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mmu_circCcdc57_1511
Basic information of circular RNA
PanCircBase ID:
mmu_circCcdc57_1511
mm39_Chr. Position ID:
chr11|120764411|120792901|-
Gene name:
Ccdc57
Transcript:
ENSMUST00000056781.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
15,14,13,12,11,10,9,8,7
Exon/intron offsets:
0,5292,8229,11647,12264,21013,21671,24223,28289
Genomic length:
28490
Exon/intron sizes in nt:
21,41,71,10,11,53,21,40,00,00,00,00,000
Flanking exon/introns:
chr11:120757502-120764411|chr11:120792901-120794141
Splice length:
1511
Other database IDs:
CIRCpedia: MMU_CIRCpedia_220665, circAtlas: mmu-Ccdc57_0006
Human Ortholog IDs:
Mature spliced Sequence:
ACATGAAGAGCTTGACCGTCAAGCCAGGGAGAAAGACACAGTGCTGGCGGCAGTGAAGCGCGCCCATGCAGAGGAGCTGCAGACGCTGGACGCCAAGGTGCTGGAGCTTCAGTTCCTCTGTGAAACCCTGGAGGGACAACTGCGCAGGGCTGAGTGCACAAGAGCAGAGGACGCCAAGGAGAAGAACGCCCTTACTGACAAATTTCGTGAAGATGCGGCAGCTCTGAAAGCTGCCTGGGACGCCCAGATCACGCAGATGTCCAAGGAGACTGTCTCCAAAGACTTTCAGATTCACACGCTGCAGGAAGAAGAGATGAAGCTCAAGGCACAGGTGGCCAGATTCCAACAGGACATAGACAGGTACAAGCAGCAGCTGTCCCTGGCAGTGGAGAGGGGACAGAGCCTGGAGCGTGAACAGGTACAGCTAGGCCTTGACTGGCAGCGTCGCTGCGATGATATTGAACGAGACCAGATCCAGAAATCGGAGACTTTGATCGAAGGGCTGACCAAGGCCAGGGATCAGGTCGCTGCTAAACTCCAGGAGACAGAGAAGGCACTGCGTCAGCAGGAGACTCTGCTGAAGGCTGTGTCACTGGAGCGAGACCAAGCTATGGAAACCCTACGTACACATGGGCTCCTTCCTGGACAGGAGGCACAGGTACCTCCTCAGCAGCATGAAGGAGAAATAAGGGCAGATTCTCCATCTACTGAGATCCAGAGGCTACAGGAACAGAATGCAGGTCTGCGGAACGCTGTTTCACAGATGAGGAGAGAGATGGAGATGCTGAGCGGTCATCTCCCCCCTGCCCAGCCAGAAGAGTGTTCAAATGCAGACCCTGATCCCAAGGCTGGAGGAGACTCCACCCCTCCAGATTATGTTCTGACCCTTGAAGCAGAAATGCAAAATCTAAAGCATAAACTTAAGGCATTGGAGGAACAACTACAAAGCACAGAAGAGCCAGTGAAGACGTCCGTGGCCACTGCTGATCCACACCATGGTGTCCACAGCTCTGCAGCAGCAGCTGACGCAGCTCTGGCAGACCAGACATCCACTGCATTAGCACTCAGAAAACTTGGAGACAGAGTGCACCTCTTGAACTTGCTGGTGACACAGCTCAAAAGGAAGCTGCGGCAGAAGCCCCGGGAGCTGGTCCCTGTCCAACACGAGGTCCCCAGTGAGGTGGACCAGGTGCACCTGGAGGTTTTGGAGCTGCAGAAGCAGGTGGCTGAGTTAAGGAAGCATCTCAAGGTGACACCCCAGGGAGAGCCTTCATCCAGGGAGCAGTTACAGAGACAGGGTGTGGCAGACCGGTACCCCATGGGCATGGAAGACCAGACGGAGTCCCCTACTTTCCCCCAGGAAGGGGCACAGCCTCCACAGACCATATATGTGACCCATCTGCAAAGGAAATTAAAGGATGCAGCTAGGAAAATACTCAGCCTCCGCCTAGAGAGGGAACAGCTCCTAGAAATGGGAAATAGACTCCGAGCTGAGCAAGGCCACGCAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TACTCAGCCTCCGCCTAGAG
60.18
GCGTCTGCAGCTCCTCTG
60.51
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TACTCAGCCTCCGCCTAGAG
60.18
CAGCGTCTGCAGCTCCTC
60.51
166
PCR template sequence:
TTAAAGGATGCAGCTAGGAAAATACTCAGCCTCCGCCTAGAGAGGGAACAGCTCCTAGAAATGGGAAATAGACTCCGAGCTGAGCAAGGCCACGCAAAAGACATGAAGAGCTTGACCGTCAAGCCAGGGAGAAAGACACAGTGCTGGCGGCAGTGAAGCGCGCCCATGCAGAGGAGCTGCAGACGCTGGACGCCAAGGTG
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-370-3p(2), mmu-miR-324-3p(2), mmu-miR-18a-5p(1), mmu-miR-143-3p(1), mmu-miR-339-5p(1), mmu-miR-127-5p(1), mmu-miR-680(1), mmu-miR-29b-2-5p(1), mmu-miR-207(1), mmu-miR-532-5p(1), mmu-miR-484(1), mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
GGCCACGCAAAAGACATGAAGAGCTT
siRNA sets
AAGCTCTTCATGTCTTTTG, AGCTCTTCATGTCTTTTGC, CTCTTCATGTCTTTTGCGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCCDC57_1511_ORF_1
1.2733
0.325786927
0.999609142
1311
ORF sequence:
ATGTCCAAGGAGACTGTCTCCAAAGACTTTCAGATTCACACGCTGCAGGAAGAAGAGATGAAGCTCAAGGCACAGGTGGCCAGATTCCAACAGGACATAGACAGGTACAAGCAGCAGCTGTCCCTGGCAGTGGAGAGGGGACAGAGCCTGGAGCGTGAACAGGTACAGCTAGGCCTTGACTGGCAGCGTCGCTGCGATGATATTGAACGAGACCAGATCCAGAAATCGGAGACTTTGATCGAAGGGCTGACCAAGGCCAGGGATCAGGTCGCTGCTAAACTCCAGGAGACAGAGAAGGCACTGCGTCAGCAGGAGACTCTGCTGAAGGCTGTGTCACTGGAGCGAGACCAAGCTATGGAAACCCTACGTACACATGGGCTCCTTCCTGGACAGGAGGCACAGGTACCTCCTCAGCAGCATGAAGGAGAAATAAGGGCAGATTCTCCATCTACTGAGATCCAGAGGCTACAGGAACAGAATGCAGGTCTGCGGAACGCTGTTTCACAGATGAGGAGAGAGATGGAGATGCTGAGCGGTCATCTCCCCCCTGCCCAGCCAGAAGAGTGTTCAAATGCAGACCCTGATCCCAAGGCTGGAGGAGACTCCACCCCTCCAGATTATGTTCTGACCCTTGAAGCAGAAATGCAAAATCTAAAGCATAAACTTAAGGCATTGGAGGAACAACTACAAAGCACAGAAGAGCCAGTGAAGACGTCCGTGGCCACTGCTGATCCACACCATGGTGTCCACAGCTCTGCAGCAGCAGCTGACGCAGCTCTGGCAGACCAGACATCCACTGCATTAGCACTCAGAAAACTTGGAGACAGAGTGCACCTCTTGAACTTGCTGGTGACACAGCTCAAAAGGAAGCTGCGGCAGAAGCCCCGGGAGCTGGTCCCTGTCCAACACGAGGTCCCCAGTGAGGTGGACCAGGTGCACCTGGAGGTTTTGGAGCTGCAGAAGCAGGTGGCTGAGTTAAGGAAGCATCTCAAGGTGACACCCCAGGGAGAGCCTTCATCCAGGGAGCAGTTACAGAGACAGGGTGTGGCAGACCGGTACCCCATGGGCATGGAAGACCAGACGGAGTCCCCTACTTTCCCCCAGGAAGGGGCACAGCCTCCACAGACCATATATGTGACCCATCTGCAAAGGAAATTAAAGGATGCAGCTAGGAAAATACTCAGCCTCCGCCTAGAGAGGGAACAGCTCCTAGAAATGGGAAATAGACTCCGAGCTGAGCAAGGCCACGCAAAAGACATGAAGAGCTTGACCGTCAAGCCAGGGAGAAAGACACAGTGCTGGCGGCAGTGA
Peptide sequence:
MSKETVSKDFQIHTLQEEEMKLKAQVARFQQDIDRYKQQLSLAVERGQSLEREQVQLGLDWQRRCDDIERDQIQKSETLIEGLTKARDQVAAKLQETEKALRQQETLLKAVSLERDQAMETLRTHGLLPGQEAQVPPQQHEGEIRADSPSTEIQRLQEQNAGLRNAVSQMRREMEMLSGHLPPAQPEECSNADPDPKAGGDSTPPDYVLTLEAEMQNLKHKLKALEEQLQSTEEPVKTSVATADPHHGVHSSAAAADAALADQTSTALALRKLGDRVHLLNLLVTQLKRKLRQKPRELVPVQHEVPSEVDQVHLEVLELQKQVAELRKHLKVTPQGEPSSREQLQRQGVADRYPMGMEDQTESPTFPQEGAQPPQTIYVTHLQRKLKDAARKILSLRLEREQLLEMGNRLRAEQGHAKDMKSLTVKPGRKTQCWRQ
IRESfinder result
IRESfinder score
0.356522548
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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