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mmu_circNotch1_1998
Basic information of circular RNA
PanCircBase ID:
mmu_circNotch1_1998
mm39_Chr. Position ID:
chr2|26363692|26371705|-
Gene name:
Notch1
Transcript:
ENSMUST00000028288.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
13
Exon/intron indexes:
17,16,15,14,13,12,11,10,9,8,7,6,5
Exon/intron offsets:
0,440,2393,2667,3266,4199,4389,4926,5766,6190,6543,7293,7890
Genomic length:
8013
Exon/intron sizes in nt:
15,31,20,11,41,46,19,30,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr2:26363024-26363692|chr2:26371705-26374279
Splice length:
1998
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTTTGCTGGACAGAACTGTGAAGAAAATGTGGATGACTGTCCAGGAAACAACTGCAAGAATGGGGGTGCCTGTGTGGACGGCGTGAATACCTACAATTGCCGCTGCCCACCGGAGTGGACGGGTCAGTACTGTACAGAGGATGTGGACGAATGTCAGCTCATGCCCAATGCCTGCCAGAATGGCGGAACCTGCCACAACACACACGGCGGCTACAACTGTGTGTGTGTCAATGGGTGGACTGGCGAGGACTGCAGTGAGAACATTGATGACTGTGCCAGTGCCGCCTGTTTCCAGGGTGCCACTTGCCACGACCGTGTGGCTTCCTTCTACTGCGAATGTCCGCATGGGCGCACAGGTCTGCTGTGCCACCTCAACGATGCGTGCATCAGCAACCCCTGCAACGAGGGCTCCAACTGTGACACCAACCCTGTCAACGGCAAAGCCATCTGCACCTGCCCCTCGGGGTACACAGGGCCAGCCTGCAGCCAGGACGTGGATGAGTGTGCTCTGGGTGCCAACCCTTGTGAGCACGCAGGCAAATGCCTCAACACACTGGGTTCTTTTGAGTGCCAGTGTCTACAGGGCTACACGGGACCCCGCTGTGAGATTGATGTTAATGAGTGCATCTCCAACCCATGTCAGAATGATGCCACTTGCCTGGACCAGATTGGGGAGTTCCAATGCATATGTATGCCAGGTTATGAAGGTGTATACTGTGAAATCAACACGGATGAGTGCGCCAGCAGCCCCTGTCTGCACAATGGCCACTGCATGGACAAGATCAATGAGTTCCAATGTCAGTGCCCCAAAGGCTTCAACGGGCACCTGTGCCAGTATGATGTGGATGAGTGTGCCAGCACACCATGCAAGAACGGTGCCAAGTGCCTGGATGGGCCCAACACCTATACCTGCGTGTGTACAGAAGGTTACACAGGGACCCACTGCGAAGTGGACATTGACGAGTGTGACCCTGACCCCTGCCACTATGGTTCCTGTAAGGATGGTGTGGCCACCTTTACCTGCCTGTGCCAGCCAGGCTACACAGGCCATCACTGTGAGACCAACATCAATGAGTGCCACAGCCAACCGTGCCGCCATGGGGGCACCTGCCAGGACCGTGACAACTCCTACCTCTGCTTATGCCTCAAGGGAACCACAGGGCCCAACTGTGAGATCAACCTGGATGACTGCGCCAGCAACCCCTGTGACTCTGGCACCTGTCTGGACAAGATTGATGGCTACGAATGTGCCTGTGAACCAGGCTACACAGGAAGCATGTGTAACGTCAACATTGACGAATGTGCGGGCAGCCCCTGCCACAACGGGGGCACTTGTGAGGATGGCATCGCGGGCTTCACTTGCCGCTGCCCCGAGGGCTACCATGACCCCACGTGCCTGTCCGAGGTCAACGAGTGCAACAGTAACCCCTGCATCCACGGAGCTTGCCGGGATGGCCTCAATGGGTACAAGTGTGACTGTGCCCCTGGGTGGAGTGGAACAAACTGTGACATCAACAACAACGAGTGTGAGTCCAACCCTTGTGTCAACGGTGGCACCTGCAAGGACATGACCAGTGGCTACGTATGCACCTGCCGAGAAGGCTTCAGTGGCCCTAATTGCCAGACCAACATCAACGAATGTGCCTCCAACCCCTGCCTGAACCAGGGGACCTGCATTGATGATGTCGCTGGATACAAGTGCAACTGTCCTCTGCCATATACAGGAGCCACGTGTGAGGTGGTGTTGGCCCCATGTGCTACCAGCCCCTGCAAAAACAGCGGGGTATGCAAGGAGTCTGAAGACTATGAGAGTTTTTCCTGTGTCTGTCCCACAGGCTGGCAAGGTCAAACCTGCGAGGTTGACATCAATGAGTGTGTGAAAAGCCCATGTCGCCATGGGGCCTCCTGCCAGAACACCAATGGCAGCTACCGCTGCCTCTGCCAGGCCGGCTATACAGGTCGCAACTGTGAGAGTGACATCGATGACTGCCGCCCCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTCCTGCCAGAACACCAAT
59.96
ACCCCCATTCTTGCAGTTGT
59.81
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTGCCAGAACACCAATGG
60.25
ACCCCCATTCTTGCAGTTGT
59.81
162
PCR template sequence:
GGGGCCTCCTGCCAGAACACCAATGGCAGCTACCGCTGCCTCTGCCAGGCCGGCTATACAGGTCGCAACTGTGAGAGTGACATCGATGACTGCCGCCCCAGTTTTGCTGGACAGAACTGTGAAGAAAATGTGGATGACTGTCCAGGAAACAACTGCAAGAATGGGGGTGCCTGTGTGGACGGCGTGAATACCTACAATTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
27
Interacting miRNAs (#binding sites)
mmu-miR-298-5p(3), mmu-let-7a-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-101a-3p(1), mmu-let-7c-5p(1), mmu-miR-33-5p(1), mmu-miR-328-3p(1), mmu-miR-216a-5p(1), mmu-miR-101b-3p(1), mmu-miR-709(1), mmu-miR-138-5p(1), mmu-miR-181b-5p(1), mmu-miR-128-3p(1), mmu-let-7d-5p(1), mmu-miR-22-3p(1), mmu-miR-96-5p(1), mmu-miR-98-5p(1), mmu-miR-680(1), mmu-miR-29b-2-5p(1), mmu-miR-129-5p(1), mmu-miR-673-5p(1), mmu-miR-490-3p(1), mmu-miR-296-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GACTGCCGCCCCAGTTTTGCTGGACA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNOTCH1_1998_ORF_1
1.2612
0.348669762
1
3834
ORF sequence:
ATGCCCAATGCCTGCCAGAATGGCGGAACCTGCCACAACACACACGGCGGCTACAACTGTGTGTGTGTCAATGGGTGGACTGGCGAGGACTGCAGTGAGAACATTGATGACTGTGCCAGTGCCGCCTGTTTCCAGGGTGCCACTTGCCACGACCGTGTGGCTTCCTTCTACTGCGAATGTCCGCATGGGCGCACAGGTCTGCTGTGCCACCTCAACGATGCGTGCATCAGCAACCCCTGCAACGAGGGCTCCAACTGTGACACCAACCCTGTCAACGGCAAAGCCATCTGCACCTGCCCCTCGGGGTACACAGGGCCAGCCTGCAGCCAGGACGTGGATGAGTGTGCTCTGGGTGCCAACCCTTGTGAGCACGCAGGCAAATGCCTCAACACACTGGGTTCTTTTGAGTGCCAGTGTCTACAGGGCTACACGGGACCCCGCTGTGAGATTGATGTTAATGAGTGCATCTCCAACCCATGTCAGAATGATGCCACTTGCCTGGACCAGATTGGGGAGTTCCAATGCATATGTATGCCAGGTTATGAAGGTGTATACTGTGAAATCAACACGGATGAGTGCGCCAGCAGCCCCTGTCTGCACAATGGCCACTGCATGGACAAGATCAATGAGTTCCAATGTCAGTGCCCCAAAGGCTTCAACGGGCACCTGTGCCAGTATGATGTGGATGAGTGTGCCAGCACACCATGCAAGAACGGTGCCAAGTGCCTGGATGGGCCCAACACCTATACCTGCGTGTGTACAGAAGGTTACACAGGGACCCACTGCGAAGTGGACATTGACGAGTGTGACCCTGACCCCTGCCACTATGGTTCCTGTAAGGATGGTGTGGCCACCTTTACCTGCCTGTGCCAGCCAGGCTACACAGGCCATCACTGTGAGACCAACATCAATGAGTGCCACAGCCAACCGTGCCGCCATGGGGGCACCTGCCAGGACCGTGACAACTCCTACCTCTGCTTATGCCTCAAGGGAACCACAGGGCCCAACTGTGAGATCAACCTGGATGACTGCGCCAGCAACCCCTGTGACTCTGGCACCTGTCTGGACAAGATTGATGGCTACGAATGTGCCTGTGAACCAGGCTACACAGGAAGCATGTGTAACGTCAACATTGACGAATGTGCGGGCAGCCCCTGCCACAACGGGGGCACTTGTGAGGATGGCATCGCGGGCTTCACTTGCCGCTGCCCCGAGGGCTACCATGACCCCACGTGCCTGTCCGAGGTCAACGAGTGCAACAGTAACCCCTGCATCCACGGAGCTTGCCGGGATGGCCTCAATGGGTACAAGTGTGACTGTGCCCCTGGGTGGAGTGGAACAAACTGTGACATCAACAACAACGAGTGTGAGTCCAACCCTTGTGTCAACGGTGGCACCTGCAAGGACATGACCAGTGGCTACGTATGCACCTGCCGAGAAGGCTTCAGTGGCCCTAATTGCCAGACCAACATCAACGAATGTGCCTCCAACCCCTGCCTGAACCAGGGGACCTGCATTGATGATGTCGCTGGATACAAGTGCAACTGTCCTCTGCCATATACAGGAGCCACGTGTGAGGTGGTGTTGGCCCCATGTGCTACCAGCCCCTGCAAAAACAGCGGGGTATGCAAGGAGTCTGAAGACTATGAGAGTTTTTCCTGTGTCTGTCCCACAGGCTGGCAAGGTCAAACCTGCGAGGTTGACATCAATGAGTGTGTGAAAAGCCCATGTCGCCATGGGGCCTCCTGCCAGAACACCAATGGCAGCTACCGCTGCCTCTGCCAGGCCGGCTATACAGGTCGCAACTGTGAGAGTGACATCGATGACTGCCGCCCCAGTTTTGCTGGACAGAACTGTGAAGAAAATGTGGATGACTGTCCAGGAAACAACTGCAAGAATGGGGGTGCCTGTGTGGACGGCGTGAATACCTACAATTGCCGCTGCCCACCGGAGTGGACGGGTCAGTACTGTACAGAGGATGTGGACGAATGTCAGCTCATGCCCAATGCCTGCCAGAATGGCGGAACCTGCCACAACACACACGGCGGCTACAACTGTGTGTGTGTCAATGGGTGGACTGGCGAGGACTGCAGTGAGAACATTGATGACTGTGCCAGTGCCGCCTGTTTCCAGGGTGCCACTTGCCACGACCGTGTGGCTTCCTTCTACTGCGAATGTCCGCATGGGCGCACAGGTCTGCTGTGCCACCTCAACGATGCGTGCATCAGCAACCCCTGCAACGAGGGCTCCAACTGTGACACCAACCCTGTCAACGGCAAAGCCATCTGCACCTGCCCCTCGGGGTACACAGGGCCAGCCTGCAGCCAGGACGTGGATGAGTGTGCTCTGGGTGCCAACCCTTGTGAGCACGCAGGCAAATGCCTCAACACACTGGGTTCTTTTGAGTGCCAGTGTCTACAGGGCTACACGGGACCCCGCTGTGAGATTGATGTTAATGAGTGCATCTCCAACCCATGTCAGAATGATGCCACTTGCCTGGACCAGATTGGGGAGTTCCAATGCATATGTATGCCAGGTTATGAAGGTGTATACTGTGAAATCAACACGGATGAGTGCGCCAGCAGCCCCTGTCTGCACAATGGCCACTGCATGGACAAGATCAATGAGTTCCAATGTCAGTGCCCCAAAGGCTTCAACGGGCACCTGTGCCAGTATGATGTGGATGAGTGTGCCAGCACACCATGCAAGAACGGTGCCAAGTGCCTGGATGGGCCCAACACCTATACCTGCGTGTGTACAGAAGGTTACACAGGGACCCACTGCGAAGTGGACATTGACGAGTGTGACCCTGACCCCTGCCACTATGGTTCCTGTAAGGATGGTGTGGCCACCTTTACCTGCCTGTGCCAGCCAGGCTACACAGGCCATCACTGTGAGACCAACATCAATGAGTGCCACAGCCAACCGTGCCGCCATGGGGGCACCTGCCAGGACCGTGACAACTCCTACCTCTGCTTATGCCTCAAGGGAACCACAGGGCCCAACTGTGAGATCAACCTGGATGACTGCGCCAGCAACCCCTGTGACTCTGGCACCTGTCTGGACAAGATTGATGGCTACGAATGTGCCTGTGAACCAGGCTACACAGGAAGCATGTGTAACGTCAACATTGACGAATGTGCGGGCAGCCCCTGCCACAACGGGGGCACTTGTGAGGATGGCATCGCGGGCTTCACTTGCCGCTGCCCCGAGGGCTACCATGACCCCACGTGCCTGTCCGAGGTCAACGAGTGCAACAGTAACCCCTGCATCCACGGAGCTTGCCGGGATGGCCTCAATGGGTACAAGTGTGACTGTGCCCCTGGGTGGAGTGGAACAAACTGTGACATCAACAACAACGAGTGTGAGTCCAACCCTTGTGTCAACGGTGGCACCTGCAAGGACATGACCAGTGGCTACGTATGCACCTGCCGAGAAGGCTTCAGTGGCCCTAATTGCCAGACCAACATCAACGAATGTGCCTCCAACCCCTGCCTGAACCAGGGGACCTGCATTGATGATGTCGCTGGATACAAGTGCAACTGTCCTCTGCCATATACAGGAGCCACGTGTGAGGTGGTGTTGGCCCCATGTGCTACCAGCCCCTGCAAAAACAGCGGGGTATGCAAGGAGTCTGAAGACTATGAGAGTTTTTCCTGTGTCTGTCCCACAGGCTGGCAAGGTCAAACCTGCGAGGTTGACATCAATGAGTGTGTGAAAAGCCCATGTCGCCATGGGGCCTCCTGCCAGAACACCAATGGCAGCTACCGCTGCCTCTGCCAGGCCGGCTATACAGGTCGCAACTGTGAGAGTGACATCGATGACTGCCGCCCC
Peptide sequence:
MPNACQNGGTCHNTHGGYNCVCVNGWTGEDCSENIDDCASAACFQGATCHDRVASFYCECPHGRTGLLCHLNDACISNPCNEGSNCDTNPVNGKAICTCPSGYTGPACSQDVDECALGANPCEHAGKCLNTLGSFECQCLQGYTGPRCEIDVNECISNPCQNDATCLDQIGEFQCICMPGYEGVYCEINTDECASSPCLHNGHCMDKINEFQCQCPKGFNGHLCQYDVDECASTPCKNGAKCLDGPNTYTCVCTEGYTGTHCEVDIDECDPDPCHYGSCKDGVATFTCLCQPGYTGHHCETNINECHSQPCRHGGTCQDRDNSYLCLCLKGTTGPNCEINLDDCASNPCDSGTCLDKIDGYECACEPGYTGSMCNVNIDECAGSPCHNGGTCEDGIAGFTCRCPEGYHDPTCLSEVNECNSNPCIHGACRDGLNGYKCDCAPGWSGTNCDINNNECESNPCVNGGTCKDMTSGYVCTCREGFSGPNCQTNINECASNPCLNQGTCIDDVAGYKCNCPLPYTGATCEVVLAPCATSPCKNSGVCKESEDYESFSCVCPTGWQGQTCEVDINECVKSPCRHGASCQNTNGSYRCLCQAGYTGRNCESDIDDCRPSFAGQNCEENVDDCPGNNCKNGGACVDGVNTYNCRCPPEWTGQYCTEDVDECQLMPNACQNGGTCHNTHGGYNCVCVNGWTGEDCSENIDDCASAACFQGATCHDRVASFYCECPHGRTGLLCHLNDACISNPCNEGSNCDTNPVNGKAICTCPSGYTGPACSQDVDECALGANPCEHAGKCLNTLGSFECQCLQGYTGPRCEIDVNECISNPCQNDATCLDQIGEFQCICMPGYEGVYCEINTDECASSPCLHNGHCMDKINEFQCQCPKGFNGHLCQYDVDECASTPCKNGAKCLDGPNTYTCVCTEGYTGTHCEVDIDECDPDPCHYGSCKDGVATFTCLCQPGYTGHHCETNINECHSQPCRHGGTCQDRDNSYLCLCLKGTTGPNCEINLDDCASNPCDSGTCLDKIDGYECACEPGYTGSMCNVNIDECAGSPCHNGGTCEDGIAGFTCRCPEGYHDPTCLSEVNECNSNPCIHGACRDGLNGYKCDCAPGWSGTNCDINNNECESNPCVNGGTCKDMTSGYVCTCREGFSGPNCQTNINECASNPCLNQGTCIDDVAGYKCNCPLPYTGATCEVVLAPCATSPCKNSGVCKESEDYESFSCVCPTGWQGQTCEVDINECVKSPCRHGASCQNTNGSYRCLCQAGYTGRNCESDIDDCRP
IRESfinder result
IRESfinder score
0.259818105
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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