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mmu_circTasp1_272
Basic information of circular RNA
PanCircBase ID:
mmu_circTasp1_272
mm39_Chr. Position ID:
chr2|139819526|139838077|-
Gene name:
Tasp1
Transcript:
ENSMUST00000046656.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
8,7,6
Exon/intron offsets:
0,7522,18466
Genomic length:
18551
Exon/intron sizes in nt:
107,80,85
Flanking exon/introns:
chr2:139793499-139819526|chr2:139838077-139850618
Splice length:
272
Other database IDs:
CIRCpedia: MMU_CIRCpedia_8872, circAtlas: mmu-Tasp1_0054
circBase: hsa_circ_0002001, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_33373
Human Ortholog IDs:
Mature spliced Sequence:
GAATCAAGAATCCAGTCTCAGTTGCTCACAGGCTCTTGTGTGAAGGGCAGAAGGGCAAGCTCTCTGCAGGCAGAATTCCTCCCTGCTTTTTAGTTGGAGAAGGAGCCTACAGATGGGCAGTGGATCATGGGATACCCTCTTGCCCTCCTAGCACCATGACCACAAGATTCAGCTTAGCTGCATTTAAAAGGAACAAGAGGAAACTAGAGCTGGCAGAAAGGGTGGAAACAGACTTCATCCAGCTGAAGAGAAGACGACAATCAAGCGCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TAGAGCTGGCAGAAAGGGTG
59.38
TCTGCCTGCAGAGAGCTTG
59.7
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTAGAGCTGGCAGAAAGGGT
59.09
TCTGCCTGCAGAGAGCTTG
59.7
143
PCR template sequence:
CTTAGCTGCATTTAAAAGGAACAAGAGGAAACTAGAGCTGGCAGAAAGGGTGGAAACAGACTTCATCCAGCTGAAGAGAAGACGACAATCAAGCGCAAAGGAATCAAGAATCCAGTCTCAGTTGCTCACAGGCTCTTGTGTGAAGGGCAGAAGGGCAAGCTCTCTGCAGGCAGAATTCCTCCCTGCTTTTTAGTTGGAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-31-5p(1), mmu-miR-377-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATCAAGCGCAAAGGAATCAAGAATCC
siRNA sets
ATTCTTGATTCCTTTGCGC, GATTCTTGATTCCTTTGCG, TTCTTGATTCCTTTGCGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTASP1_272_ORF_1
0.8211
0.050739467
0.118573164
210
ORF sequence:
ATGACCACAAGATTCAGCTTAGCTGCATTTAAAAGGAACAAGAGGAAACTAGAGCTGGCAGAAAGGGTGGAAACAGACTTCATCCAGCTGAAGAGAAGACGACAATCAAGCGCAAAGGAATCAAGAATCCAGTCTCAGTTGCTCACAGGCTCTTGTGTGAAGGGCAGAAGGGCAAGCTCTCTGCAGGCAGAATTCCTCCCTGCTTTTTAG
Peptide sequence:
MTTRFSLAAFKRNKRKLELAERVETDFIQLKRRRQSSAKESRIQSQLLTGSCVKGRRASSLQAEFLPAF
IRESfinder result
IRESfinder score
0.477660436
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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