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mmu_circChd9_1052
Basic information of circular RNA
PanCircBase ID:
mmu_circChd9_1052
mm39_Chr. Position ID:
chr8|91728247|91738083|+
Gene name:
Chd9
Transcript:
ENSMUST00000048665.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
18,19,20,21,22,23
Exon/intron offsets:
0,4094,4911,7100,8992,9636
Genomic length:
9836
Exon/intron sizes in nt:
1,96,16,81,80,11,11,97,000
Flanking exon/introns:
chr8:91725334-91728247|chr8:91738083-91741726
Splice length:
1052
Other database IDs:
circAtlas: mmu-Chd9_0041
Human Ortholog IDs:
Mature spliced Sequence:
ATATTTATATGAGCGAATTGATGGTAGAGTCAGAGGAAATCTTCGACAAGCAGCCATAGATCGATTTAGTAAACCTGATTCAGATCGATTCGTTTTCCTCCTGTGTACCCGAGCTGGTGGTCTGGGCATCAACCTAACTGCAGCAGATACATGCATTATTTTTGATTCTGATTGGAATCCTCAAAATGACCTCCAGGCCCAAGCTCGTTGCCACAGAATTGGTCAGAACAAAGCAGTTAAAGTCTACAGATTAGTAACTCGAAACTCCTATGAAAGAGAGATGTTTGACCGAGCCAGCTTGAAACTGGGCCTAGATAAAGCCGTGCTACAGAGCATGAGTGGAAGAGACAGTAATGTCAGCGGTATTCAGCAGCTTTCCAAAAAAGAAATAGAAGACCTGCTTCGAAGAGGGGCATATGGAGCCATTATGGAGGAGGAAGATGAAGGCTCTAAGTTCTGTGAGGAAGATATCGACCAGATTTTACTTCGTCGTACAAAAACTATCACAATTGAATCAGAAGGACGTGGGTCAACATTTGCTAAGGCAAGTTTTGTAGCATCTGGGAACCGGACAGATATTTCCTTAGATGATCCCAACTTCTGGCAAAAATGGGCTAAAAAAGCAGAACTAGATATAGACACCATCAGTGGCAGAAACAGTTTAGTTATTGACACCCCAAGAATTCGGAAGCAAACCAGACCCTTTAGTGCCACAAAAGATGAATTGGCTGAATTATCTGAAGCTGAAAGTGAAGGAGAAGAAAAACCCAAACTCCGGAGACCCTGTGACCGGTCCGGTGGCTATGGAAGGACTGAATGCTTTAGAGTGGAGAAAAATCTACTGGTTTATGGGTGGGGCCGATGGCGAGAGATCCTGTCTCACGGGCGTTTTAAGCGGCAGCTGAATGAGCACGATGTGGAAGTCATTTGCCGGGCCCTCCTAGCCTATTGCCTCATTCACTATCGGGGCGATGAGAAAATTAAAGGCTTCATATGGGATCTTATCACCCCCACTGAAGACGGCCAGACTCGAGAGCTGCAGAATCACTTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCACTATCGGGGCGATGAGA
60.18
GGCTGCTTGTCGAAGATTTCC
59.87
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCACTATCGGGGCGATGAGA
60.18
CGATCTATGGCTGCTTGTCG
58.86
158
PCR template sequence:
CTCATTCACTATCGGGGCGATGAGAAAATTAAAGGCTTCATATGGGATCTTATCACCCCCACTGAAGACGGCCAGACTCGAGAGCTGCAGAATCACTTAGATATTTATATGAGCGAATTGATGGTAGAGTCAGAGGAAATCTTCGACAAGCAGCCATAGATCGATTTAGTAAACCTGATTCAGATCGATTCGTTTTCCTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-709(1), mmu-miR-149-5p(1), mmu-miR-22-3p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
CAGAATCACTTAGATATTTATATGAG
siRNA sets
ATATAAATATCTAAGTGAT,TAAATATCTAAGTGATTCT,ATAAATATCTAAGTGATTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCHD9_1052_ORF_1
0.8115
0.239559545
0.960570758
831
ORF sequence:
ATGTTTGACCGAGCCAGCTTGAAACTGGGCCTAGATAAAGCCGTGCTACAGAGCATGAGTGGAAGAGACAGTAATGTCAGCGGTATTCAGCAGCTTTCCAAAAAAGAAATAGAAGACCTGCTTCGAAGAGGGGCATATGGAGCCATTATGGAGGAGGAAGATGAAGGCTCTAAGTTCTGTGAGGAAGATATCGACCAGATTTTACTTCGTCGTACAAAAACTATCACAATTGAATCAGAAGGACGTGGGTCAACATTTGCTAAGGCAAGTTTTGTAGCATCTGGGAACCGGACAGATATTTCCTTAGATGATCCCAACTTCTGGCAAAAATGGGCTAAAAAAGCAGAACTAGATATAGACACCATCAGTGGCAGAAACAGTTTAGTTATTGACACCCCAAGAATTCGGAAGCAAACCAGACCCTTTAGTGCCACAAAAGATGAATTGGCTGAATTATCTGAAGCTGAAAGTGAAGGAGAAGAAAAACCCAAACTCCGGAGACCCTGTGACCGGTCCGGTGGCTATGGAAGGACTGAATGCTTTAGAGTGGAGAAAAATCTACTGGTTTATGGGTGGGGCCGATGGCGAGAGATCCTGTCTCACGGGCGTTTTAAGCGGCAGCTGAATGAGCACGATGTGGAAGTCATTTGCCGGGCCCTCCTAGCCTATTGCCTCATTCACTATCGGGGCGATGAGAAAATTAAAGGCTTCATATGGGATCTTATCACCCCCACTGAAGACGGCCAGACTCGAGAGCTGCAGAATCACTTAGATATTTATATGAGCGAATTGATGGTAGAGTCAGAGGAAATCTTCGACAAGCAGCCATAG
Peptide sequence:
MFDRASLKLGLDKAVLQSMSGRDSNVSGIQQLSKKEIEDLLRRGAYGAIMEEEDEGSKFCEEDIDQILLRRTKTITIESEGRGSTFAKASFVASGNRTDISLDDPNFWQKWAKKAELDIDTISGRNSLVIDTPRIRKQTRPFSATKDELAELSEAESEGEEKPKLRRPCDRSGGYGRTECFRVEKNLLVYGWGRWREILSHGRFKRQLNEHDVEVICRALLAYCLIHYRGDEKIKGFIWDLITPTEDGQTRELQNHLDIYMSELMVESEEIFDKQP
IRESfinder result
IRESfinder score
0.567085949
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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