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mmu_circCacna2d1_919
Basic information of circular RNA
PanCircBase ID:
mmu_circCacna2d1_919
mm39_Chr. Position ID:
chr5|16518639|16557676|+
Gene name:
Cacna2d1
Transcript:
ENSMUST00000167946.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
13
Exon/intron indexes:
14,15,16,17,18,19,20,21,22,23,24,25,26
Exon/intron offsets:
0,1264,3993,5596,6442,12670,14331,20122,27065,28910,29033,35770,38949
Genomic length:
39037
Exon/intron sizes in nt:
50,90,78,75,75,72,72,62,81,9,69,98,88
Flanking exon/introns:
chr5:16517577-16518639|chr5:16557676-16558820
Splice length:
919
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GTTACTATTATGAGATTCCCTCCATTGGTGCAATAAGAATCAATACTCAGGAATATCTAGATGTTCTGGGAAGACCAATGGTTTTAGCTGGTGACAAAGCGAAGCAAGTTCAATGGACAAATGTGTATTTGGACGCCCTGGAACTGGGACTTGTCATTACTGGAACTCTACCAGTCTTCAACGTCACTGGCCAATCTGAAAATAAGACAAACTTGAAGAACCAGTTGATTCTTGGTGTGATGGGCGTTGATGTGTCTCTGGAAGATATCAAGAGATTGACACCACGTTTTACACTCTGTCCCAATGGCTACTATTTTGCAATTGATCCTAATGGCTATGTCTTATTGCATCCAAATCTTCAGCCAAAGAACCCCAAATCTCAGGAGCCAGTCACACTGGATTTTCTCGATGCTGAGTTAGAGAATGAAATTAAAGTGGAGATTCGAAATAAAATGATAGATGGAGAAAGTGGAGAAAAAACGTTCAGAACTCTGGTCAAGTCTCAAGATGAGAGATACATTGACAAAGGAAATCGAACATACACATGGACGCCTGTCAATGGCACAGATTACAGTTTGGCCTTGGTATTGCCAACCTACAGTTTTTACTATATAAAAGCCAAACTAGAAGAGACAATAACTCAGGCCAGATGTAACTTGGGGATATTTTCAGATTCAGAAACCCTGAAGCCAGACAATTTTGAAGAATCTGGCTATACTTTCATAGCACCAAGGGAATACTGCAATGATCTTAAACCTTCAGATAATAACACTGAATTTCTTTTGAATTTCAATGAATTTATTGATAGGAAAACTCCAAACAACCCCTCCTGTAATACAGATTTGATTAATAGAATCTTGCTGGATGCAGGTTTTACAAATGAACTTGTCCAAAATTATTGGAGTAAGCAGAAAAATAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGGATGCAGGTTTTACAA
56.61
ACCATTGGTCTTCCCAGAACA
59.22
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGGATGCAGGTTTTACAAA
57.34
ACCATTGGTCTTCCCAGAACA
59.22
142
PCR template sequence:
ACAACCCCTCCTGTAATACAGATTTGATTAATAGAATCTTGCTGGATGCAGGTTTTACAAATGAACTTGTCCAAAATTATTGGAGTAAGCAGAAAAATATGTTACTATTATGAGATTCCCTCCATTGGTGCAATAAGAATCAATACTCAGGAATATCTAGATGTTCTGGGAAGACCAATGGTTTTAGCTGGTGACAAAGC
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-134-5p(1), mmu-miR-199a-5p(1), mmu-miR-122-5p(1), mmu-miR-216a-5p(1), mmu-miR-182-5p(1), mmu-miR-297a-5p(1), mmu-miR-5101(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGCAGAAAAATATGTTACTATTATGA
siRNA sets
TAGTAACATATTTTTCTGC, AATAGTAACATATTTTTCT, ATAGTAACATATTTTTCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCACNA2D1_919_ORF_1
0.8469
0.045438366
0.970370452
972
ORF sequence:
ATGCAGGTTTTACAAATGAACTTGTCCAAAATTATTGGAGTAAGCAGAAAAATATGTTACTATTATGAGATTCCCTCCATTGGTGCAATAAGAATCAATACTCAGGAATATCTAGATGTTCTGGGAAGACCAATGGTTTTAGCTGGTGACAAAGCGAAGCAAGTTCAATGGACAAATGTGTATTTGGACGCCCTGGAACTGGGACTTGTCATTACTGGAACTCTACCAGTCTTCAACGTCACTGGCCAATCTGAAAATAAGACAAACTTGAAGAACCAGTTGATTCTTGGTGTGATGGGCGTTGATGTGTCTCTGGAAGATATCAAGAGATTGACACCACGTTTTACACTCTGTCCCAATGGCTACTATTTTGCAATTGATCCTAATGGCTATGTCTTATTGCATCCAAATCTTCAGCCAAAGAACCCCAAATCTCAGGAGCCAGTCACACTGGATTTTCTCGATGCTGAGTTAGAGAATGAAATTAAAGTGGAGATTCGAAATAAAATGATAGATGGAGAAAGTGGAGAAAAAACGTTCAGAACTCTGGTCAAGTCTCAAGATGAGAGATACATTGACAAAGGAAATCGAACATACACATGGACGCCTGTCAATGGCACAGATTACAGTTTGGCCTTGGTATTGCCAACCTACAGTTTTTACTATATAAAAGCCAAACTAGAAGAGACAATAACTCAGGCCAGATGTAACTTGGGGATATTTTCAGATTCAGAAACCCTGAAGCCAGACAATTTTGAAGAATCTGGCTATACTTTCATAGCACCAAGGGAATACTGCAATGATCTTAAACCTTCAGATAATAACACTGAATTTCTTTTGAATTTCAATGAATTTATTGATAGGAAAACTCCAAACAACCCCTCCTGTAATACAGATTTGATTAATAGAATCTTGCTGGATGCAGGTTTTACAAATGAACTTGTCCAAAATTATTGGAGTAAGCAGAAAAAT
Peptide sequence:
MQVLQMNLSKIIGVSRKICYYYEIPSIGAIRINTQEYLDVLGRPMVLAGDKAKQVQWTNVYLDALELGLVITGTLPVFNVTGQSENKTNLKNQLILGVMGVDVSLEDIKRLTPRFTLCPNGYYFAIDPNGYVLLHPNLQPKNPKSQEPVTLDFLDAELENEIKVEIRNKMIDGESGEKTFRTLVKSQDERYIDKGNRTYTWTPVNGTDYSLALVLPTYSFYYIKAKLEETITQARCNLGIFSDSETLKPDNFEESGYTFIAPREYCNDLKPSDNNTEFLLNFNEFIDRKTPNNPSCNTDLINRILLDAGFTNELVQNYWSKQKN
IRESfinder result
IRESfinder score
0.718401169
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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