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mmu_circSmchd1_502
Basic information of circular RNA
PanCircBase ID:
mmu_circSmchd1_502
mm39_Chr. Position ID:
chr17|71722029|71734538|-
Gene name:
Smchd1
Transcript:
ENSMUST00000127430.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
19,18,17,16,15
Exon/intron offsets:
0,566,11120,11405,12402
Genomic length:
12509
Exon/intron sizes in nt:
12,07,81,14,83,107
Flanking exon/introns:
chr17:71718909-71722029|chr17:71734538-71735166
Splice length:
502
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GAACCCCAGGCACTGTATGATGAAATAAAAACTGTGCCCATTGCAAAGCTGGATAGGACAGTAGCCGAGAAAACAATTAGGAAATATGTAGAAGATGAAATGGCAAGGCTCCCTGATAGATTGTCTGTAACTTGGCCTGAAGGAGATGAATTATTGCCAAATGAAGTTAGGCCTGCTGGAACACCAATCGGTGCATTAAGAATTGAAATTCTAAACAAAAAGGGGGAAGCAATGCAGAAACTCCCAGGGACAAGTCATGGAGGGTCAAAGAAGCTGCTGGTGGAACTTAAAGTCATACTGCACACTTCAAGTGGAAATAAAGAAATCATTTCACATATCAGTCAGCATGGAGGGAAATGGCCTTACTGGTTTAAAAAAATGGAAAATATCCAGAAACTGGGTAATTATACATTGAAATTACAAGTTGTATTGAATGAAAGTAATGCAGATACCTATGCAGGAAGATCACTACCGTCCAAAGTAATTAAATTCTCTGTTAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCAGATACCTATGCAGGAAGA
58.69
CCTAATTGTTTTCTCGGCTACTGT
59.06
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCAGATACCTATGCAGGAAGA
58.69
CCTAATTGTTTTCTCGGCTACTGTC
59.94
140
PCR template sequence:
AATTATACATTGAAATTACAAGTTGTATTGAATGAAAGTAATGCAGATACCTATGCAGGAAGATCACTACCGTCCAAAGTAATTAAATTCTCTGTTAAAGGAACCCCAGGCACTGTATGATGAAATAAAAACTGTGCCCATTGCAAAGCTGGATAGGACAGTAGCCGAGAAAACAATTAGGAAATATGTAGAAGATGAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-203-3p(1), mmu-miR-182-5p(1), mmu-miR-190b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTCTCTGTTAAAGGAACCCCAGGCAC
siRNA sets
TGGGGTTCCTTTAACAGAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMCHD1_502_ORF_1
0.8317
-0.109317033
0.247058849
423
ORF sequence:
ATGGCAAGGCTCCCTGATAGATTGTCTGTAACTTGGCCTGAAGGAGATGAATTATTGCCAAATGAAGTTAGGCCTGCTGGAACACCAATCGGTGCATTAAGAATTGAAATTCTAAACAAAAAGGGGGAAGCAATGCAGAAACTCCCAGGGACAAGTCATGGAGGGTCAAAGAAGCTGCTGGTGGAACTTAAAGTCATACTGCACACTTCAAGTGGAAATAAAGAAATCATTTCACATATCAGTCAGCATGGAGGGAAATGGCCTTACTGGTTTAAAAAAATGGAAAATATCCAGAAACTGGGTAATTATACATTGAAATTACAAGTTGTATTGAATGAAAGTAATGCAGATACCTATGCAGGAAGATCACTACCGTCCAAAGTAATTAAATTCTCTGTTAAAGGAACCCCAGGCACTGTATGA
Peptide sequence:
MARLPDRLSVTWPEGDELLPNEVRPAGTPIGALRIEILNKKGEAMQKLPGTSHGGSKKLLVELKVILHTSSGNKEIISHISQHGGKWPYWFKKMENIQKLGNYTLKLQVVLNESNADTYAGRSLPSKVIKFSVKGTPGTV
IRESfinder result
IRESfinder score
0.606327757
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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