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mmu_circMapkap1_387
Basic information of circular RNA
PanCircBase ID:
mmu_circMapkap1_387
mm39_Chr. Position ID:
chr2|34453066|34487572|+
Gene name:
Mapkap1
Transcript:
ENSMUST00000124443.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
7,8,9
Exon/intron offsets:
0,18137,34368
Genomic length:
34506
Exon/intron sizes in nt:
10,81,41,138
Flanking exon/introns:
chr2:34423909-34453066|chr2:34487572-34509856
Splice length:
387
Other database IDs:
circAtlas: mmu-Mapkap1_0012
circBase: hsa_circ_0003984, circAtlas: hsa-MAPKAP1_0013, CIRCpedia: HSA_CIRCpedia_62829
Human Ortholog IDs:
Mature spliced Sequence:
GCCCTCAGTACCGCCTGGAGAAGCAGAGTGAGCCTAACATCGCTGTGGACCTGGAGAGCACGCTGGAGAGCCAGAACGCCTGGGAGTTCTGCCTGGTTCGCGAGAACAGTTCAAGGGCAGACGGAGTTTTCGAGGAGGATTCACAAATTGACATCGCTACAGTACAGGATATGCTTAGCAGCCACCATTACAAGTCATTCAAAGTCAGCATGATCCACAGACTGCGATTCACGACGGATGTGCAGTTAGGTATCTCTGGAGACAAAGTAGAGATAGACCCTGTTACGAATCAGAAAGCCAGCACTAAGTTTTGGATTAAGCAGAAACCCATCTCAATCGATTGTGACCTGCTCTGTGCCTGTGACCTTGCCGAGGAGAAGAGCCCCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATTGTGACCTGCTCTGTGCC
60.61
GAACCAGGCAGAACTCCCAG
60.32
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GATTGTGACCTGCTCTGTGC
59.2
GAACCAGGCAGAACTCCCAG
60.32
148
PCR template sequence:
AATCAGAAAGCCAGCACTAAGTTTTGGATTAAGCAGAAACCCATCTCAATCGATTGTGACCTGCTCTGTGCCTGTGACCTTGCCGAGGAGAAGAGCCCCAGCCCTCAGTACCGCCTGGAGAAGCAGAGTGAGCCTAACATCGCTGTGGACCTGGAGAGCACGCTGGAGAGCCAGAACGCCTGGGAGTTCTGCCTGGTTCG
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-207(2), mmu-miR-149-5p(1), mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
GAGAAGAGCCCCAGCCCTCAGTACCG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMAPKAP1_387_ORF_1
1.1407
0.375542031
0.939741517
603
ORF sequence:
ATGCTTAGCAGCCACCATTACAAGTCATTCAAAGTCAGCATGATCCACAGACTGCGATTCACGACGGATGTGCAGTTAGGTATCTCTGGAGACAAAGTAGAGATAGACCCTGTTACGAATCAGAAAGCCAGCACTAAGTTTTGGATTAAGCAGAAACCCATCTCAATCGATTGTGACCTGCTCTGTGCCTGTGACCTTGCCGAGGAGAAGAGCCCCAGCCCTCAGTACCGCCTGGAGAAGCAGAGTGAGCCTAACATCGCTGTGGACCTGGAGAGCACGCTGGAGAGCCAGAACGCCTGGGAGTTCTGCCTGGTTCGCGAGAACAGTTCAAGGGCAGACGGAGTTTTCGAGGAGGATTCACAAATTGACATCGCTACAGTACAGGATATGCTTAGCAGCCACCATTACAAGTCATTCAAAGTCAGCATGATCCACAGACTGCGATTCACGACGGATGTGCAGTTAGGTATCTCTGGAGACAAAGTAGAGATAGACCCTGTTACGAATCAGAAAGCCAGCACTAAGTTTTGGATTAAGCAGAAACCCATCTCAATCGATTGTGACCTGCTCTGTGCCTGTGACCTTGCCGAGGAGAAGAGCCCC
Peptide sequence:
MLSSHHYKSFKVSMIHRLRFTTDVQLGISGDKVEIDPVTNQKASTKFWIKQKPISIDCDLLCACDLAEEKSPSPQYRLEKQSEPNIAVDLESTLESQNAWEFCLVRENSSRADGVFEEDSQIDIATVQDMLSSHHYKSFKVSMIHRLRFTTDVQLGISGDKVEIDPVTNQKASTKFWIKQKPISIDCDLLCACDLAEEKSP
IRESfinder result
IRESfinder score
0.514522965
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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