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mmu_circSmchd1_366
Basic information of circular RNA
PanCircBase ID:
mmu_circSmchd1_366
mm39_Chr. Position ID:
chr17|71755507|71762730|-
Gene name:
Smchd1
Transcript:
ENSMUST00000127430.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
7,6,5
Exon/intron offsets:
0,219,7092
Genomic length:
7223
Exon/intron sizes in nt:
12,01,15,131
Flanking exon/introns:
chr17:71751043-71755507|chr17:71762730-71763412
Splice length:
366
Other database IDs:
circAtlas: mmu-Smchd1_0037
Human Ortholog IDs:
Mature spliced Sequence:
CTTTTTGATGAAACACAAGGAAAACCTGCTGTCGCAGTGGTAGATAATGGAAGAGGAATGACCTCTAAGCAGCTTAACAACTGGGCTGTGTATAGGCTGTCAAAATTTACAAGACAAGGTGACTTTGAAAGTGATCACTCAGGGTATGTCCGGCCATTACCAGTACCACGCAGTTTGAACAGTGACATTTCCTATTTTGGTGTTGGAGGCAAACAGGCTGTTTTCTTTGTTGGGCAATCAGCCAGAATGATAAGCAAGCCTATCGACTCCAAGGATGTTCATGAGCTGGTGCTTTCTAAAGAAGATTTTGAGAAGAAGGAAAAAAATAAAGAGGCGATATATAGTGGATATATTAGAAACAGAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGATGTTCATGAGCTGGTGC
59.26
GCCCAGTTGTTAAGCTGCTT
59.04
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGATGTTCATGAGCTGGTGC
59.26
GCCCAGTTGTTAAGCTGCTTA
58.84
180
PCR template sequence:
CTCCAAGGATGTTCATGAGCTGGTGCTTTCTAAAGAAGATTTTGAGAAGAAGGAAAAAAATAAAGAGGCGATATATAGTGGATATATTAGAAACAGAAAGCTTTTTGATGAAACACAAGGAAAACCTGCTGTCGCAGTGGTAGATAATGGAAGAGGAATGACCTCTAAGCAGCTTAACAACTGGGCTGTGTATAGGCTGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-351-5p(1), mmu-miR-362-5p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TAGAAACAGAAAGCTTTTTGATGAAA
siRNA sets
TTTCATCAAAAAGCTTTCT, TTCATCAAAAAGCTTTCTG, TCATCAAAAAGCTTTCTGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMCHD1_366_ORF_1
0.9157
0.039246502
0.81368448
675
ORF sequence:
ATGACCTCTAAGCAGCTTAACAACTGGGCTGTGTATAGGCTGTCAAAATTTACAAGACAAGGTGACTTTGAAAGTGATCACTCAGGGTATGTCCGGCCATTACCAGTACCACGCAGTTTGAACAGTGACATTTCCTATTTTGGTGTTGGAGGCAAACAGGCTGTTTTCTTTGTTGGGCAATCAGCCAGAATGATAAGCAAGCCTATCGACTCCAAGGATGTTCATGAGCTGGTGCTTTCTAAAGAAGATTTTGAGAAGAAGGAAAAAAATAAAGAGGCGATATATAGTGGATATATTAGAAACAGAAAGCTTTTTGATGAAACACAAGGAAAACCTGCTGTCGCAGTGGTAGATAATGGAAGAGGAATGACCTCTAAGCAGCTTAACAACTGGGCTGTGTATAGGCTGTCAAAATTTACAAGACAAGGTGACTTTGAAAGTGATCACTCAGGGTATGTCCGGCCATTACCAGTACCACGCAGTTTGAACAGTGACATTTCCTATTTTGGTGTTGGAGGCAAACAGGCTGTTTTCTTTGTTGGGCAATCAGCCAGAATGATAAGCAAGCCTATCGACTCCAAGGATGTTCATGAGCTGGTGCTTTCTAAAGAAGATTTTGAGAAGAAGGAAAAAAATAAAGAGGCGATATATAGTGGATATATTAGAAACAGAAAG
Peptide sequence:
MTSKQLNNWAVYRLSKFTRQGDFESDHSGYVRPLPVPRSLNSDISYFGVGGKQAVFFVGQSARMISKPIDSKDVHELVLSKEDFEKKEKNKEAIYSGYIRNRKLFDETQGKPAVAVVDNGRGMTSKQLNNWAVYRLSKFTRQGDFESDHSGYVRPLPVPRSLNSDISYFGVGGKQAVFFVGQSARMISKPIDSKDVHELVLSKEDFEKKEKNKEAIYSGYIRNRK
IRESfinder result
IRESfinder score
0.462568849
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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