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mmu_circSmchd1_1639
Basic information of circular RNA
PanCircBase ID:
mmu_circSmchd1_1639
mm39_Chr. Position ID:
chr17|71734431|71763495|-
Gene name:
Smchd1
Transcript:
ENSMUST00000127430.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
15,14,13,12,11,10,9,8,7,6,5,4
Exon/intron offsets:
0,735,2025,3785,9269,13467,14439,16445,21076,21295,28168,28981
Genomic length:
29064
Exon/intron sizes in nt:
107,114,195,184,121,211,91,167,120,115,131,83
Flanking exon/introns:
chr17:71733517-71734431|chr17:71763495-71770756
Splice length:
1639
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CATTTGCTCTTGCAGAGTTAATCGACAATTCATTGTCAGCTACTTCTCGAAATAATGGTGTTAGGAGAATACAGATCAAATTGCTTTTTGATGAAACACAAGGAAAACCTGCTGTCGCAGTGGTAGATAATGGAAGAGGAATGACCTCTAAGCAGCTTAACAACTGGGCTGTGTATAGGCTGTCAAAATTTACAAGACAAGGTGACTTTGAAAGTGATCACTCAGGGTATGTCCGGCCATTACCAGTACCACGCAGTTTGAACAGTGACATTTCCTATTTTGGTGTTGGAGGCAAACAGGCTGTTTTCTTTGTTGGGCAATCAGCCAGAATGATAAGCAAGCCTATCGACTCCAAGGATGTTCATGAGCTGGTGCTTTCTAAAGAAGATTTTGAGAAGAAGGAAAAAAATAAAGAGGCGATATATAGTGGATATATTAGAAACAGAAAGCCAGCTGATTCTGCTCACATTACAAATGATGATGAAAGATTCCTACACAATCTTATTGAGGAAGAGAAAGAGAAAGACAGCTTTACAGCTGTGGTTATTACAGGGGTACAGCCAGAACACATACAGTACTTGAAAAATTATTTACATCTTTGGACACGACAGCTAACGCATATTTATCATTACTATATTCATGGACCAAAAGGAAATGAAATAAGTACAGCCAAAGCCATTGGACCTTTCAACAATATTGATATTGAAATTTCTTTGTTTGAAAAGGGGAAGACACCTAAGATTATCAACCTAAGGGAAATACAAGATGACATGCAGACATTGTATATAAACACAGCGTCTGATAGTTTTGAGTTCAAGGCTCACGTTGAAGGAGACGGTGTAGTGGAAGGGGTTATCCGGTACCATCCCTTCTTATATGATAGAGAAACCTTTCCTGATGACCCATGCTTTCCATCAAAGCTAAAGGATGAAGACGACGATGATGACTGTTTCATATCCGAGAAAGCAGCTCGAGGGAAGAGGCCGATCTTTGAGTGTTTTTGGAATGGACGGTTAATACCATATACATCAGTAGGAGACTTTGACTGGTGTGCTCCTCCTAAGAAGAGAGGGCTTGTCCCAATTGAGTGCTTTAATAGAATATCTGGTGCATTATTCACTAATGACAAATTTCAGGTCAGCACAAATAAACTGACATTTATGGATCTTGAGCTGAAATTGAAAGATAAGAACACCCTCTTTACAAGAATCTTAAATGGACAGGAGCAGAGAATGAAAATTGACAGAGAATTTGCTTTATGGCTGAAGGATTGTCATGAAAAGCATGACAAACAAATAAAATTCACGCTTTTTAAAGGAATAATTACCCGTCCAGATCTTCCCACTAAAAAGCAAGGCCCCTGGGCAACATTTTCAGCAATAGAATGGGATGGGAAAATATACAAAGCAGGCCAACTGGTCAAGACAATCAAGACACTTCCTCTCTGTTATGGAAGCATTGTTAGATTTTTCCTTCATGGTGATCATGATGGAGAAGTGTATGCGACGGGAGGTGAAGTTCAGATTGCCATGGAACCCCAGGCACTGTATGATGAAATAAAAACTGTGCCCATTGCAAAGCTGGATAGGACAGTAGCCGAGAAAACAATTAGGAAATATGTAGAAGATGAAATGGCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGGATAGGACAGTAGCCG
59.68
TTTGATCTGTATTCTCCTAACACCA
57.75
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCCCATTGCAAAGCTGGATAG
59.93
TGATCTGTATTCTCCTAACACCA
56.46
150
PCR template sequence:
AGGCACTGTATGATGAAATAAAAACTGTGCCCATTGCAAAGCTGGATAGGACAGTAGCCGAGAAAACAATTAGGAAATATGTAGAAGATGAAATGGCAAGCATTTGCTCTTGCAGAGTTAATCGACAATTCATTGTCAGCTACTTCTCGAAATAATGGTGTTAGGAGAATACAGATCAAATTGCTTTTTGATGAAACACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(2), mmu-miR-335-3p(2), mmu-miR-137-3p(1), mmu-miR-223-3p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-335-5p(1), mmu-miR-29c-3p(1), mmu-miR-351-5p(1), mmu-miR-362-5p(1), mmu-miR-297a-5p(1), mmu-miR-1198-5p(1), mmu-miR-5101(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATGAAATGGCAAGCATTTGCTCTTGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMCHD1_1639_ORF_1
0.9326
0.037164079
0.999791108
1650
ORF sequence:
ATGAAATGGCAAGCATTTGCTCTTGCAGAGTTAATCGACAATTCATTGTCAGCTACTTCTCGAAATAATGGTGTTAGGAGAATACAGATCAAATTGCTTTTTGATGAAACACAAGGAAAACCTGCTGTCGCAGTGGTAGATAATGGAAGAGGAATGACCTCTAAGCAGCTTAACAACTGGGCTGTGTATAGGCTGTCAAAATTTACAAGACAAGGTGACTTTGAAAGTGATCACTCAGGGTATGTCCGGCCATTACCAGTACCACGCAGTTTGAACAGTGACATTTCCTATTTTGGTGTTGGAGGCAAACAGGCTGTTTTCTTTGTTGGGCAATCAGCCAGAATGATAAGCAAGCCTATCGACTCCAAGGATGTTCATGAGCTGGTGCTTTCTAAAGAAGATTTTGAGAAGAAGGAAAAAAATAAAGAGGCGATATATAGTGGATATATTAGAAACAGAAAGCCAGCTGATTCTGCTCACATTACAAATGATGATGAAAGATTCCTACACAATCTTATTGAGGAAGAGAAAGAGAAAGACAGCTTTACAGCTGTGGTTATTACAGGGGTACAGCCAGAACACATACAGTACTTGAAAAATTATTTACATCTTTGGACACGACAGCTAACGCATATTTATCATTACTATATTCATGGACCAAAAGGAAATGAAATAAGTACAGCCAAAGCCATTGGACCTTTCAACAATATTGATATTGAAATTTCTTTGTTTGAAAAGGGGAAGACACCTAAGATTATCAACCTAAGGGAAATACAAGATGACATGCAGACATTGTATATAAACACAGCGTCTGATAGTTTTGAGTTCAAGGCTCACGTTGAAGGAGACGGTGTAGTGGAAGGGGTTATCCGGTACCATCCCTTCTTATATGATAGAGAAACCTTTCCTGATGACCCATGCTTTCCATCAAAGCTAAAGGATGAAGACGACGATGATGACTGTTTCATATCCGAGAAAGCAGCTCGAGGGAAGAGGCCGATCTTTGAGTGTTTTTGGAATGGACGGTTAATACCATATACATCAGTAGGAGACTTTGACTGGTGTGCTCCTCCTAAGAAGAGAGGGCTTGTCCCAATTGAGTGCTTTAATAGAATATCTGGTGCATTATTCACTAATGACAAATTTCAGGTCAGCACAAATAAACTGACATTTATGGATCTTGAGCTGAAATTGAAAGATAAGAACACCCTCTTTACAAGAATCTTAAATGGACAGGAGCAGAGAATGAAAATTGACAGAGAATTTGCTTTATGGCTGAAGGATTGTCATGAAAAGCATGACAAACAAATAAAATTCACGCTTTTTAAAGGAATAATTACCCGTCCAGATCTTCCCACTAAAAAGCAAGGCCCCTGGGCAACATTTTCAGCAATAGAATGGGATGGGAAAATATACAAAGCAGGCCAACTGGTCAAGACAATCAAGACACTTCCTCTCTGTTATGGAAGCATTGTTAGATTTTTCCTTCATGGTGATCATGATGGAGAAGTGTATGCGACGGGAGGTGAAGTTCAGATTGCCATGGAACCCCAGGCACTGTATGATGAAATAAAAACTGTGCCCATTGCAAAGCTGGATAGGACAGTAGCCGAGAAAACAATTAGGAAATATGTAGAAGATGAAATGGCA
Peptide sequence:
MKWQAFALAELIDNSLSATSRNNGVRRIQIKLLFDETQGKPAVAVVDNGRGMTSKQLNNWAVYRLSKFTRQGDFESDHSGYVRPLPVPRSLNSDISYFGVGGKQAVFFVGQSARMISKPIDSKDVHELVLSKEDFEKKEKNKEAIYSGYIRNRKPADSAHITNDDERFLHNLIEEEKEKDSFTAVVITGVQPEHIQYLKNYLHLWTRQLTHIYHYYIHGPKGNEISTAKAIGPFNNIDIEISLFEKGKTPKIINLREIQDDMQTLYINTASDSFEFKAHVEGDGVVEGVIRYHPFLYDRETFPDDPCFPSKLKDEDDDDDCFISEKAARGKRPIFECFWNGRLIPYTSVGDFDWCAPPKKRGLVPIECFNRISGALFTNDKFQVSTNKLTFMDLELKLKDKNTLFTRILNGQEQRMKIDREFALWLKDCHEKHDKQIKFTLFKGIITRPDLPTKKQGPWATFSAIEWDGKIYKAGQLVKTIKTLPLCYGSIVRFFLHGDHDGEVYATGGEVQIAMEPQALYDEIKTVPIAKLDRTVAEKTIRKYVEDEMA
IRESfinder result
IRESfinder score
0.610623122
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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