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mmu_circChd1_2121_2
Basic information of circular RNA
PanCircBase ID:
mmu_circChd1_2121_2
mm39_Chr. Position ID:
chr17|15948448|15963492|+
Gene name:
Chd1
Transcript:
ENSMUST00000024627.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
13
Exon/intron indexes:
5,6,7,8,9,10,11,12,13,14,15,16,17
Exon/intron offsets:
0,2296,2562,3667,4352,4798,6044,7441,8673,10295,11319,13970,14891
Genomic length:
15044
Exon/intron sizes in nt:
65,15,02,69,22,61,01,10,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr17:15946624-15948448|chr17:15963492-15967396
Splice length:
2121
Other database IDs:
circAtlas: mmu-Chd1_0087
Human Ortholog IDs:
Mature spliced Sequence:
GACTCGTCCAGCAGTGAAGACTCCGACGACTCGTCCAGCGGTGCCAAGAGGAAGAAGCACAATGATGAAGACTGGCAGATGTCTGGGTCCGGATCTCCATCTCAGTCTGGTTCAGACTCAGAATCTGAAGAAGAGCGAGATAAAAGCAGCTGCGACGGGACAGAGTCCGACTACGAGCCGAAAAACAAAGTCAGAAGCCGAAAGCCTCAGAATAGATCTAAGTCAAAAAATGGGAAAAAAATTCTTGGACAAAAAAAGAGACAGATTGATTCATCTGAGGATGAAGATGATGAAGATTATGATAATGATAAACGAAGCTCTCGCCGCCAAGCCACCGTCAATGTGAGCTACAAGGAGGATGAAGAAATGAAAACCGACTCCGATGACCTGCTGGAGGTCTGCGGCGAGGACGTCCCTCAGCCTGAGGACGAGGAGTTTGAGACAATAGAGAGGGTTATGGATTGCAGAGTGGGGCGGAAAGGAGCTACTGGTGCTACTACAACCATTTATGCTGTCGAAGCAGATGGTGACCCAAATGCAGGATTTGAAAGAAACAAAGAGCCAGGAGACATACAGTATTTAATTAAGTGGAAAGGATGGTCTCACATCCACAACACATGGGAGACAGAAGAGACCCTGAAGCAGCAGAACGTTAGAGGGATGAAAAAATTGGATAATTATAAGAAAAAAGATCAAGAGACGAAACGATGGCTGAAAAATGCTTCTCCAGAAGATGTGGAATATTATAATTGCCAGCAAGAGCTTACAGATGATCTACACAAACAGTATCAGATAGTGGAGCGCATAATTGCTCATTCCAATCAAAAATCAGCAGCTGGTCTTCCTGATTATTATTGCAAATGGCAGGGGCTTCCATACTCAGAGTGCAGCTGGGAGGATGGAGCTCTCATTTCCAAAAAGTTTCAGACATGCATCGATGAATATTTTAGCAGGAATCAGTCAAAAACGACACCTTTTAAAGATTGCAAAGTATTGAAACAAAGACCAAGATTTGTAGCTCTGAAGAAACAACCATCCTATATTGGAGGACATGAGGGCTTAGAACTGAGAGACTATCAGCTGAATGGTTTAAACTGGCTCGCTCACTCTTGGTGCAAAGGAAATAGTTGCATACTTGCTGATGAAATGGGCCTTGGGAAAACAATACAGACGATCTCATTTTTGAACTATTTGTTCCATGAACATCAGTTATATGGGCCGTTTCTACTAGTTGTCCCGCTCTCCACTCTGACTTCCTGGCAGAGGGAGATACAGACGTGGGCGTCTCAGATGAATGCTGTGGTTTACTTAGGCGACATTAACAGCAGAAACATGATAAGAACTCATGAATGGATGCATCCCCAGACCAAACGGTTAAAATTTAATATACTTTTAACAACGTATGAAATTTTATTGAAGGATAAGGCATTCCTTGGTGGTCTGAATTGGGCATTCATAGGTGTTGATGAAGCGCATCGATTAAAGAATGATGATTCCCTTCTGTACAAAACTTTAATCGACTTTAAATCTAACCATCGCCTTCTGATCACTGGAACCCCTCTACAGAACTCCCTGAAGGAGCTCTGGTCACTGCTGCACTTCATTATGCCGGAGAAGTTTTCTTCATGGGAAGATTTTGAAGAAGAACATGGCAAAGGCAGAGAATATGGTTATGCAAGCCTCCACAAGGAGCTTGAGCCATTTCTGTTACGCAGAGTTAAGAAAGATGTGGAAAAATCTCTTCCTGCCAAGGTGGAGCAGATTTTAAGAATGGAGATGAGTGCTTTACAGAAGCAATATTACAAGTGGATTTTAACTAGGAATTATAAAGCCCTCAGCAAAGGTTCCAAGGGCAGTACCTCAGGCTTTTTGAACATTATGATGGAGCTAAAGAAATGTTGTAACCATTGCTACCTCATTAAACCACCAGATAATAATGAATTCTATAATAAACAGGAGGCCTTACAACACTTAATCCGTAGTAGCGGAAAACTCATCCTTCTCGACAAGCTGTTGATTCGCCTAAGAGAAAGAGGCAACCGAGTGCTCATTTTCTCTCAGATGGTGCGGATGTTAGACATACTCGCAGAGTATTTGAAGTACCGCCAGTTCCCCTTTCAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGCAACCGAGTGCTCATTT
60.25
GACCCAGACATCTGCCAGTC
60.11
177
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGCAACCGAGTGCTCATTT
60.25
TGCTTCTTCCTCTTGGCACC
60.25
147
PCR template sequence:
CCTAAGAGAAAGAGGCAACCGAGTGCTCATTTTCTCTCAGATGGTGCGGATGTTAGACATACTCGCAGAGTATTTGAAGTACCGCCAGTTCCCCTTTCAAGACTCGTCCAGCAGTGAAGACTCCGACGACTCGTCCAGCGGTGCCAAGAGGAAGAAGCACAATGATGAAGACTGGCAGATGTCTGGGTCCGGATCTCCAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
22
Interacting miRNAs (#binding sites)
mmu-miR-137-3p(1), mmu-miR-23b-3p(1), mmu-let-7a-5p(1), mmu-miR-7b-5p(1), mmu-miR-429-3p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-7a-5p(1), mmu-miR-23a-3p(1), mmu-let-7d-5p(1), mmu-miR-149-5p(1), mmu-miR-351-5p(1), mmu-miR-182-5p(1), mmu-miR-383-5p(1), mmu-miR-98-5p(1), mmu-miR-384-3p(1), mmu-miR-1198-5p(1), mmu-miR-335-3p(1), mmu-miR-3470b(1), mmu-miR-1904(1), mmu-miR-202-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTTCCCCTTTCAAGACTCGTCCAGCA
siRNA sets
GGACGAGTCTTGAAAGGGG, CTGGACGAGTCTTGAAAGG, TGGACGAGTCTTGAAAGGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCHD1_2121_2_ORF_1
0.8454
0.1325132
1
4164
ORF sequence:
ATGTCTGGGTCCGGATCTCCATCTCAGTCTGGTTCAGACTCAGAATCTGAAGAAGAGCGAGATAAAAGCAGCTGCGACGGGACAGAGTCCGACTACGAGCCGAAAAACAAAGTCAGAAGCCGAAAGCCTCAGAATAGATCTAAGTCAAAAAATGGGAAAAAAATTCTTGGACAAAAAAAGAGACAGATTGATTCATCTGAGGATGAAGATGATGAAGATTATGATAATGATAAACGAAGCTCTCGCCGCCAAGCCACCGTCAATGTGAGCTACAAGGAGGATGAAGAAATGAAAACCGACTCCGATGACCTGCTGGAGGTCTGCGGCGAGGACGTCCCTCAGCCTGAGGACGAGGAGTTTGAGACAATAGAGAGGGTTATGGATTGCAGAGTGGGGCGGAAAGGAGCTACTGGTGCTACTACAACCATTTATGCTGTCGAAGCAGATGGTGACCCAAATGCAGGATTTGAAAGAAACAAAGAGCCAGGAGACATACAGTATTTAATTAAGTGGAAAGGATGGTCTCACATCCACAACACATGGGAGACAGAAGAGACCCTGAAGCAGCAGAACGTTAGAGGGATGAAAAAATTGGATAATTATAAGAAAAAAGATCAAGAGACGAAACGATGGCTGAAAAATGCTTCTCCAGAAGATGTGGAATATTATAATTGCCAGCAAGAGCTTACAGATGATCTACACAAACAGTATCAGATAGTGGAGCGCATAATTGCTCATTCCAATCAAAAATCAGCAGCTGGTCTTCCTGATTATTATTGCAAATGGCAGGGGCTTCCATACTCAGAGTGCAGCTGGGAGGATGGAGCTCTCATTTCCAAAAAGTTTCAGACATGCATCGATGAATATTTTAGCAGGAATCAGTCAAAAACGACACCTTTTAAAGATTGCAAAGTATTGAAACAAAGACCAAGATTTGTAGCTCTGAAGAAACAACCATCCTATATTGGAGGACATGAGGGCTTAGAACTGAGAGACTATCAGCTGAATGGTTTAAACTGGCTCGCTCACTCTTGGTGCAAAGGAAATAGTTGCATACTTGCTGATGAAATGGGCCTTGGGAAAACAATACAGACGATCTCATTTTTGAACTATTTGTTCCATGAACATCAGTTATATGGGCCGTTTCTACTAGTTGTCCCGCTCTCCACTCTGACTTCCTGGCAGAGGGAGATACAGACGTGGGCGTCTCAGATGAATGCTGTGGTTTACTTAGGCGACATTAACAGCAGAAACATGATAAGAACTCATGAATGGATGCATCCCCAGACCAAACGGTTAAAATTTAATATACTTTTAACAACGTATGAAATTTTATTGAAGGATAAGGCATTCCTTGGTGGTCTGAATTGGGCATTCATAGGTGTTGATGAAGCGCATCGATTAAAGAATGATGATTCCCTTCTGTACAAAACTTTAATCGACTTTAAATCTAACCATCGCCTTCTGATCACTGGAACCCCTCTACAGAACTCCCTGAAGGAGCTCTGGTCACTGCTGCACTTCATTATGCCGGAGAAGTTTTCTTCATGGGAAGATTTTGAAGAAGAACATGGCAAAGGCAGAGAATATGGTTATGCAAGCCTCCACAAGGAGCTTGAGCCATTTCTGTTACGCAGAGTTAAGAAAGATGTGGAAAAATCTCTTCCTGCCAAGGTGGAGCAGATTTTAAGAATGGAGATGAGTGCTTTACAGAAGCAATATTACAAGTGGATTTTAACTAGGAATTATAAAGCCCTCAGCAAAGGTTCCAAGGGCAGTACCTCAGGCTTTTTGAACATTATGATGGAGCTAAAGAAATGTTGTAACCATTGCTACCTCATTAAACCACCAGATAATAATGAATTCTATAATAAACAGGAGGCCTTACAACACTTAATCCGTAGTAGCGGAAAACTCATCCTTCTCGACAAGCTGTTGATTCGCCTAAGAGAAAGAGGCAACCGAGTGCTCATTTTCTCTCAGATGGTGCGGATGTTAGACATACTCGCAGAGTATTTGAAGTACCGCCAGTTCCCCTTTCAAGACTCGTCCAGCAGTGAAGACTCCGACGACTCGTCCAGCGGTGCCAAGAGGAAGAAGCACAATGATGAAGACTGGCAGATGTCTGGGTCCGGATCTCCATCTCAGTCTGGTTCAGACTCAGAATCTGAAGAAGAGCGAGATAAAAGCAGCTGCGACGGGACAGAGTCCGACTACGAGCCGAAAAACAAAGTCAGAAGCCGAAAGCCTCAGAATAGATCTAAGTCAAAAAATGGGAAAAAAATTCTTGGACAAAAAAAGAGACAGATTGATTCATCTGAGGATGAAGATGATGAAGATTATGATAATGATAAACGAAGCTCTCGCCGCCAAGCCACCGTCAATGTGAGCTACAAGGAGGATGAAGAAATGAAAACCGACTCCGATGACCTGCTGGAGGTCTGCGGCGAGGACGTCCCTCAGCCTGAGGACGAGGAGTTTGAGACAATAGAGAGGGTTATGGATTGCAGAGTGGGGCGGAAAGGAGCTACTGGTGCTACTACAACCATTTATGCTGTCGAAGCAGATGGTGACCCAAATGCAGGATTTGAAAGAAACAAAGAGCCAGGAGACATACAGTATTTAATTAAGTGGAAAGGATGGTCTCACATCCACAACACATGGGAGACAGAAGAGACCCTGAAGCAGCAGAACGTTAGAGGGATGAAAAAATTGGATAATTATAAGAAAAAAGATCAAGAGACGAAACGATGGCTGAAAAATGCTTCTCCAGAAGATGTGGAATATTATAATTGCCAGCAAGAGCTTACAGATGATCTACACAAACAGTATCAGATAGTGGAGCGCATAATTGCTCATTCCAATCAAAAATCAGCAGCTGGTCTTCCTGATTATTATTGCAAATGGCAGGGGCTTCCATACTCAGAGTGCAGCTGGGAGGATGGAGCTCTCATTTCCAAAAAGTTTCAGACATGCATCGATGAATATTTTAGCAGGAATCAGTCAAAAACGACACCTTTTAAAGATTGCAAAGTATTGAAACAAAGACCAAGATTTGTAGCTCTGAAGAAACAACCATCCTATATTGGAGGACATGAGGGCTTAGAACTGAGAGACTATCAGCTGAATGGTTTAAACTGGCTCGCTCACTCTTGGTGCAAAGGAAATAGTTGCATACTTGCTGATGAAATGGGCCTTGGGAAAACAATACAGACGATCTCATTTTTGAACTATTTGTTCCATGAACATCAGTTATATGGGCCGTTTCTACTAGTTGTCCCGCTCTCCACTCTGACTTCCTGGCAGAGGGAGATACAGACGTGGGCGTCTCAGATGAATGCTGTGGTTTACTTAGGCGACATTAACAGCAGAAACATGATAAGAACTCATGAATGGATGCATCCCCAGACCAAACGGTTAAAATTTAATATACTTTTAACAACGTATGAAATTTTATTGAAGGATAAGGCATTCCTTGGTGGTCTGAATTGGGCATTCATAGGTGTTGATGAAGCGCATCGATTAAAGAATGATGATTCCCTTCTGTACAAAACTTTAATCGACTTTAAATCTAACCATCGCCTTCTGATCACTGGAACCCCTCTACAGAACTCCCTGAAGGAGCTCTGGTCACTGCTGCACTTCATTATGCCGGAGAAGTTTTCTTCATGGGAAGATTTTGAAGAAGAACATGGCAAAGGCAGAGAATATGGTTATGCAAGCCTCCACAAGGAGCTTGAGCCATTTCTGTTACGCAGAGTTAAGAAAGATGTGGAAAAATCTCTTCCTGCCAAGGTGGAGCAGATTTTAAGAATGGAGATGAGTGCTTTACAGAAGCAATATTACAAGTGGATTTTAACTAGGAATTATAAAGCCCTCAGCAAAGGTTCCAAGGGCAGTACCTCAGGCTTTTTGAACATTATGATGGAGCTAAAGAAATGTTGTAACCATTGCTACCTCATTAAACCACCAGATAATAATGAATTCTATAATAAACAGGAGGCCTTACAACACTTAATCCGTAGTAGCGGAAAACTCATCCTTCTCGACAAGCTGTTGATTCGCCTAAGAGAAAGAGGCAACCGAGTGCTCATTTTCTCTCAGATGGTGCGGATGTTAGACATACTCGCAGAGTATTTGAAGTACCGCCAGTTCCCCTTTCAA
Peptide sequence:
MSGSGSPSQSGSDSESEEERDKSSCDGTESDYEPKNKVRSRKPQNRSKSKNGKKILGQKKRQIDSSEDEDDEDYDNDKRSSRRQATVNVSYKEDEEMKTDSDDLLEVCGEDVPQPEDEEFETIERVMDCRVGRKGATGATTTIYAVEADGDPNAGFERNKEPGDIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKKKDQETKRWLKNASPEDVEYYNCQQELTDDLHKQYQIVERIIAHSNQKSAAGLPDYYCKWQGLPYSECSWEDGALISKKFQTCIDEYFSRNQSKTTPFKDCKVLKQRPRFVALKKQPSYIGGHEGLELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWASQMNAVVYLGDINSRNMIRTHEWMHPQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGREYGYASLHKELEPFLLRRVKKDVEKSLPAKVEQILRMEMSALQKQYYKWILTRNYKALSKGSKGSTSGFLNIMMELKKCCNHCYLIKPPDNNEFYNKQEALQHLIRSSGKLILLDKLLIRLRERGNRVLIFSQMVRMLDILAEYLKYRQFPFQDSSSSEDSDDSSSGAKRKKHNDEDWQMSGSGSPSQSGSDSESEEERDKSSCDGTESDYEPKNKVRSRKPQNRSKSKNGKKILGQKKRQIDSSEDEDDEDYDNDKRSSRRQATVNVSYKEDEEMKTDSDDLLEVCGEDVPQPEDEEFETIERVMDCRVGRKGATGATTTIYAVEADGDPNAGFERNKEPGDIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKKKDQETKRWLKNASPEDVEYYNCQQELTDDLHKQYQIVERIIAHSNQKSAAGLPDYYCKWQGLPYSECSWEDGALISKKFQTCIDEYFSRNQSKTTPFKDCKVLKQRPRFVALKKQPSYIGGHEGLELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWASQMNAVVYLGDINSRNMIRTHEWMHPQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGREYGYASLHKELEPFLLRRVKKDVEKSLPAKVEQILRMEMSALQKQYYKWILTRNYKALSKGSKGSTSGFLNIMMELKKCCNHCYLIKPPDNNEFYNKQEALQHLIRSSGKLILLDKLLIRLRERGNRVLIFSQMVRMLDILAEYLKYRQFPFQ
IRESfinder result
IRESfinder score
0.535643454
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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