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mmu_circNipbl_2040
Basic information of circular RNA
PanCircBase ID:
mmu_circNipbl_2040
mm39_Chr. Position ID:
chr15|8348940|8364754|-
Gene name:
Nipbl
Transcript:
ENSMUST00000052965.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
16
Exon/intron indexes:
31,30,29,28,27,26,25,24,23,22,21,20,19,18,17,16
Exon/intron offsets:
0,3029,3952,4195,4791,4988,6227,7542,8288,8935,10721,12932,13551,14124,15393,15727
Genomic length:
15814
Exon/intron sizes in nt:
99,135,147,99,103,215,90,144,133,83,139,101,81,152,232,87
Flanking exon/introns:
chr15:8347900-8348940|chr15:8364754-8366337
Splice length:
2040
Other database IDs:
CIRCpedia: MMU_CIRCpedia_31215, circAtlas: mmu-Nipbl_0025
Human Ortholog IDs:
Mature spliced Sequence:
CTTTCAACTGACAAAACTGTGAAAGTCCTAAATATATTGGAGAAGAATATTCAGGATGGATCAAAGCTTTCCACTTTGTTAAATCATAATAATGATACTGAAGAAGAAGAAAGATTGTGGAGAGACCTAATTATGGAAAGAGTTACAAAGTCAGCAGATGCCTGTCTTACAACTATCAACATTATGACATCTCCTAACATGCCAAAAGCTGTATACATTGAAGATGTAATTGAAAGGGTTATACAGTACACTAAGTTTCATTTACAGAACACACTCTATCCCCAGTATGACCCTGTTTACAGAGTAGATCCACATGGAGGAGGGTTATTAAGTTCAAAGGCCAAACGGGCTAAATGTTCTACTCATAAGCAGAGAGTAATTGTAATGCTTTACAACAAAGTTTGTGACATTGTTAGCAGTTTATCAGAATTGCTAGAGATACAGCTTCTTACAGACACAACAATTCTTCAGGTTTCATCAATGGGAATAACACCCTTTTTTGTGGAAAATGTCAGTGAACTACAATTGTGTGCCATTAAGTTAGTCACTGCAGTATTTTCAAGATATGAAAAGCATAGGCAGTTAATATTGGAAGAAATTTTTACTTCACTTGCAAGATTACCAACTAGCAAGAGAAGTTTAAGGAATTTCAGGTTAAATAGTAGTGATGTGGATGGAGAACCTATGTATATTCAGATGGTTACAGCTCTAGTTTTACAACTTATTCAGTGCGTAGTTCACTTACCATCATCGGAGAAGGATCCTAATTCAGAAGAAGACTCAAACAAAAAAGTTGATCAGGATGTTGTCATTACGAACTCTTACGAAACAGCTATGAGAACAGCCCAAAACTTTCTCTCCATCTTTCTTAAAAAATGTGGTAGTAAACAAGGAGAAGAAGATTACAGACCGCTTTTTGAAAACTTTGTTCAAGACCTTCTCTCAACAGTCAATAAGCCCGAGTGGCCGGCTGCTGAACTACTCCTTAGCTTGTTAGGGAGGCTGTTGGTTCATCAGTTCAGTAACAAGTCAACAGAAATGGCTTTAAGAGTGGCATCTCTTGATTACCTTGGGACTGTTGCTGCGCGACTGAGAAAAGATGCTGTCACCAGCAAGATGGATCAAGGGTCTATAGAACGAATTTTAAAACAGGTTTCTGGAGGAGAAGATGAGATCCAACAATTGCAAAAAGCATTGCTTGATTATCTGGATGAGAACACTGAAACTGACCCTTCGCTAGTGTTTTCTCGTAAATTCTATATAGCCCAGTGGTTCCGTGACACAACTCTGGAAACAGAAAAAGCAATGAAATCACAAAAAGATGAAGAATCATCTGACGCAACACATCATGCAAAAGAACTTGAGACAACTGGGCAGATCATGCATCGCGCTGAGAACCGGAAAAAGTTTCTTCGAAGCATTATCAAAACCACACCTTCTCAGTTCAGCACATTAAAGATGAACTCTGACACTGTGGACTATGATGATGCGTGCTTGATTGTTCGATATTTGGCCTCTATGAGGCCGTTTGCCCAGAGCTTTGATATTTATTTGACACAGATACTACGAGTTCTTGGTGAAAATGCAATTGCCGTTCGAACAAAAGCCATGAAGTGTTTGTCTGAGGTTGTTGCTGTAGACCCCAGTATTCTAGCAAGGCTTGACATGCAGCGCGGAGTTCATGGGCGACTAATGGATAACTCCACTAGTGTTCGAGAGGCAGCAGTGGAATTGCTAGGTCGCTTTGTCCTGTGTCGCCCTCAGCTTGCTGAGCAGTATTATGACATGCTGATTGAAAGAATATTGGATACTGGGATCAGTGTCAGGAAAAGAGTAATAAAGATTTTAAGAGACATCTGTATTGAACAACCAACATTTCCAAAAATTACAGAAATGTGTGTAAAAATGATTCGTAGAGTCAATGATGAAGAGGGCATTAAGAAATTAGTAAATGAAACATTCCAAAAGCTCTGGTTTACTCCAACTCCACATAATGACAAAGAAGCAATGACAAGGAAGATTTTAAACATCACTGATGTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTCTGGTTTACTCCAACTCCA
59.96
TGGAAAGCTTTGATCCATCCTGA
59.99
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTCTGGTTTACTCCAACTCCA
59.96
AGTGGAAAGCTTTGATCCATCCT
59.99
148
PCR template sequence:
GAAATTAGTAAATGAAACATTCCAAAAGCTCTGGTTTACTCCAACTCCACATAATGACAAAGAAGCAATGACAAGGAAGATTTTAAACATCACTGATGTGCTTTCAACTGACAAAACTGTGAAAGTCCTAAATATATTGGAGAAGAATATTCAGGATGGATCAAAGCTTTCCACTTTGTTAAATCATAATAATGATACTG
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-200b-3p(2), mmu-miR-200c-3p(2), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-429-3p(1), mmu-miR-375-3p(1), mmu-miR-135a-5p(1), mmu-miR-30e-5p(1), mmu-miR-30a-5p(1), mmu-miR-185-5p(1), mmu-miR-30d-5p(1), mmu-miR-212-3p(1), mmu-miR-183-5p(1), mmu-miR-27a-5p(1), mmu-miR-680(1), mmu-miR-129-5p(1), mmu-miR-207(1), mmu-miR-5101(1), mmu-miR-335-3p(1), mmu-miR-697(1), mmu-miR-3105-3p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CATCACTGATGTGCTTTCAACTGACA
siRNA sets
TCAGTTGAAAGCACATCAG, GTTGAAAGCACATCAGTGA, AGTTGAAAGCACATCAGTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNIPBL_2040_ORF_1
0.9438
0.008311691
1
3948
ORF sequence:
ATGGAAAGAGTTACAAAGTCAGCAGATGCCTGTCTTACAACTATCAACATTATGACATCTCCTAACATGCCAAAAGCTGTATACATTGAAGATGTAATTGAAAGGGTTATACAGTACACTAAGTTTCATTTACAGAACACACTCTATCCCCAGTATGACCCTGTTTACAGAGTAGATCCACATGGAGGAGGGTTATTAAGTTCAAAGGCCAAACGGGCTAAATGTTCTACTCATAAGCAGAGAGTAATTGTAATGCTTTACAACAAAGTTTGTGACATTGTTAGCAGTTTATCAGAATTGCTAGAGATACAGCTTCTTACAGACACAACAATTCTTCAGGTTTCATCAATGGGAATAACACCCTTTTTTGTGGAAAATGTCAGTGAACTACAATTGTGTGCCATTAAGTTAGTCACTGCAGTATTTTCAAGATATGAAAAGCATAGGCAGTTAATATTGGAAGAAATTTTTACTTCACTTGCAAGATTACCAACTAGCAAGAGAAGTTTAAGGAATTTCAGGTTAAATAGTAGTGATGTGGATGGAGAACCTATGTATATTCAGATGGTTACAGCTCTAGTTTTACAACTTATTCAGTGCGTAGTTCACTTACCATCATCGGAGAAGGATCCTAATTCAGAAGAAGACTCAAACAAAAAAGTTGATCAGGATGTTGTCATTACGAACTCTTACGAAACAGCTATGAGAACAGCCCAAAACTTTCTCTCCATCTTTCTTAAAAAATGTGGTAGTAAACAAGGAGAAGAAGATTACAGACCGCTTTTTGAAAACTTTGTTCAAGACCTTCTCTCAACAGTCAATAAGCCCGAGTGGCCGGCTGCTGAACTACTCCTTAGCTTGTTAGGGAGGCTGTTGGTTCATCAGTTCAGTAACAAGTCAACAGAAATGGCTTTAAGAGTGGCATCTCTTGATTACCTTGGGACTGTTGCTGCGCGACTGAGAAAAGATGCTGTCACCAGCAAGATGGATCAAGGGTCTATAGAACGAATTTTAAAACAGGTTTCTGGAGGAGAAGATGAGATCCAACAATTGCAAAAAGCATTGCTTGATTATCTGGATGAGAACACTGAAACTGACCCTTCGCTAGTGTTTTCTCGTAAATTCTATATAGCCCAGTGGTTCCGTGACACAACTCTGGAAACAGAAAAAGCAATGAAATCACAAAAAGATGAAGAATCATCTGACGCAACACATCATGCAAAAGAACTTGAGACAACTGGGCAGATCATGCATCGCGCTGAGAACCGGAAAAAGTTTCTTCGAAGCATTATCAAAACCACACCTTCTCAGTTCAGCACATTAAAGATGAACTCTGACACTGTGGACTATGATGATGCGTGCTTGATTGTTCGATATTTGGCCTCTATGAGGCCGTTTGCCCAGAGCTTTGATATTTATTTGACACAGATACTACGAGTTCTTGGTGAAAATGCAATTGCCGTTCGAACAAAAGCCATGAAGTGTTTGTCTGAGGTTGTTGCTGTAGACCCCAGTATTCTAGCAAGGCTTGACATGCAGCGCGGAGTTCATGGGCGACTAATGGATAACTCCACTAGTGTTCGAGAGGCAGCAGTGGAATTGCTAGGTCGCTTTGTCCTGTGTCGCCCTCAGCTTGCTGAGCAGTATTATGACATGCTGATTGAAAGAATATTGGATACTGGGATCAGTGTCAGGAAAAGAGTAATAAAGATTTTAAGAGACATCTGTATTGAACAACCAACATTTCCAAAAATTACAGAAATGTGTGTAAAAATGATTCGTAGAGTCAATGATGAAGAGGGCATTAAGAAATTAGTAAATGAAACATTCCAAAAGCTCTGGTTTACTCCAACTCCACATAATGACAAAGAAGCAATGACAAGGAAGATTTTAAACATCACTGATGTGCTTTCAACTGACAAAACTGTGAAAGTCCTAAATATATTGGAGAAGAATATTCAGGATGGATCAAAGCTTTCCACTTTGTTAAATCATAATAATGATACTGAAGAAGAAGAAAGATTGTGGAGAGACCTAATTATGGAAAGAGTTACAAAGTCAGCAGATGCCTGTCTTACAACTATCAACATTATGACATCTCCTAACATGCCAAAAGCTGTATACATTGAAGATGTAATTGAAAGGGTTATACAGTACACTAAGTTTCATTTACAGAACACACTCTATCCCCAGTATGACCCTGTTTACAGAGTAGATCCACATGGAGGAGGGTTATTAAGTTCAAAGGCCAAACGGGCTAAATGTTCTACTCATAAGCAGAGAGTAATTGTAATGCTTTACAACAAAGTTTGTGACATTGTTAGCAGTTTATCAGAATTGCTAGAGATACAGCTTCTTACAGACACAACAATTCTTCAGGTTTCATCAATGGGAATAACACCCTTTTTTGTGGAAAATGTCAGTGAACTACAATTGTGTGCCATTAAGTTAGTCACTGCAGTATTTTCAAGATATGAAAAGCATAGGCAGTTAATATTGGAAGAAATTTTTACTTCACTTGCAAGATTACCAACTAGCAAGAGAAGTTTAAGGAATTTCAGGTTAAATAGTAGTGATGTGGATGGAGAACCTATGTATATTCAGATGGTTACAGCTCTAGTTTTACAACTTATTCAGTGCGTAGTTCACTTACCATCATCGGAGAAGGATCCTAATTCAGAAGAAGACTCAAACAAAAAAGTTGATCAGGATGTTGTCATTACGAACTCTTACGAAACAGCTATGAGAACAGCCCAAAACTTTCTCTCCATCTTTCTTAAAAAATGTGGTAGTAAACAAGGAGAAGAAGATTACAGACCGCTTTTTGAAAACTTTGTTCAAGACCTTCTCTCAACAGTCAATAAGCCCGAGTGGCCGGCTGCTGAACTACTCCTTAGCTTGTTAGGGAGGCTGTTGGTTCATCAGTTCAGTAACAAGTCAACAGAAATGGCTTTAAGAGTGGCATCTCTTGATTACCTTGGGACTGTTGCTGCGCGACTGAGAAAAGATGCTGTCACCAGCAAGATGGATCAAGGGTCTATAGAACGAATTTTAAAACAGGTTTCTGGAGGAGAAGATGAGATCCAACAATTGCAAAAAGCATTGCTTGATTATCTGGATGAGAACACTGAAACTGACCCTTCGCTAGTGTTTTCTCGTAAATTCTATATAGCCCAGTGGTTCCGTGACACAACTCTGGAAACAGAAAAAGCAATGAAATCACAAAAAGATGAAGAATCATCTGACGCAACACATCATGCAAAAGAACTTGAGACAACTGGGCAGATCATGCATCGCGCTGAGAACCGGAAAAAGTTTCTTCGAAGCATTATCAAAACCACACCTTCTCAGTTCAGCACATTAAAGATGAACTCTGACACTGTGGACTATGATGATGCGTGCTTGATTGTTCGATATTTGGCCTCTATGAGGCCGTTTGCCCAGAGCTTTGATATTTATTTGACACAGATACTACGAGTTCTTGGTGAAAATGCAATTGCCGTTCGAACAAAAGCCATGAAGTGTTTGTCTGAGGTTGTTGCTGTAGACCCCAGTATTCTAGCAAGGCTTGACATGCAGCGCGGAGTTCATGGGCGACTAATGGATAACTCCACTAGTGTTCGAGAGGCAGCAGTGGAATTGCTAGGTCGCTTTGTCCTGTGTCGCCCTCAGCTTGCTGAGCAGTATTATGACATGCTGATTGAAAGAATATTGGATACTGGGATCAGTGTCAGGAAAAGAGTAATAAAGATTTTAAGAGACATCTGTATTGAACAACCAACATTTCCAAAAATTACAGAAATGTGTGTAAAAATGATTCGTAGAGTCAATGATGAAGAGGGCATTAAGAAATTAGTAAATGAAACATTCCAAAAGCTCTGGTTTACTCCAACTCCACATAATGACAAAGAAGCAATGACAAGGAAGATTTTAAACATCACTGATGTG
Peptide sequence:
MERVTKSADACLTTINIMTSPNMPKAVYIEDVIERVIQYTKFHLQNTLYPQYDPVYRVDPHGGGLLSSKAKRAKCSTHKQRVIVMLYNKVCDIVSSLSELLEIQLLTDTTILQVSSMGITPFFVENVSELQLCAIKLVTAVFSRYEKHRQLILEEIFTSLARLPTSKRSLRNFRLNSSDVDGEPMYIQMVTALVLQLIQCVVHLPSSEKDPNSEEDSNKKVDQDVVITNSYETAMRTAQNFLSIFLKKCGSKQGEEDYRPLFENFVQDLLSTVNKPEWPAAELLLSLLGRLLVHQFSNKSTEMALRVASLDYLGTVAARLRKDAVTSKMDQGSIERILKQVSGGEDEIQQLQKALLDYLDENTETDPSLVFSRKFYIAQWFRDTTLETEKAMKSQKDEESSDATHHAKELETTGQIMHRAENRKKFLRSIIKTTPSQFSTLKMNSDTVDYDDACLIVRYLASMRPFAQSFDIYLTQILRVLGENAIAVRTKAMKCLSEVVAVDPSILARLDMQRGVHGRLMDNSTSVREAAVELLGRFVLCRPQLAEQYYDMLIERILDTGISVRKRVIKILRDICIEQPTFPKITEMCVKMIRRVNDEEGIKKLVNETFQKLWFTPTPHNDKEAMTRKILNITDVLSTDKTVKVLNILEKNIQDGSKLSTLLNHNNDTEEEERLWRDLIMERVTKSADACLTTINIMTSPNMPKAVYIEDVIERVIQYTKFHLQNTLYPQYDPVYRVDPHGGGLLSSKAKRAKCSTHKQRVIVMLYNKVCDIVSSLSELLEIQLLTDTTILQVSSMGITPFFVENVSELQLCAIKLVTAVFSRYEKHRQLILEEIFTSLARLPTSKRSLRNFRLNSSDVDGEPMYIQMVTALVLQLIQCVVHLPSSEKDPNSEEDSNKKVDQDVVITNSYETAMRTAQNFLSIFLKKCGSKQGEEDYRPLFENFVQDLLSTVNKPEWPAAELLLSLLGRLLVHQFSNKSTEMALRVASLDYLGTVAARLRKDAVTSKMDQGSIERILKQVSGGEDEIQQLQKALLDYLDENTETDPSLVFSRKFYIAQWFRDTTLETEKAMKSQKDEESSDATHHAKELETTGQIMHRAENRKKFLRSIIKTTPSQFSTLKMNSDTVDYDDACLIVRYLASMRPFAQSFDIYLTQILRVLGENAIAVRTKAMKCLSEVVAVDPSILARLDMQRGVHGRLMDNSTSVREAAVELLGRFVLCRPQLAEQYYDMLIERILDTGISVRKRVIKILRDICIEQPTFPKITEMCVKMIRRVNDEEGIKKLVNETFQKLWFTPTPHNDKEAMTRKILNITDV
IRESfinder result
IRESfinder score
0.716345179
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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