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mmu_circChd6_1059
Basic information of circular RNA
PanCircBase ID:
mmu_circChd6_1059
mm39_Chr. Position ID:
chr2|160819378|160830287|-
Gene name:
Chd6
Transcript:
ENSMUST00000039782.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
27,26,25,24,23,22,21,20
Exon/intron offsets:
0,1910,4116,5165,5599,6204,6999,10798
Genomic length:
10909
Exon/intron sizes in nt:
6,11,30,10,49,01,60,20,00,00,000
Flanking exon/introns:
chr2:160812126-160819378|chr2:160830287-160832164
Splice length:
1059
Other database IDs:
circAtlas: mmu-Chd6_0032
Human Ortholog IDs:
Mature spliced Sequence:
GCTAGTTTCGTGGCTTCAGGAAACAGAACAGATATTTCCTTGGATGACCCTAATTTTTGGCAGAAATGGGCTAAAATAGCTGAATTAGACACTGAAGCAAATAATGAAAAGGAAAGCTTAGTGATTGACCGGCCGCGTGTGAGGAAGCAGACCAAGCACTACAACTCTTTTGAGGAGGACGAGCTCATGGAGTTCTCAGAGTTAGACAGCGACTCAGACGAAAGGCCCACACGGTCCAGACGCCTCAGCGACAGAGCCCGACGCTACCTCCGCGCTGAGTGCTTCCGAGTGGAGAAGAACCTGCTCATCTTTGGCTGGGGCCGGTGGAAGGACATCCTGACTCACGGGCGATTCAAGTGGCCCCTGAATGAGAAGGATATGGAGATGATTTGCAGGGCTCTGCTGGTGTACTGTGTCAAGCATTACAAAGGGGATGAGAAAATCAAAAGTTTTATTTGGGAACTAATCACACCTTCCAAAGACGGGCAAGTTCAGACCCTCCAGAACCACTCAGGCTTGTCTGCCCCAGTCCCCAGAGGGAGGAAAGGAAAAAAGACAAAAAACCAGCTCTTGCTCCCAGAACTGAAGAATGCAGACTGGCTGGCCACCTGCAATCCTGAGGTGGTCTTACATGATGATGGATACAAGAAACACCTCAAACAGCATTGCAATAAGGTGCTTTTGAGAGTCCGGATGCTGTACTACCTAAAAGCTGAAATACTGGGAGAAGCAGCTGATAAAGCATTCGAGGGAACTCCTGCCAGAGAGCTGGATGTGCTTCTGCCTGACATTGACTATGTGGAGATCCCAGTGGATTGGTGGGACGCTGAAGCTGATAAGTCCCTTCTCATTGGCGTGTTCAAGCACGGGTATGAGAGGTACAATGCCATGCGGGCTGACCCAGCGCTCTGCTTCCTAGAGAAAGTTGGCATGCCTGATGAGAAGTCCCTTTCTGCAGAGCAGGGAGTTACAGATGGAACTTCGGACATTCCTGAAAGAGGCAACATAGATAAAGAAGACAGTGCTGAGGACAAGTTGGATGGTCTCCAGAAGCAAACG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCGGACATTCCTGAAAGAGGC
60.07
GCTATTTTAGCCCATTTCTGCCA
59.62
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCGGACATTCCTGAAAGAGGC
60.07
AGCCCATTTCTGCCAAAAAT
56.45
150
PCR template sequence:
GCAGGGAGTTACAGATGGAACTTCGGACATTCCTGAAAGAGGCAACATAGATAAAGAAGACAGTGCTGAGGACAAGTTGGATGGTCTCCAGAAGCAAACGGCTAGTTTCGTGGCTTCAGGAAACAGAACAGATATTTCCTTGGATGACCCTAATTTTTGGCAGAAATGGGCTAAAATAGCTGAATTAGACACTGAAGCAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-1a-3p(1), mmu-miR-206-3p(1), mmu-let-7b-5p(1), mmu-miR-211-5p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-335-3p(1), mmu-miR-1199-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCAGAAGCAAACGGCTAGTTTCGTGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCHD6_1059_ORF_1
1.1008
0.313292474
0.999993715
1932
ORF sequence:
ATGGAGTTCTCAGAGTTAGACAGCGACTCAGACGAAAGGCCCACACGGTCCAGACGCCTCAGCGACAGAGCCCGACGCTACCTCCGCGCTGAGTGCTTCCGAGTGGAGAAGAACCTGCTCATCTTTGGCTGGGGCCGGTGGAAGGACATCCTGACTCACGGGCGATTCAAGTGGCCCCTGAATGAGAAGGATATGGAGATGATTTGCAGGGCTCTGCTGGTGTACTGTGTCAAGCATTACAAAGGGGATGAGAAAATCAAAAGTTTTATTTGGGAACTAATCACACCTTCCAAAGACGGGCAAGTTCAGACCCTCCAGAACCACTCAGGCTTGTCTGCCCCAGTCCCCAGAGGGAGGAAAGGAAAAAAGACAAAAAACCAGCTCTTGCTCCCAGAACTGAAGAATGCAGACTGGCTGGCCACCTGCAATCCTGAGGTGGTCTTACATGATGATGGATACAAGAAACACCTCAAACAGCATTGCAATAAGGTGCTTTTGAGAGTCCGGATGCTGTACTACCTAAAAGCTGAAATACTGGGAGAAGCAGCTGATAAAGCATTCGAGGGAACTCCTGCCAGAGAGCTGGATGTGCTTCTGCCTGACATTGACTATGTGGAGATCCCAGTGGATTGGTGGGACGCTGAAGCTGATAAGTCCCTTCTCATTGGCGTGTTCAAGCACGGGTATGAGAGGTACAATGCCATGCGGGCTGACCCAGCGCTCTGCTTCCTAGAGAAAGTTGGCATGCCTGATGAGAAGTCCCTTTCTGCAGAGCAGGGAGTTACAGATGGAACTTCGGACATTCCTGAAAGAGGCAACATAGATAAAGAAGACAGTGCTGAGGACAAGTTGGATGGTCTCCAGAAGCAAACGGCTAGTTTCGTGGCTTCAGGAAACAGAACAGATATTTCCTTGGATGACCCTAATTTTTGGCAGAAATGGGCTAAAATAGCTGAATTAGACACTGAAGCAAATAATGAAAAGGAAAGCTTAGTGATTGACCGGCCGCGTGTGAGGAAGCAGACCAAGCACTACAACTCTTTTGAGGAGGACGAGCTCATGGAGTTCTCAGAGTTAGACAGCGACTCAGACGAAAGGCCCACACGGTCCAGACGCCTCAGCGACAGAGCCCGACGCTACCTCCGCGCTGAGTGCTTCCGAGTGGAGAAGAACCTGCTCATCTTTGGCTGGGGCCGGTGGAAGGACATCCTGACTCACGGGCGATTCAAGTGGCCCCTGAATGAGAAGGATATGGAGATGATTTGCAGGGCTCTGCTGGTGTACTGTGTCAAGCATTACAAAGGGGATGAGAAAATCAAAAGTTTTATTTGGGAACTAATCACACCTTCCAAAGACGGGCAAGTTCAGACCCTCCAGAACCACTCAGGCTTGTCTGCCCCAGTCCCCAGAGGGAGGAAAGGAAAAAAGACAAAAAACCAGCTCTTGCTCCCAGAACTGAAGAATGCAGACTGGCTGGCCACCTGCAATCCTGAGGTGGTCTTACATGATGATGGATACAAGAAACACCTCAAACAGCATTGCAATAAGGTGCTTTTGAGAGTCCGGATGCTGTACTACCTAAAAGCTGAAATACTGGGAGAAGCAGCTGATAAAGCATTCGAGGGAACTCCTGCCAGAGAGCTGGATGTGCTTCTGCCTGACATTGACTATGTGGAGATCCCAGTGGATTGGTGGGACGCTGAAGCTGATAAGTCCCTTCTCATTGGCGTGTTCAAGCACGGGTATGAGAGGTACAATGCCATGCGGGCTGACCCAGCGCTCTGCTTCCTAGAGAAAGTTGGCATGCCTGATGAGAAGTCCCTTTCTGCAGAGCAGGGAGTTACAGATGGAACTTCGGACATTCCTGAAAGAGGCAACATAGATAAAGAAGACAGTGCTGAGGACAAGTTGGATGGTCTCCAGAAGCAAACG
Peptide sequence:
MEFSELDSDSDERPTRSRRLSDRARRYLRAECFRVEKNLLIFGWGRWKDILTHGRFKWPLNEKDMEMICRALLVYCVKHYKGDEKIKSFIWELITPSKDGQVQTLQNHSGLSAPVPRGRKGKKTKNQLLLPELKNADWLATCNPEVVLHDDGYKKHLKQHCNKVLLRVRMLYYLKAEILGEAADKAFEGTPARELDVLLPDIDYVEIPVDWWDAEADKSLLIGVFKHGYERYNAMRADPALCFLEKVGMPDEKSLSAEQGVTDGTSDIPERGNIDKEDSAEDKLDGLQKQTASFVASGNRTDISLDDPNFWQKWAKIAELDTEANNEKESLVIDRPRVRKQTKHYNSFEEDELMEFSELDSDSDERPTRSRRLSDRARRYLRAECFRVEKNLLIFGWGRWKDILTHGRFKWPLNEKDMEMICRALLVYCVKHYKGDEKIKSFIWELITPSKDGQVQTLQNHSGLSAPVPRGRKGKKTKNQLLLPELKNADWLATCNPEVVLHDDGYKKHLKQHCNKVLLRVRMLYYLKAEILGEAADKAFEGTPARELDVLLPDIDYVEIPVDWWDAEADKSLLIGVFKHGYERYNAMRADPALCFLEKVGMPDEKSLSAEQGVTDGTSDIPERGNIDKEDSAEDKLDGLQKQT
IRESfinder result
IRESfinder score
0.412709261
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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