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mmu_circSmchd1_825
Basic information of circular RNA
PanCircBase ID:
mmu_circSmchd1_825
mm39_Chr. Position ID:
chr17|71743700|71755841|-
Gene name:
Smchd1
Transcript:
ENSMUST00000127430.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
11,10,9,8,7,6
Exon/intron offsets:
0,4198,5170,7176,11807,12026
Genomic length:
12141
Exon/intron sizes in nt:
121,211,91,167,120,115
Flanking exon/introns:
chr17:71738400-71743700|chr17:71755841-71762599
Splice length:
825
Other database IDs:
circBase: mmu_circ_0000812, CIRCpedia: MMU_CIRCpedia_27815, circAtlas: mmu-Smchd1_0028
Human Ortholog IDs:
Mature spliced Sequence:
TGATCACTCAGGGTATGTCCGGCCATTACCAGTACCACGCAGTTTGAACAGTGACATTTCCTATTTTGGTGTTGGAGGCAAACAGGCTGTTTTCTTTGTTGGGCAATCAGCCAGAATGATAAGCAAGCCTATCGACTCCAAGGATGTTCATGAGCTGGTGCTTTCTAAAGAAGATTTTGAGAAGAAGGAAAAAAATAAAGAGGCGATATATAGTGGATATATTAGAAACAGAAAGCCAGCTGATTCTGCTCACATTACAAATGATGATGAAAGATTCCTACACAATCTTATTGAGGAAGAGAAAGAGAAAGACAGCTTTACAGCTGTGGTTATTACAGGGGTACAGCCAGAACACATACAGTACTTGAAAAATTATTTACATCTTTGGACACGACAGCTAACGCATATTTATCATTACTATATTCATGGACCAAAAGGAAATGAAATAAGTACAGCCAAAGCCATTGGACCTTTCAACAATATTGATATTGAAATTTCTTTGTTTGAAAAGGGGAAGACACCTAAGATTATCAACCTAAGGGAAATACAAGATGACATGCAGACATTGTATATAAACACAGCGTCTGATAGTTTTGAGTTCAAGGCTCACGTTGAAGGAGACGGTGTAGTGGAAGGGGTTATCCGGTACCATCCCTTCTTATATGATAGAGAAACCTTTCCTGATGACCCATGCTTTCCATCAAAGCTAAAGGATGAAGACGACGATGATGACTGTTTCATATCCGAGAAAGCAGCTCGAGGGAAGAGGCCGATCTTTGAGTGTTTTTGGAATGGACGGTTAATACCATATACATCAGTAGGAGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAAAGCAGCTCGAGGGAAGA
59.75
AACAGCCTGTTTGCCTCCAA
60.4
169
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGAAAGCAGCTCGAGGGAA
59.75
AACAGCCTGTTTGCCTCCAA
60.4
171
PCR template sequence:
ATGATGACTGTTTCATATCCGAGAAAGCAGCTCGAGGGAAGAGGCCGATCTTTGAGTGTTTTTGGAATGGACGGTTAATACCATATACATCAGTAGGAGATGATCACTCAGGGTATGTCCGGCCATTACCAGTACCACGCAGTTTGAACAGTGACATTTCCTATTTTGGTGTTGGAGGCAAACAGGCTGTTTTCTTTGTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(2), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-362-5p(1), mmu-miR-297a-5p(1), mmu-miR-1198-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CATCAGTAGGAGATGATCACTCAGGG
siRNA sets
TGAGTGATCATCTCCTACT, GAGTGATCATCTCCTACTG, AGTGATCATCTCCTACTGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMCHD1_825_ORF_1
0.9538
0.082093674
0.999625794
1533
ORF sequence:
ATGATAAGCAAGCCTATCGACTCCAAGGATGTTCATGAGCTGGTGCTTTCTAAAGAAGATTTTGAGAAGAAGGAAAAAAATAAAGAGGCGATATATAGTGGATATATTAGAAACAGAAAGCCAGCTGATTCTGCTCACATTACAAATGATGATGAAAGATTCCTACACAATCTTATTGAGGAAGAGAAAGAGAAAGACAGCTTTACAGCTGTGGTTATTACAGGGGTACAGCCAGAACACATACAGTACTTGAAAAATTATTTACATCTTTGGACACGACAGCTAACGCATATTTATCATTACTATATTCATGGACCAAAAGGAAATGAAATAAGTACAGCCAAAGCCATTGGACCTTTCAACAATATTGATATTGAAATTTCTTTGTTTGAAAAGGGGAAGACACCTAAGATTATCAACCTAAGGGAAATACAAGATGACATGCAGACATTGTATATAAACACAGCGTCTGATAGTTTTGAGTTCAAGGCTCACGTTGAAGGAGACGGTGTAGTGGAAGGGGTTATCCGGTACCATCCCTTCTTATATGATAGAGAAACCTTTCCTGATGACCCATGCTTTCCATCAAAGCTAAAGGATGAAGACGACGATGATGACTGTTTCATATCCGAGAAAGCAGCTCGAGGGAAGAGGCCGATCTTTGAGTGTTTTTGGAATGGACGGTTAATACCATATACATCAGTAGGAGATGATCACTCAGGGTATGTCCGGCCATTACCAGTACCACGCAGTTTGAACAGTGACATTTCCTATTTTGGTGTTGGAGGCAAACAGGCTGTTTTCTTTGTTGGGCAATCAGCCAGAATGATAAGCAAGCCTATCGACTCCAAGGATGTTCATGAGCTGGTGCTTTCTAAAGAAGATTTTGAGAAGAAGGAAAAAAATAAAGAGGCGATATATAGTGGATATATTAGAAACAGAAAGCCAGCTGATTCTGCTCACATTACAAATGATGATGAAAGATTCCTACACAATCTTATTGAGGAAGAGAAAGAGAAAGACAGCTTTACAGCTGTGGTTATTACAGGGGTACAGCCAGAACACATACAGTACTTGAAAAATTATTTACATCTTTGGACACGACAGCTAACGCATATTTATCATTACTATATTCATGGACCAAAAGGAAATGAAATAAGTACAGCCAAAGCCATTGGACCTTTCAACAATATTGATATTGAAATTTCTTTGTTTGAAAAGGGGAAGACACCTAAGATTATCAACCTAAGGGAAATACAAGATGACATGCAGACATTGTATATAAACACAGCGTCTGATAGTTTTGAGTTCAAGGCTCACGTTGAAGGAGACGGTGTAGTGGAAGGGGTTATCCGGTACCATCCCTTCTTATATGATAGAGAAACCTTTCCTGATGACCCATGCTTTCCATCAAAGCTAAAGGATGAAGACGACGATGATGACTGTTTCATATCCGAGAAAGCAGCTCGAGGGAAGAGGCCGATCTTTGAGTGTTTTTGGAATGGACGGTTAATACCATATACATCAGTAGGA
Peptide sequence:
MISKPIDSKDVHELVLSKEDFEKKEKNKEAIYSGYIRNRKPADSAHITNDDERFLHNLIEEEKEKDSFTAVVITGVQPEHIQYLKNYLHLWTRQLTHIYHYYIHGPKGNEISTAKAIGPFNNIDIEISLFEKGKTPKIINLREIQDDMQTLYINTASDSFEFKAHVEGDGVVEGVIRYHPFLYDRETFPDDPCFPSKLKDEDDDDDCFISEKAARGKRPIFECFWNGRLIPYTSVGDDHSGYVRPLPVPRSLNSDISYFGVGGKQAVFFVGQSARMISKPIDSKDVHELVLSKEDFEKKEKNKEAIYSGYIRNRKPADSAHITNDDERFLHNLIEEEKEKDSFTAVVITGVQPEHIQYLKNYLHLWTRQLTHIYHYYIHGPKGNEISTAKAIGPFNNIDIEISLFEKGKTPKIINLREIQDDMQTLYINTASDSFEFKAHVEGDGVVEGVIRYHPFLYDRETFPDDPCFPSKLKDEDDDDDCFISEKAARGKRPIFECFWNGRLIPYTSVG
IRESfinder result
IRESfinder score
0.569909443
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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