top of page
mmu_circChd6_1572
Basic information of circular RNA
PanCircBase ID:
mmu_circChd6_1572
mm39_Chr. Position ID:
chr2|160850274|160868255|-
Gene name:
Chd6
Transcript:
ENSMUST00000039782.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
17,16,15,14,13,12,11,10,9
Exon/intron offsets:
0,4667,5729,8821,9671,11097,12612,17584,17894
Genomic length:
17981
Exon/intron sizes in nt:
196,211,256,144,177,244,122,135,87
Flanking exon/introns:
chr2:160834199-160850274|chr2:160868255-160871097
Splice length:
1572
Other database IDs:
circBase: mmu_circ_0009538, CIRCpedia: MMU_CIRCpedia_11175, circAtlas: mmu-Chd6_0011
Human Ortholog IDs:
Mature spliced Sequence:
CCTGATGAAGACTTGTTCAATCCAGATTATATAGAAATTGATCGTATCTTAGAAGTGGCCCACACCAAGGATGCAGAAACAGGGGAGGAAGTAACACATTACCTGGTAAAATGGTGCTCCCTGCCATATGAGGAAAGCACCTGGGAGCTAGAAGAAGATGTGGATCCTGCAAAAGTGAAGGAATTTGAATCTCTACAAATTCTCCCTGAAGTTAAACATGTGGAACGACCTGCCTCTGATGCGTGGCAGAAACTGGAGACATCCCGTGAGTATAGGAACAGTAACCGGCTGCGAGAGTACCAACTCGAGGGGATGAACTGGCTTCTTTTCAACTGGTACAACAGAAAAAACTGTATATTGGCTGATGAAATGGGCCTAGGGAAAACCATCCAGTCCATCGCATTCCTTTCAGAAATCTTTGTCAGAGGAATCCACGGCCCCTTTCTCATCATTGCCCCACTTTCCACCATCACTAACTGGGAGCGAGAATTCCGGACATGGACGGAGATGAATGCTATTGTGTACCACGGCAGCCAGATCAGCAGGCAGATGATCCAGCAGTACGAAATGGTATACAGAGATGCACAGGGAAACCCCCTTTCAGGAGTCTTCAAGTTCCACGTCGTCATCACAACGTTTGAGATGATCCTGGCAGATTGCCCAGAGCTGAAGAAAATTCACTGGAGCTGTGTGATAATTGATGAGGCCCACAGACTGAAGAATAGGAACTGCAAACTTCTGGAAGGGTTAAAGCTCATGGCCCTGGAACACAAAGTGCTGCTCACAGGAACACCCTTGCAGAACTCTGTGGAAGAGCTCTTCAGTTTGCTTAACTTTCTGGAGCCCTCGCAGTTCCCTTCAGAGACTGCCTTCTTAGAGGAGTTTGGTGATCTCAAAACAGAAGAACAGGTAAAGAAATTGCAGTCTATCCTAAAACCAATGATGCTTCGGCGCCTGAAAGATGATGTGGAGAAGAACCTTGCTCCTAAGCAAGAGACCATCATTGAAGTAGAACTGACCAATATCCAGAAAAAGTACTATCGTGCTATCCTAGAGAAAAACTTTTCCTTCCTGACCAAAGGTGCAAATCAACACAACATGCCCAATCTTATCAATACTATGATGGAGCTCAGAAAATGCTGTAACCACCCCTACCTGATCAATGGGGCCGAGGAAAAGATTCTGGAAGATTTCAGAAAAGCGCACAGCTCCGAAGCCTCTGACTTCCAGCTGCAGGCCATGATCCAGGCGGCCGGGAAGCTGGTGCTGATTGACAAGCTTCTCCCCAAGCTCATTGCCGGGGGCCACAAAGTGCTCATCTTCTCGCAGATGGTGCGCTGCCTCGACATCCTGGAAGATTATCTCATCCAGAGGAGATACACCTATGAGCGAATTGATGGGCGAGTACGGGGAAACCTGCGCCAGGCAGCCATCGACCGGTTCTGTAAGCCAGACTCAGACCGCTTTGTCTTTCTTCTGTGCACCAGAGCGGGAGGCCTGGGAATCAATCTCACAGCTGCTGATACCTGCATCATATTTGATTCTGACTGGAACCCACAAAATGACTTGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCACAGCTGCTGATACCTGC
60.11
TTCTGCATCCTTGGTGTGGG
60.25
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGAGGCCTGGGAATCAATC
60.18
TTCTGCATCCTTGGTGTGGG
60.25
160
PCR template sequence:
TCTTCTGTGCACCAGAGCGGGAGGCCTGGGAATCAATCTCACAGCTGCTGATACCTGCATCATATTTGATTCTGACTGGAACCCACAAAATGACTTGCAGCCTGATGAAGACTTGTTCAATCCAGATTATATAGAAATTGATCGTATCTTAGAAGTGGCCCACACCAAGGATGCAGAAACAGGGGAGGAAGTAACACATT
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-15a-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-324-5p(1), mmu-miR-181b-5p(1), mmu-miR-370-3p(1), mmu-miR-1198-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAATGACTTGCAGCCTGATGAAGACT
siRNA sets
TTCATCAGGCTGCAAGTCA, TCTTCATCAGGCTGCAAGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCHD6_1572_ORF_1
1.2678
0.338347801
0.999999994
2832
ORF sequence:
ATGAACTGGCTTCTTTTCAACTGGTACAACAGAAAAAACTGTATATTGGCTGATGAAATGGGCCTAGGGAAAACCATCCAGTCCATCGCATTCCTTTCAGAAATCTTTGTCAGAGGAATCCACGGCCCCTTTCTCATCATTGCCCCACTTTCCACCATCACTAACTGGGAGCGAGAATTCCGGACATGGACGGAGATGAATGCTATTGTGTACCACGGCAGCCAGATCAGCAGGCAGATGATCCAGCAGTACGAAATGGTATACAGAGATGCACAGGGAAACCCCCTTTCAGGAGTCTTCAAGTTCCACGTCGTCATCACAACGTTTGAGATGATCCTGGCAGATTGCCCAGAGCTGAAGAAAATTCACTGGAGCTGTGTGATAATTGATGAGGCCCACAGACTGAAGAATAGGAACTGCAAACTTCTGGAAGGGTTAAAGCTCATGGCCCTGGAACACAAAGTGCTGCTCACAGGAACACCCTTGCAGAACTCTGTGGAAGAGCTCTTCAGTTTGCTTAACTTTCTGGAGCCCTCGCAGTTCCCTTCAGAGACTGCCTTCTTAGAGGAGTTTGGTGATCTCAAAACAGAAGAACAGGTAAAGAAATTGCAGTCTATCCTAAAACCAATGATGCTTCGGCGCCTGAAAGATGATGTGGAGAAGAACCTTGCTCCTAAGCAAGAGACCATCATTGAAGTAGAACTGACCAATATCCAGAAAAAGTACTATCGTGCTATCCTAGAGAAAAACTTTTCCTTCCTGACCAAAGGTGCAAATCAACACAACATGCCCAATCTTATCAATACTATGATGGAGCTCAGAAAATGCTGTAACCACCCCTACCTGATCAATGGGGCCGAGGAAAAGATTCTGGAAGATTTCAGAAAAGCGCACAGCTCCGAAGCCTCTGACTTCCAGCTGCAGGCCATGATCCAGGCGGCCGGGAAGCTGGTGCTGATTGACAAGCTTCTCCCCAAGCTCATTGCCGGGGGCCACAAAGTGCTCATCTTCTCGCAGATGGTGCGCTGCCTCGACATCCTGGAAGATTATCTCATCCAGAGGAGATACACCTATGAGCGAATTGATGGGCGAGTACGGGGAAACCTGCGCCAGGCAGCCATCGACCGGTTCTGTAAGCCAGACTCAGACCGCTTTGTCTTTCTTCTGTGCACCAGAGCGGGAGGCCTGGGAATCAATCTCACAGCTGCTGATACCTGCATCATATTTGATTCTGACTGGAACCCACAAAATGACTTGCAGCCTGATGAAGACTTGTTCAATCCAGATTATATAGAAATTGATCGTATCTTAGAAGTGGCCCACACCAAGGATGCAGAAACAGGGGAGGAAGTAACACATTACCTGGTAAAATGGTGCTCCCTGCCATATGAGGAAAGCACCTGGGAGCTAGAAGAAGATGTGGATCCTGCAAAAGTGAAGGAATTTGAATCTCTACAAATTCTCCCTGAAGTTAAACATGTGGAACGACCTGCCTCTGATGCGTGGCAGAAACTGGAGACATCCCGTGAGTATAGGAACAGTAACCGGCTGCGAGAGTACCAACTCGAGGGGATGAACTGGCTTCTTTTCAACTGGTACAACAGAAAAAACTGTATATTGGCTGATGAAATGGGCCTAGGGAAAACCATCCAGTCCATCGCATTCCTTTCAGAAATCTTTGTCAGAGGAATCCACGGCCCCTTTCTCATCATTGCCCCACTTTCCACCATCACTAACTGGGAGCGAGAATTCCGGACATGGACGGAGATGAATGCTATTGTGTACCACGGCAGCCAGATCAGCAGGCAGATGATCCAGCAGTACGAAATGGTATACAGAGATGCACAGGGAAACCCCCTTTCAGGAGTCTTCAAGTTCCACGTCGTCATCACAACGTTTGAGATGATCCTGGCAGATTGCCCAGAGCTGAAGAAAATTCACTGGAGCTGTGTGATAATTGATGAGGCCCACAGACTGAAGAATAGGAACTGCAAACTTCTGGAAGGGTTAAAGCTCATGGCCCTGGAACACAAAGTGCTGCTCACAGGAACACCCTTGCAGAACTCTGTGGAAGAGCTCTTCAGTTTGCTTAACTTTCTGGAGCCCTCGCAGTTCCCTTCAGAGACTGCCTTCTTAGAGGAGTTTGGTGATCTCAAAACAGAAGAACAGGTAAAGAAATTGCAGTCTATCCTAAAACCAATGATGCTTCGGCGCCTGAAAGATGATGTGGAGAAGAACCTTGCTCCTAAGCAAGAGACCATCATTGAAGTAGAACTGACCAATATCCAGAAAAAGTACTATCGTGCTATCCTAGAGAAAAACTTTTCCTTCCTGACCAAAGGTGCAAATCAACACAACATGCCCAATCTTATCAATACTATGATGGAGCTCAGAAAATGCTGTAACCACCCCTACCTGATCAATGGGGCCGAGGAAAAGATTCTGGAAGATTTCAGAAAAGCGCACAGCTCCGAAGCCTCTGACTTCCAGCTGCAGGCCATGATCCAGGCGGCCGGGAAGCTGGTGCTGATTGACAAGCTTCTCCCCAAGCTCATTGCCGGGGGCCACAAAGTGCTCATCTTCTCGCAGATGGTGCGCTGCCTCGACATCCTGGAAGATTATCTCATCCAGAGGAGATACACCTATGAGCGAATTGATGGGCGAGTACGGGGAAACCTGCGCCAGGCAGCCATCGACCGGTTCTGTAAGCCAGACTCAGACCGCTTTGTCTTTCTTCTGTGCACCAGAGCGGGAGGCCTGGGAATCAATCTCACAGCTGCTGATACCTGCATCATATTTGATTCTGACTGGAACCCACAAAATGACTTGCAG
Peptide sequence:
MNWLLFNWYNRKNCILADEMGLGKTIQSIAFLSEIFVRGIHGPFLIIAPLSTITNWEREFRTWTEMNAIVYHGSQISRQMIQQYEMVYRDAQGNPLSGVFKFHVVITTFEMILADCPELKKIHWSCVIIDEAHRLKNRNCKLLEGLKLMALEHKVLLTGTPLQNSVEELFSLLNFLEPSQFPSETAFLEEFGDLKTEEQVKKLQSILKPMMLRRLKDDVEKNLAPKQETIIEVELTNIQKKYYRAILEKNFSFLTKGANQHNMPNLINTMMELRKCCNHPYLINGAEEKILEDFRKAHSSEASDFQLQAMIQAAGKLVLIDKLLPKLIAGGHKVLIFSQMVRCLDILEDYLIQRRYTYERIDGRVRGNLRQAAIDRFCKPDSDRFVFLLCTRAGGLGINLTAADTCIIFDSDWNPQNDLQPDEDLFNPDYIEIDRILEVAHTKDAETGEEVTHYLVKWCSLPYEESTWELEEDVDPAKVKEFESLQILPEVKHVERPASDAWQKLETSREYRNSNRLREYQLEGMNWLLFNWYNRKNCILADEMGLGKTIQSIAFLSEIFVRGIHGPFLIIAPLSTITNWEREFRTWTEMNAIVYHGSQISRQMIQQYEMVYRDAQGNPLSGVFKFHVVITTFEMILADCPELKKIHWSCVIIDEAHRLKNRNCKLLEGLKLMALEHKVLLTGTPLQNSVEELFSLLNFLEPSQFPSETAFLEEFGDLKTEEQVKKLQSILKPMMLRRLKDDVEKNLAPKQETIIEVELTNIQKKYYRAILEKNFSFLTKGANQHNMPNLINTMMELRKCCNHPYLINGAEEKILEDFRKAHSSEASDFQLQAMIQAAGKLVLIDKLLPKLIAGGHKVLIFSQMVRCLDILEDYLIQRRYTYERIDGRVRGNLRQAAIDRFCKPDSDRFVFLLCTRAGGLGINLTAADTCIIFDSDWNPQNDLQ
IRESfinder result
IRESfinder score
0.558237687
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page