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mmu_circHnf1b_798
Basic information of circular RNA
PanCircBase ID:
mmu_circHnf1b_798
mm39_Chr. Position ID:
chr11|83752541|83780010|+
Gene name:
Hnf1b
Transcript:
ENSMUST00000021016.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
3,4,5,6
Exon/intron offsets:
0,2227,20937,27333
Genomic length:
27469
Exon/intron sizes in nt:
2,65,23,61,61,136
Flanking exon/introns:
chr11:83746929-83752541|chr11:83780010-83784207
Splice length:
798
Other database IDs:
circAtlas: mmu-Hnf1b_0012
Human Ortholog IDs:
Mature spliced Sequence:
AGTTCAACCAGACAGTCCAGAGCTCTGGAAACATGACAGACAAAAGCAGTCAGGATCAGCTGCTGTTTCTCTTTCCAGAGTTCAGTCAACAGAACCAGGGGCCTGGGCAGTCGGAGGACACCTGCTCCGAGCCCACCAACAAGAAGATGCGCCGCAACCGGTTTAAATGGGGGCCCGCATCCCAGCAAATTTTGTACCAGGCCTACGACCGGCAAAAGAATCCCAGCAAGGAAGAGAGGGAGGCCTTAGTGGAGGAGTGTAACAGGGCAGAATGTTTGCAACGAGGGGTCTCCCCTTCCAAAGCCCACGGCCTAGGCTCCAACTTGGTCACGGAGGTCCGTGTCTACAACTGGTTCGCAAACCGCCGGAAGGAAGAGGCGTTCAGGCAGAAGCTGGCCATGGATGCCTATAGCTCCAACCAGACGCACAACCTGAACCCCCTGCTCACCCATGGCTCCCCTCACCATCAGCCAAGCTCCTCTCCACCCAACAAGATGTCAGGAGTGCGCTACAACCAGCCGGGAAACAATGAGGTCACTTCCTCTTCGACAATCAGTCACCATGGTAACAGTGCCATGGTGACCAGCCAGTCGGTTTTACAGCAAGTCTCCCCAGCCAGCCTGGACCCAGGCCACAGTCTCCTCTCACCTGACAGTAAAATGCAGATCACAGTGTCGGGAGGAGGACTGCCTCCCGTCAGCACCTTGACGAATATCCACAGCCTCTCCCACCACAATCCCCAGCAATCTCAGAACCTCATCATGACCCCCCTGTCTGGAGTCATGGCCATTGCACAGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCCTCTCCCACCACAATC
60.39
ACAGCAGCTGATCCTGACTG
59.75
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TATCCACAGCCTCTCCCACC
60.69
ACAGCAGCTGATCCTGACTG
59.75
152
PCR template sequence:
AGCACCTTGACGAATATCCACAGCCTCTCCCACCACAATCCCCAGCAATCTCAGAACCTCATCATGACCCCCCTGTCTGGAGTCATGGCCATTGCACAGAAGTTCAACCAGACAGTCCAGAGCTCTGGAAACATGACAGACAAAAGCAGTCAGGATCAGCTGCTGTTTCTCTTTCCAGAGTTCAGTCAACAGAACCAGGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-210-3p(1), mmu-miR-134-5p(1), mmu-miR-296-5p(1), mmu-miR-433-3p(1), mmu-miR-183-5p(1), mmu-miR-541-5p(1), mmu-miR-705(1), mmu-miR-129-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCCATTGCACAGAAGTTCAACCAGAC
siRNA sets
TCTGGTTGAACTTCTGTGC, CTGGTTGAACTTCTGTGCA, GTCTGGTTGAACTTCTGTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHNF1B_798_ORF_1
1.0579
0.359813541
0.999920298
1563
ORF sequence:
ATGACAGACAAAAGCAGTCAGGATCAGCTGCTGTTTCTCTTTCCAGAGTTCAGTCAACAGAACCAGGGGCCTGGGCAGTCGGAGGACACCTGCTCCGAGCCCACCAACAAGAAGATGCGCCGCAACCGGTTTAAATGGGGGCCCGCATCCCAGCAAATTTTGTACCAGGCCTACGACCGGCAAAAGAATCCCAGCAAGGAAGAGAGGGAGGCCTTAGTGGAGGAGTGTAACAGGGCAGAATGTTTGCAACGAGGGGTCTCCCCTTCCAAAGCCCACGGCCTAGGCTCCAACTTGGTCACGGAGGTCCGTGTCTACAACTGGTTCGCAAACCGCCGGAAGGAAGAGGCGTTCAGGCAGAAGCTGGCCATGGATGCCTATAGCTCCAACCAGACGCACAACCTGAACCCCCTGCTCACCCATGGCTCCCCTCACCATCAGCCAAGCTCCTCTCCACCCAACAAGATGTCAGGAGTGCGCTACAACCAGCCGGGAAACAATGAGGTCACTTCCTCTTCGACAATCAGTCACCATGGTAACAGTGCCATGGTGACCAGCCAGTCGGTTTTACAGCAAGTCTCCCCAGCCAGCCTGGACCCAGGCCACAGTCTCCTCTCACCTGACAGTAAAATGCAGATCACAGTGTCGGGAGGAGGACTGCCTCCCGTCAGCACCTTGACGAATATCCACAGCCTCTCCCACCACAATCCCCAGCAATCTCAGAACCTCATCATGACCCCCCTGTCTGGAGTCATGGCCATTGCACAGAAGTTCAACCAGACAGTCCAGAGCTCTGGAAACATGACAGACAAAAGCAGTCAGGATCAGCTGCTGTTTCTCTTTCCAGAGTTCAGTCAACAGAACCAGGGGCCTGGGCAGTCGGAGGACACCTGCTCCGAGCCCACCAACAAGAAGATGCGCCGCAACCGGTTTAAATGGGGGCCCGCATCCCAGCAAATTTTGTACCAGGCCTACGACCGGCAAAAGAATCCCAGCAAGGAAGAGAGGGAGGCCTTAGTGGAGGAGTGTAACAGGGCAGAATGTTTGCAACGAGGGGTCTCCCCTTCCAAAGCCCACGGCCTAGGCTCCAACTTGGTCACGGAGGTCCGTGTCTACAACTGGTTCGCAAACCGCCGGAAGGAAGAGGCGTTCAGGCAGAAGCTGGCCATGGATGCCTATAGCTCCAACCAGACGCACAACCTGAACCCCCTGCTCACCCATGGCTCCCCTCACCATCAGCCAAGCTCCTCTCCACCCAACAAGATGTCAGGAGTGCGCTACAACCAGCCGGGAAACAATGAGGTCACTTCCTCTTCGACAATCAGTCACCATGGTAACAGTGCCATGGTGACCAGCCAGTCGGTTTTACAGCAAGTCTCCCCAGCCAGCCTGGACCCAGGCCACAGTCTCCTCTCACCTGACAGTAAAATGCAGATCACAGTGTCGGGAGGAGGACTGCCTCCCGTCAGCACCTTGACGAATATCCACAGCCTCTCCCACCACAATCCCCAGCAATCTCAGAACCTCATCATGACCCCCCTGTCTGGAGTCATGGCCATTGCACAG
Peptide sequence:
MTDKSSQDQLLFLFPEFSQQNQGPGQSEDTCSEPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEAFRQKLAMDAYSSNQTHNLNPLLTHGSPHHQPSSSPPNKMSGVRYNQPGNNEVTSSSTISHHGNSAMVTSQSVLQQVSPASLDPGHSLLSPDSKMQITVSGGGLPPVSTLTNIHSLSHHNPQQSQNLIMTPLSGVMAIAQKFNQTVQSSGNMTDKSSQDQLLFLFPEFSQQNQGPGQSEDTCSEPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEAFRQKLAMDAYSSNQTHNLNPLLTHGSPHHQPSSSPPNKMSGVRYNQPGNNEVTSSSTISHHGNSAMVTSQSVLQQVSPASLDPGHSLLSPDSKMQITVSGGGLPPVSTLTNIHSLSHHNPQQSQNLIMTPLSGVMAIAQ
IRESfinder result
IRESfinder score
0.416266502
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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