAGATGGGGAAAATAAATCCATGCAGCTTTCTCAGTTAGATATGGTTTTAGATCAAACAAAAACAGAACTAGAAAAGACAACAAATTCAGTGAAGGAGTTAGAAAGGTTACAACACCACACAGAAACTGAATTAACAGAAACCATGCAGAAACGGGAAGCTCTCGAAAACGAACTACAGAATGCTCATGGAGAATTGAAAAGTACCTTAAGACAACTACAGGAATTGAGAGATGTATTACAAAAGGCTCAGTTATCATTAGAGGAAAAATACACTACAATAAAGGATCTCACTGCTGAACTGAGAGAATGTAAGATGGAGATTGAAGACAAAAAACAAGAACTTATTGAAATGGATCAGGCGCTTAAGGAGAGAAATTGGGAGCTAAAGCAAAGAGCAGCTCAGGTTACACATTTGGATATGACTATTCGTGAACACAGAGGAGAAATGGAGCAAAAAATAATCAAATTGGAGGGTACCCTGGAAAAATCAGAATTAGAACTTAAAGAATGCAACAAACAGGTAGAAAGCTTAAATGAAAAGTTGCAAAATGCCAAAGAACAGCTTCGAGAAAAGGAGTTTATAATGCTCCAAAATGAACAGGAGATATCACAACTGAAAAAGGAAATCGAAAGAACACAGCAAAGGATGAAAGAAATGGAAAGTGATTAA
Peptide sequence:
MAHRTSQFQLIQEELLEKASNASKLENEMTKKCSQLLILEKQLEEKIIAYSSIAAKNAELEQELMEKNEKIRSLESNINTEHEKICFAFEKAKKIHLEQHKEMEKQIEQLETQLEKRDQQFKEQEKTMSILQQDILCKQHHLESLDRLLTESKVEMEKENMKKDEALKALQIHVSEETIKVRQLDSALEICKEELALHLNQLERNKEKFERQLKKKSEEVYCLQKELKIKTHNLEETSEQNAILQHTLQQQQQMLQQETMRNGELEDTQSKLEKQVSKQEQELQKQRESSTEKLRKMEEKYETAIREVDLKRQKIIELTGTARQAKLEMDQYKEELSKMEKEIIHLKRDGENKSMQLSQLDMVLDQTKTELEKTTNSVKELERLQHHTETELTETMQKREALENELQNAHGELKSTLRQLQELRDVLQKAQLSLEEKYTTIKDLTAELRECKMEIEDKKQELIEMDQALKERNWELKQRAAQVTHLDMTIREHRGEMEQKIIKLEGTLEKSELELKECNKQVESLNEKLQNAKEQLREKEFIMLQNEQEISQLKKEIERTQQRMKEMESD
IRESfinder result
IRESfinder score
0.580772512
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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