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mmu_circTasp1_530
Basic information of circular RNA
PanCircBase ID:
mmu_circTasp1_530
mm39_Chr. Position ID:
chr2|139819526|139890229|-
Gene name:
Tasp1
Transcript:
ENSMUST00000046656.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
8,7,6,5,4,3
Exon/intron offsets:
0,7522,18466,31092,64487,70635
Genomic length:
70703
Exon/intron sizes in nt:
107,80,85,121,69,68
Flanking exon/introns:
chr2:139793499-139819526|chr2:139890229-139899206
Splice length:
530
Other database IDs:
circBase: mmu_circ_0009390, CIRCpedia: MMU_CIRCpedia_8875, circAtlas: mmu-Tasp1_0030
Human Ortholog IDs:
Mature spliced Sequence:
GTGCAGGCTATCATTCTGAATCCAAAGCCAAGGAATATAAACATGTATGCAAACGAGCTTGTCAGAAGGCAATTGAGAAGCTACAGGCTGGTGCTCTTGCTACAGATGCAGTGGCTGCTGCTCTGGTGGAACTTGAGGATTCTCCTTTTACAAATGCAGGAATAGGATCTAATCTAAATCTCTTAGGAGAGATTGAATGTGATGCCAGCATAATGGATGGAAAGTCCTTAAACTTTGGAGCCGTTGGAGCACTGAGTGGAATCAAGAATCCAGTCTCAGTTGCTCACAGGCTCTTGTGTGAAGGGCAGAAGGGCAAGCTCTCTGCAGGCAGAATTCCTCCCTGCTTTTTAGTTGGAGAAGGAGCCTACAGATGGGCAGTGGATCATGGGATACCCTCTTGCCCTCCTAGCACCATGACCACAAGATTCAGCTTAGCTGCATTTAAAAGGAACAAGAGGAAACTAGAGCTGGCAGAAAGGGTGGAAACAGACTTCATCCAGCTGAAGAGAAGACGACAATCAAGCGCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TAGAGCTGGCAGAAAGGGTG
59.38
TTGCCTTCTGACAAGCTCGT
59.89
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTAGAGCTGGCAGAAAGGGT
59.09
TGCCTTCTGACAAGCTCGTT
59.89
140
PCR template sequence:
CTTAGCTGCATTTAAAAGGAACAAGAGGAAACTAGAGCTGGCAGAAAGGGTGGAAACAGACTTCATCCAGCTGAAGAGAAGACGACAATCAAGCGCAAAGGTGCAGGCTATCATTCTGAATCCAAAGCCAAGGAATATAAACATGTATGCAAACGAGCTTGTCAGAAGGCAATTGAGAAGCTACAGGCTGGTGCTCTTGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-15a-5p(1), mmu-miR-181a-5p(1), mmu-miR-31-5p(1), mmu-miR-322-5p(1), mmu-miR-335-5p(1), mmu-miR-217-5p(1), mmu-miR-181b-5p(1), mmu-miR-377-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATCAAGCGCAAAGGTGCAGGCTATCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTASP1_530_ORF_1
0.8074
0.021190856
0.45157778
483
ORF sequence:
ATGGATGGAAAGTCCTTAAACTTTGGAGCCGTTGGAGCACTGAGTGGAATCAAGAATCCAGTCTCAGTTGCTCACAGGCTCTTGTGTGAAGGGCAGAAGGGCAAGCTCTCTGCAGGCAGAATTCCTCCCTGCTTTTTAGTTGGAGAAGGAGCCTACAGATGGGCAGTGGATCATGGGATACCCTCTTGCCCTCCTAGCACCATGACCACAAGATTCAGCTTAGCTGCATTTAAAAGGAACAAGAGGAAACTAGAGCTGGCAGAAAGGGTGGAAACAGACTTCATCCAGCTGAAGAGAAGACGACAATCAAGCGCAAAGGTGCAGGCTATCATTCTGAATCCAAAGCCAAGGAATATAAACATGTATGCAAACGAGCTTGTCAGAAGGCAATTGAGAAGCTACAGGCTGGTGCTCTTGCTACAGATGCAGTGGCTGCTGCTCTGGTGGAACTTGAGGATTCTCCTTTTACAAATGCAGGAATAG
Peptide sequence:
MDGKSLNFGAVGALSGIKNPVSVAHRLLCEGQKGKLSAGRIPPCFLVGEGAYRWAVDHGIPSCPPSTMTTRFSLAAFKRNKRKLELAERVETDFIQLKRRRQSSAKVQAIILNPKPRNINMYANELVRRQLRSYRLVLLLQMQWLLLWWNLRILLLQMQE
IRESfinder result
IRESfinder score
0.452150709
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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