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mmu_circChd1_2121_1
Basic information of circular RNA
PanCircBase ID:
mmu_circChd1_2121_1
mm39_Chr. Position ID:
chr17|15945530|15959956|+
Gene name:
Chd1
Transcript:
ENSMUST00000024627.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
13
Exon/intron indexes:
3,4,5,6,7,8,9,10,11,12,13,14,15
Exon/intron offsets:
0,980,2918,5214,5480,6585,7270,7716,8962,10359,11591,13213,14237
Genomic length:
14426
Exon/intron sizes in nt:
20,21,14,65,15,02,69,20,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr17:15927401-15945530|chr17:15959956-15962418
Splice length:
2121
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_53111
Human Ortholog IDs:
Mature spliced Sequence:
TCAGTCAGGTGATGATTGTGGGTCAGCATCAGGCTCTGGATCTGGCTCGAGTTCTGGCAGCAGCAGTGACGGAAGCAGCAGCCAATCCGGGAGCAGCGACTCTGATTCTGGCTCTGACTCAGGAAGTCAATCAGAGTCTGAATCAGACACATCCCGAGAGAACAAGGTTCAAGCAAAACCACCAAAAGTCGACGGAGCCGAGTTTTGGAAATCTAGCCCCAGTATTCTGGCTGTCCAGAGATCTGCAATGCTTAGGAAGCAGCCACAGCAGGCCCAGCAGCAGCGCCCAGCTTCATCTAATAGTGGATCCGAAGAAGACTCGTCCAGCAGTGAAGACTCCGACGACTCGTCCAGCGGTGCCAAGAGGAAGAAGCACAATGATGAAGACTGGCAGATGTCTGGGTCCGGATCTCCATCTCAGTCTGGTTCAGACTCAGAATCTGAAGAAGAGCGAGATAAAAGCAGCTGCGACGGGACAGAGTCCGACTACGAGCCGAAAAACAAAGTCAGAAGCCGAAAGCCTCAGAATAGATCTAAGTCAAAAAATGGGAAAAAAATTCTTGGACAAAAAAAGAGACAGATTGATTCATCTGAGGATGAAGATGATGAAGATTATGATAATGATAAACGAAGCTCTCGCCGCCAAGCCACCGTCAATGTGAGCTACAAGGAGGATGAAGAAATGAAAACCGACTCCGATGACCTGCTGGAGGTCTGCGGCGAGGACGTCCCTCAGCCTGAGGACGAGGAGTTTGAGACAATAGAGAGGGTTATGGATTGCAGAGTGGGGCGGAAAGGAGCTACTGGTGCTACTACAACCATTTATGCTGTCGAAGCAGATGGTGACCCAAATGCAGGATTTGAAAGAAACAAAGAGCCAGGAGACATACAGTATTTAATTAAGTGGAAAGGATGGTCTCACATCCACAACACATGGGAGACAGAAGAGACCCTGAAGCAGCAGAACGTTAGAGGGATGAAAAAATTGGATAATTATAAGAAAAAAGATCAAGAGACGAAACGATGGCTGAAAAATGCTTCTCCAGAAGATGTGGAATATTATAATTGCCAGCAAGAGCTTACAGATGATCTACACAAACAGTATCAGATAGTGGAGCGCATAATTGCTCATTCCAATCAAAAATCAGCAGCTGGTCTTCCTGATTATTATTGCAAATGGCAGGGGCTTCCATACTCAGAGTGCAGCTGGGAGGATGGAGCTCTCATTTCCAAAAAGTTTCAGACATGCATCGATGAATATTTTAGCAGGAATCAGTCAAAAACGACACCTTTTAAAGATTGCAAAGTATTGAAACAAAGACCAAGATTTGTAGCTCTGAAGAAACAACCATCCTATATTGGAGGACATGAGGGCTTAGAACTGAGAGACTATCAGCTGAATGGTTTAAACTGGCTCGCTCACTCTTGGTGCAAAGGAAATAGTTGCATACTTGCTGATGAAATGGGCCTTGGGAAAACAATACAGACGATCTCATTTTTGAACTATTTGTTCCATGAACATCAGTTATATGGGCCGTTTCTACTAGTTGTCCCGCTCTCCACTCTGACTTCCTGGCAGAGGGAGATACAGACGTGGGCGTCTCAGATGAATGCTGTGGTTTACTTAGGCGACATTAACAGCAGAAACATGATAAGAACTCATGAATGGATGCATCCCCAGACCAAACGGTTAAAATTTAATATACTTTTAACAACGTATGAAATTTTATTGAAGGATAAGGCATTCCTTGGTGGTCTGAATTGGGCATTCATAGGTGTTGATGAAGCGCATCGATTAAAGAATGATGATTCCCTTCTGTACAAAACTTTAATCGACTTTAAATCTAACCATCGCCTTCTGATCACTGGAACCCCTCTACAGAACTCCCTGAAGGAGCTCTGGTCACTGCTGCACTTCATTATGCCGGAGAAGTTTTCTTCATGGGAAGATTTTGAAGAAGAACATGGCAAAGGCAGAGAATATGGTTATGCAAGCCTCCACAAGGAGCTTGAGCCATTTCTGTTACGCAGAGTTAAGAAAGATGTGGAAAAATCTCTTCCTGCCAAGGTGGAGCAGATTTTAAGAATGGAGATGAGTGCTTTACAGAAGCAATATTACAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCTTCCTGCCAAGGTGGAG
60.04
GATTGGCTGCTGCTTCCGTC
61.99
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTCTTCCTGCCAAGGTGGAG
60.04
ATTGGCTGCTGCTTCCGT
59.97
153
PCR template sequence:
TGTTACGCAGAGTTAAGAAAGATGTGGAAAAATCTCTTCCTGCCAAGGTGGAGCAGATTTTAAGAATGGAGATGAGTGCTTTACAGAAGCAATATTACAATCAGTCAGGTGATGATTGTGGGTCAGCATCAGGCTCTGGATCTGGCTCGAGTTCTGGCAGCAGCAGTGACGGAAGCAGCAGCCAATCCGGGAGCAGCGAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-miR-137-3p(1), mmu-miR-23b-3p(1), mmu-miR-7b-5p(1), mmu-miR-429-3p(1), mmu-miR-200c-3p(1), mmu-miR-7a-5p(1), mmu-miR-23a-3p(1), mmu-miR-149-5p(1), mmu-miR-127-5p(1), mmu-miR-182-5p(1), mmu-miR-370-3p(1), mmu-miR-383-5p(1), mmu-miR-1198-5p(1), mmu-miR-335-3p(1), mmu-miR-3470b(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
AGCAATATTACAATCAGTCAGGTGAT
siRNA sets
TGACTGATTGTAATATTGC, GACTGATTGTAATATTGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCHD1_2121_1_ORF_1
0.8634
0.156900508
1
3993
ORF sequence:
ATGCTTAGGAAGCAGCCACAGCAGGCCCAGCAGCAGCGCCCAGCTTCATCTAATAGTGGATCCGAAGAAGACTCGTCCAGCAGTGAAGACTCCGACGACTCGTCCAGCGGTGCCAAGAGGAAGAAGCACAATGATGAAGACTGGCAGATGTCTGGGTCCGGATCTCCATCTCAGTCTGGTTCAGACTCAGAATCTGAAGAAGAGCGAGATAAAAGCAGCTGCGACGGGACAGAGTCCGACTACGAGCCGAAAAACAAAGTCAGAAGCCGAAAGCCTCAGAATAGATCTAAGTCAAAAAATGGGAAAAAAATTCTTGGACAAAAAAAGAGACAGATTGATTCATCTGAGGATGAAGATGATGAAGATTATGATAATGATAAACGAAGCTCTCGCCGCCAAGCCACCGTCAATGTGAGCTACAAGGAGGATGAAGAAATGAAAACCGACTCCGATGACCTGCTGGAGGTCTGCGGCGAGGACGTCCCTCAGCCTGAGGACGAGGAGTTTGAGACAATAGAGAGGGTTATGGATTGCAGAGTGGGGCGGAAAGGAGCTACTGGTGCTACTACAACCATTTATGCTGTCGAAGCAGATGGTGACCCAAATGCAGGATTTGAAAGAAACAAAGAGCCAGGAGACATACAGTATTTAATTAAGTGGAAAGGATGGTCTCACATCCACAACACATGGGAGACAGAAGAGACCCTGAAGCAGCAGAACGTTAGAGGGATGAAAAAATTGGATAATTATAAGAAAAAAGATCAAGAGACGAAACGATGGCTGAAAAATGCTTCTCCAGAAGATGTGGAATATTATAATTGCCAGCAAGAGCTTACAGATGATCTACACAAACAGTATCAGATAGTGGAGCGCATAATTGCTCATTCCAATCAAAAATCAGCAGCTGGTCTTCCTGATTATTATTGCAAATGGCAGGGGCTTCCATACTCAGAGTGCAGCTGGGAGGATGGAGCTCTCATTTCCAAAAAGTTTCAGACATGCATCGATGAATATTTTAGCAGGAATCAGTCAAAAACGACACCTTTTAAAGATTGCAAAGTATTGAAACAAAGACCAAGATTTGTAGCTCTGAAGAAACAACCATCCTATATTGGAGGACATGAGGGCTTAGAACTGAGAGACTATCAGCTGAATGGTTTAAACTGGCTCGCTCACTCTTGGTGCAAAGGAAATAGTTGCATACTTGCTGATGAAATGGGCCTTGGGAAAACAATACAGACGATCTCATTTTTGAACTATTTGTTCCATGAACATCAGTTATATGGGCCGTTTCTACTAGTTGTCCCGCTCTCCACTCTGACTTCCTGGCAGAGGGAGATACAGACGTGGGCGTCTCAGATGAATGCTGTGGTTTACTTAGGCGACATTAACAGCAGAAACATGATAAGAACTCATGAATGGATGCATCCCCAGACCAAACGGTTAAAATTTAATATACTTTTAACAACGTATGAAATTTTATTGAAGGATAAGGCATTCCTTGGTGGTCTGAATTGGGCATTCATAGGTGTTGATGAAGCGCATCGATTAAAGAATGATGATTCCCTTCTGTACAAAACTTTAATCGACTTTAAATCTAACCATCGCCTTCTGATCACTGGAACCCCTCTACAGAACTCCCTGAAGGAGCTCTGGTCACTGCTGCACTTCATTATGCCGGAGAAGTTTTCTTCATGGGAAGATTTTGAAGAAGAACATGGCAAAGGCAGAGAATATGGTTATGCAAGCCTCCACAAGGAGCTTGAGCCATTTCTGTTACGCAGAGTTAAGAAAGATGTGGAAAAATCTCTTCCTGCCAAGGTGGAGCAGATTTTAAGAATGGAGATGAGTGCTTTACAGAAGCAATATTACAATCAGTCAGGTGATGATTGTGGGTCAGCATCAGGCTCTGGATCTGGCTCGAGTTCTGGCAGCAGCAGTGACGGAAGCAGCAGCCAATCCGGGAGCAGCGACTCTGATTCTGGCTCTGACTCAGGAAGTCAATCAGAGTCTGAATCAGACACATCCCGAGAGAACAAGGTTCAAGCAAAACCACCAAAAGTCGACGGAGCCGAGTTTTGGAAATCTAGCCCCAGTATTCTGGCTGTCCAGAGATCTGCAATGCTTAGGAAGCAGCCACAGCAGGCCCAGCAGCAGCGCCCAGCTTCATCTAATAGTGGATCCGAAGAAGACTCGTCCAGCAGTGAAGACTCCGACGACTCGTCCAGCGGTGCCAAGAGGAAGAAGCACAATGATGAAGACTGGCAGATGTCTGGGTCCGGATCTCCATCTCAGTCTGGTTCAGACTCAGAATCTGAAGAAGAGCGAGATAAAAGCAGCTGCGACGGGACAGAGTCCGACTACGAGCCGAAAAACAAAGTCAGAAGCCGAAAGCCTCAGAATAGATCTAAGTCAAAAAATGGGAAAAAAATTCTTGGACAAAAAAAGAGACAGATTGATTCATCTGAGGATGAAGATGATGAAGATTATGATAATGATAAACGAAGCTCTCGCCGCCAAGCCACCGTCAATGTGAGCTACAAGGAGGATGAAGAAATGAAAACCGACTCCGATGACCTGCTGGAGGTCTGCGGCGAGGACGTCCCTCAGCCTGAGGACGAGGAGTTTGAGACAATAGAGAGGGTTATGGATTGCAGAGTGGGGCGGAAAGGAGCTACTGGTGCTACTACAACCATTTATGCTGTCGAAGCAGATGGTGACCCAAATGCAGGATTTGAAAGAAACAAAGAGCCAGGAGACATACAGTATTTAATTAAGTGGAAAGGATGGTCTCACATCCACAACACATGGGAGACAGAAGAGACCCTGAAGCAGCAGAACGTTAGAGGGATGAAAAAATTGGATAATTATAAGAAAAAAGATCAAGAGACGAAACGATGGCTGAAAAATGCTTCTCCAGAAGATGTGGAATATTATAATTGCCAGCAAGAGCTTACAGATGATCTACACAAACAGTATCAGATAGTGGAGCGCATAATTGCTCATTCCAATCAAAAATCAGCAGCTGGTCTTCCTGATTATTATTGCAAATGGCAGGGGCTTCCATACTCAGAGTGCAGCTGGGAGGATGGAGCTCTCATTTCCAAAAAGTTTCAGACATGCATCGATGAATATTTTAGCAGGAATCAGTCAAAAACGACACCTTTTAAAGATTGCAAAGTATTGAAACAAAGACCAAGATTTGTAGCTCTGAAGAAACAACCATCCTATATTGGAGGACATGAGGGCTTAGAACTGAGAGACTATCAGCTGAATGGTTTAAACTGGCTCGCTCACTCTTGGTGCAAAGGAAATAGTTGCATACTTGCTGATGAAATGGGCCTTGGGAAAACAATACAGACGATCTCATTTTTGAACTATTTGTTCCATGAACATCAGTTATATGGGCCGTTTCTACTAGTTGTCCCGCTCTCCACTCTGACTTCCTGGCAGAGGGAGATACAGACGTGGGCGTCTCAGATGAATGCTGTGGTTTACTTAGGCGACATTAACAGCAGAAACATGATAAGAACTCATGAATGGATGCATCCCCAGACCAAACGGTTAAAATTTAATATACTTTTAACAACGTATGAAATTTTATTGAAGGATAAGGCATTCCTTGGTGGTCTGAATTGGGCATTCATAGGTGTTGATGAAGCGCATCGATTAAAGAATGATGATTCCCTTCTGTACAAAACTTTAATCGACTTTAAATCTAACCATCGCCTTCTGATCACTGGAACCCCTCTACAGAACTCCCTGAAGGAGCTCTGGTCACTGCTGCACTTCATTATGCCGGAGAAGTTTTCTTCATGGGAAGATTTTGAAGAAGAACATGGCAAAGGCAGAGAATATGGTTATGCAAGCCTCCACAAGGAGCTTGAGCCATTTCTGTTACGCAGAGTTAAGAAAGATGTGGAAAAATCTCTTCCTGCCAAGGTGGAGCAGATTTTAAGAATGGAGATGAGTGCTTTACAGAAGCAATATTAC
Peptide sequence:
MLRKQPQQAQQQRPASSNSGSEEDSSSSEDSDDSSSGAKRKKHNDEDWQMSGSGSPSQSGSDSESEEERDKSSCDGTESDYEPKNKVRSRKPQNRSKSKNGKKILGQKKRQIDSSEDEDDEDYDNDKRSSRRQATVNVSYKEDEEMKTDSDDLLEVCGEDVPQPEDEEFETIERVMDCRVGRKGATGATTTIYAVEADGDPNAGFERNKEPGDIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKKKDQETKRWLKNASPEDVEYYNCQQELTDDLHKQYQIVERIIAHSNQKSAAGLPDYYCKWQGLPYSECSWEDGALISKKFQTCIDEYFSRNQSKTTPFKDCKVLKQRPRFVALKKQPSYIGGHEGLELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWASQMNAVVYLGDINSRNMIRTHEWMHPQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGREYGYASLHKELEPFLLRRVKKDVEKSLPAKVEQILRMEMSALQKQYYNQSGDDCGSASGSGSGSSSGSSSDGSSSQSGSSDSDSGSDSGSQSESESDTSRENKVQAKPPKVDGAEFWKSSPSILAVQRSAMLRKQPQQAQQQRPASSNSGSEEDSSSSEDSDDSSSGAKRKKHNDEDWQMSGSGSPSQSGSDSESEEERDKSSCDGTESDYEPKNKVRSRKPQNRSKSKNGKKILGQKKRQIDSSEDEDDEDYDNDKRSSRRQATVNVSYKEDEEMKTDSDDLLEVCGEDVPQPEDEEFETIERVMDCRVGRKGATGATTTIYAVEADGDPNAGFERNKEPGDIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKKKDQETKRWLKNASPEDVEYYNCQQELTDDLHKQYQIVERIIAHSNQKSAAGLPDYYCKWQGLPYSECSWEDGALISKKFQTCIDEYFSRNQSKTTPFKDCKVLKQRPRFVALKKQPSYIGGHEGLELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWASQMNAVVYLGDINSRNMIRTHEWMHPQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGREYGYASLHKELEPFLLRRVKKDVEKSLPAKVEQILRMEMSALQKQYY
IRESfinder result
IRESfinder score
0.50018544
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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