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mmu_circC2cd5_1175
Basic information of circular RNA
PanCircBase ID:
mmu_circC2cd5_1175
mm39_Chr. Position ID:
chr6|142974885|142987269|-
Gene name:
C2cd5
Transcript:
ENSMUST00000087485.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
22,21,20,19,18,17,16,15,14,13
Exon/intron offsets:
0,413,962,1618,2085,2402,5862,7075,9663,12192
Genomic length:
12384
Exon/intron sizes in nt:
87,88,90,99,62,64,141,165,187,192
Flanking exon/introns:
chr6:142963799-142974885|chr6:142987269-142992768
Splice length:
1175
Other database IDs:
circBase: mmu_circ_0013160, CIRCpedia: MMU_CIRCpedia_9282, circAtlas: mmu-C2cd5_0027
circBase: hsa_circ_0098147, circAtlas: hsa-C2CD5_0015, CIRCpedia: HSA_CIRCpedia_7957
Human Ortholog IDs:
Mature spliced Sequence:
GATTGAAGAGAATTTACCGGTGGGCTGCGGATTCTGCCATATACCATATGATGAACTGAACATGCCGTTTCCCGCTCATCTCACATATTGCTATAACTGCAGGAAGCAAAAAGTCCCTGATGTTCTCTTCACAACTATCGATCTGCCCACAGACGCAGTGGTTGTTGGTAAAGGTTGTCTTATTCAGGCAAGGTTATGTCGATTAAAAAAGAAAGCACAGGCAGAAGCCAATGCCACAGCTATCAGTAATCTCTTGCCGTTTATGGAATATGAAGTACACACTCAACTGATGAACAAGCTCAAACTCAAAGGAATGAATGCTTTGTTTGGACTGAGAATTCAGATCACAGTGGGCGAGACCATGCTGATGGGCTTAGCGTCGGCCACAGGAGTCTACTTAGCAGCCTTACCCACACCCGGTGGAATCCAGATCGCTGGGAAGACCCCTAATGATGGCTCCTATGAACAGCACATCTCCCACATGCAGAAGAGAATAAACGACACCATTGCAAAAAACAAAGAGCTGTATGAGATCACCCCCCCGGAGGTGTCTGAGGAGATGATAGGATCCCCCATCCCAGAACCCAGACAGCGCTCCAGACTTCTAAGATCACAGTCGGAAAGTTCTGATGAAGTTACAGAGTTAGATCTTTCACACGGGAAAAAGGATGCTTTTGTTTTAGAGATCGATGACACCGATGCCATGGAAGATGTGCACTCCCTCCTTACTGACGCCCCGCCCCCTTCAGGTTTTTATAGTTGTAATACAGAAATTATGCCTGGCATAAATAACTGGACATCAGAAATACAGATGTTCACGTCAGTAAGAGTGGTCAGACTAAGTAGCCTCAACTTGACTAACCAAGCTCTCAATAAGAACTTCAACGGCCTATGTGAGAACTTGCTCAAGAGCCTGTATTTCAAACTTCGGTCCATGACCCCCTGCTGCCTCTGCCATGTGAACTTTACAGTGTCTCTGCCTGAAGATGAGTTAATCCAGGTCACAGTCACAGCAGTTGCAATAACTTTTGATAAAAACCAGGCCTTACAGACCACAAAACCCCACGTTGAAAAGTCACTACAAAGAGCCTCCACAGATAACGAAGAACTGCTGCAGTTCCCACTGGAGCTCTGCTCAGACTCACTGCCTCCTCATCCTTTCCCAGCAGCTAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTTCCCACTGGAGCTCTGC
60.38
GTGAGATGAGCGGGAAACGG
61.08
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTTCCCACTGGAGCTCTGC
60.38
TGAGATGAGCGGGAAACGG
59.78
142
PCR template sequence:
TCACTACAAAGAGCCTCCACAGATAACGAAGAACTGCTGCAGTTCCCACTGGAGCTCTGCTCAGACTCACTGCCTCCTCATCCTTTCCCAGCAGCTAAAGGATTGAAGAGAATTTACCGGTGGGCTGCGGATTCTGCCATATACCATATGATGAACTGAACATGCCGTTTCCCGCTCATCTCACATATTGCTATAACTGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-134-5p(1), mmu-let-7b-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-31-5p(1), mmu-let-7c-5p(1), mmu-miR-541-5p(1), mmu-miR-34b-5p(1), mmu-miR-705(1), mmu-miR-129-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCAGCAGCTAAAGGATTGAAGAGAAT
siRNA sets
TTCTCTTCAATCCTTTAGC, ATTCTCTTCAATCCTTTAG, TCAATCCTTTAGCTGCTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCC2CD5_1175_ORF_1
0.9038
0.156219978
0.99587344
1173
ORF sequence:
ATGCCGTTTCCCGCTCATCTCACATATTGCTATAACTGCAGGAAGCAAAAAGTCCCTGATGTTCTCTTCACAACTATCGATCTGCCCACAGACGCAGTGGTTGTTGGTAAAGGTTGTCTTATTCAGGCAAGGTTATGTCGATTAAAAAAGAAAGCACAGGCAGAAGCCAATGCCACAGCTATCAGTAATCTCTTGCCGTTTATGGAATATGAAGTACACACTCAACTGATGAACAAGCTCAAACTCAAAGGAATGAATGCTTTGTTTGGACTGAGAATTCAGATCACAGTGGGCGAGACCATGCTGATGGGCTTAGCGTCGGCCACAGGAGTCTACTTAGCAGCCTTACCCACACCCGGTGGAATCCAGATCGCTGGGAAGACCCCTAATGATGGCTCCTATGAACAGCACATCTCCCACATGCAGAAGAGAATAAACGACACCATTGCAAAAAACAAAGAGCTGTATGAGATCACCCCCCCGGAGGTGTCTGAGGAGATGATAGGATCCCCCATCCCAGAACCCAGACAGCGCTCCAGACTTCTAAGATCACAGTCGGAAAGTTCTGATGAAGTTACAGAGTTAGATCTTTCACACGGGAAAAAGGATGCTTTTGTTTTAGAGATCGATGACACCGATGCCATGGAAGATGTGCACTCCCTCCTTACTGACGCCCCGCCCCCTTCAGGTTTTTATAGTTGTAATACAGAAATTATGCCTGGCATAAATAACTGGACATCAGAAATACAGATGTTCACGTCAGTAAGAGTGGTCAGACTAAGTAGCCTCAACTTGACTAACCAAGCTCTCAATAAGAACTTCAACGGCCTATGTGAGAACTTGCTCAAGAGCCTGTATTTCAAACTTCGGTCCATGACCCCCTGCTGCCTCTGCCATGTGAACTTTACAGTGTCTCTGCCTGAAGATGAGTTAATCCAGGTCACAGTCACAGCAGTTGCAATAACTTTTGATAAAAACCAGGCCTTACAGACCACAAAACCCCACGTTGAAAAGTCACTACAAAGAGCCTCCACAGATAACGAAGAACTGCTGCAGTTCCCACTGGAGCTCTGCTCAGACTCACTGCCTCCTCATCCTTTCCCAGCAGCTAAAGGATTGAAGAGAATTTACCGGTGGGCTGCGGATTCTGCCATATACCATATGATGAACTGA
Peptide sequence:
MPFPAHLTYCYNCRKQKVPDVLFTTIDLPTDAVVVGKGCLIQARLCRLKKKAQAEANATAISNLLPFMEYEVHTQLMNKLKLKGMNALFGLRIQITVGETMLMGLASATGVYLAALPTPGGIQIAGKTPNDGSYEQHISHMQKRINDTIAKNKELYEITPPEVSEEMIGSPIPEPRQRSRLLRSQSESSDEVTELDLSHGKKDAFVLEIDDTDAMEDVHSLLTDAPPPSGFYSCNTEIMPGINNWTSEIQMFTSVRVVRLSSLNLTNQALNKNFNGLCENLLKSLYFKLRSMTPCCLCHVNFTVSLPEDELIQVTVTAVAITFDKNQALQTTKPHVEKSLQRASTDNEELLQFPLELCSDSLPPHPFPAAKGLKRIYRWAADSAIYHMMN
IRESfinder result
IRESfinder score
0.498587424
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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