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mmu_circGpatch2_393
Basic information of circular RNA
PanCircBase ID:
mmu_circGpatch2_393
mm39_Chr. Position ID:
chr1|186962980|187036594|+
Gene name:
Gpatch2
Transcript:
ENSMUST00000160481.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
3,4,5,6
Exon/intron offsets:
0,2347,2963,73546
Genomic length:
73614
Exon/intron sizes in nt:
62,183,80,68
Flanking exon/introns:
chr1:186958416-186962980|chr1:187036594-187047555
Splice length:
393
Other database IDs:
circBase: mmu_circ_0008543, CIRCpedia: MMU_CIRCpedia_40773, circAtlas: mmu-Gpatch2_0008
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
TGACACCAGCAGTCTCAGCAGCACTGACGCGGGCTTGTTCACCAACGATGAGGGAAGACAAGGTGATGATGAGCAGAGTGACTGGTTCTATGAGAAGGAGTCAGGCGGAGCGTGCGGGATTGCTGGAGTCGTGCCCTGGTGGGAAAAGGATGAGCCAGCAGAGCTGGACACCAACCTGCCCGACCCTGTGTTTGAGAGTATCTTAAGTGGCTCCTTCCCTCTCATGTCCCATCCTGGCAGAGGAGGTTTCCAAGCTAGACTCAGTCGCCTTCATGGAACGCCTTCAAAGAATATTAAAAAGTCTTCAGGGGCTCCACCTTCAATGCTGTCTGCTCCTGGCCCTGGCAGTAACAAGAGGATGGTTCACTTCTCCCCAGACGCCCATCGCCATGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAAGTCTTCAGGGGCTCCAC
59.6
CATCGTTGGTGAACAAGCCC
59.76
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCAGGGGCTCCACCTTCAA
61.07
CATCGTTGGTGAACAAGCCC
59.76
140
PCR template sequence:
TTAAAAAGTCTTCAGGGGCTCCACCTTCAATGCTGTCTGCTCCTGGCCCTGGCAGTAACAAGAGGATGGTTCACTTCTCCCCAGACGCCCATCGCCATGATGACACCAGCAGTCTCAGCAGCACTGACGCGGGCTTGTTCACCAACGATGAGGGAAGACAAGGTGATGATGAGCAGAGTGACTGGTTCTATGAGAAGGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-149-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCCATCGCCATGATGACACCAGCAGT
siRNA sets
ACTGCTGGTGTCATCATGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGPATCH2_393_ORF_1
0.9788
0.192230325
0.801075957
561
ORF sequence:
ATGTCCCATCCTGGCAGAGGAGGTTTCCAAGCTAGACTCAGTCGCCTTCATGGAACGCCTTCAAAGAATATTAAAAAGTCTTCAGGGGCTCCACCTTCAATGCTGTCTGCTCCTGGCCCTGGCAGTAACAAGAGGATGGTTCACTTCTCCCCAGACGCCCATCGCCATGATGACACCAGCAGTCTCAGCAGCACTGACGCGGGCTTGTTCACCAACGATGAGGGAAGACAAGGTGATGATGAGCAGAGTGACTGGTTCTATGAGAAGGAGTCAGGCGGAGCGTGCGGGATTGCTGGAGTCGTGCCCTGGTGGGAAAAGGATGAGCCAGCAGAGCTGGACACCAACCTGCCCGACCCTGTGTTTGAGAGTATCTTAAGTGGCTCCTTCCCTCTCATGTCCCATCCTGGCAGAGGAGGTTTCCAAGCTAGACTCAGTCGCCTTCATGGAACGCCTTCAAAGAATATTAAAAAGTCTTCAGGGGCTCCACCTTCAATGCTGTCTGCTCCTGGCCCTGGCAGTAACAAGAGGATGGTTCACTTCTCCCCAGACGCCCATCGCCAT
Peptide sequence:
MSHPGRGGFQARLSRLHGTPSKNIKKSSGAPPSMLSAPGPGSNKRMVHFSPDAHRHDDTSSLSSTDAGLFTNDEGRQGDDEQSDWFYEKESGGACGIAGVVPWWEKDEPAELDTNLPDPVFESILSGSFPLMSHPGRGGFQARLSRLHGTPSKNIKKSSGAPPSMLSAPGPGSNKRMVHFSPDAHRH
IRESfinder result
IRESfinder score
0.531207152
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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