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mmu_circDepdc5_655
Basic information of circular RNA
PanCircBase ID:
mmu_circDepdc5_655
mm39_Chr. Position ID:
chr5|33053223|33061876|+
Gene name:
Depdc5
Transcript:
ENSMUST00000049780.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
10,11,12,13,14,15,16,17
Exon/intron offsets:
0,1999,3112,5576,5950,7897,8395,8579
Genomic length:
8653
Exon/intron sizes in nt:
62,70,73,104,75,135,62,74
Flanking exon/introns:
chr5:33050797-33053223|chr5:33061876-33067800
Splice length:
655
Other database IDs:
CIRCpedia: MMU_CIRCpedia_218797, circAtlas: mmu-Depdc5_0011
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GGGATCTGTACTTTGAGAAAGCTGTGAACGGTTTCCTCGCCGACCTGTTTACTAAATGGAAGGAGAAGAACTGTAGTCATGAAGTGACTGTGGTCCTGTTTTCCAGAACTTTCTATGATGCAAAATCTATTGATGAATTTCCTGAAATAAACCGAGCTTCAATTCAAGAGGATCACAAAGGGAGATTCTATGAGGACTTTTACAAAGTGGTGGTGCAGAATGAGAGAAGGGAAGAGTGGACTTCACTCCTCGTGACCATTAAAAAACTCTTCATCCAGTATCCAGTGTTGGTGCGACTGGAACAGGCAGGGGGCTTTCCTCAAGGAGACAATTCTACCTCAGCACAAGGAAACTACCTAGAGGCCATCAACTTGTCATTCAATGTGTTTGACAAGCACTACATCAACCGAAACTTTGACCGAACTGGGCAGATGTCTGTGGTGATCACGCCGGGGGTGGGTGTCTTTGAAGTGGACCGCCTACTCATGATCTTGACCAAGCAGCGGATGATTGATAATGGAATTGGTGTGGACTTAGTGTGCATGGGAGAGCAGCCACTACATGCTGTGCCATTATTCAAGCTACATAACCGGAGTGTTCCGAGGGATTCTCGACTGGGTGATGATTATAATATTCCTCACTGGATAAACCATAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGGATTCTCGACTGGGTGA
59.96
ACAGGACCACAGTCACTTCA
58.5
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGGATTCTCGACTGGGTGA
59.96
AACAGGACCACAGTCACTTCA
59.16
153
PCR template sequence:
CACTACATGCTGTGCCATTATTCAAGCTACATAACCGGAGTGTTCCGAGGGATTCTCGACTGGGTGATGATTATAATATTCCTCACTGGATAAACCATAGGGGATCTGTACTTTGAGAAAGCTGTGAACGGTTTCCTCGCCGACCTGTTTACTAAATGGAAGGAGAAGAACTGTAGTCATGAAGTGACTGTGGTCCTGTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-let-7a-5p(1), mmu-miR-141-3p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-196a-5p(1), mmu-miR-98-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGATAAACCATAGGGGATCTGTACTT
siRNA sets
AAGTACAGATCCCCTATGG, AGTACAGATCCCCTATGGT, GATCCCCTATGGTTTATCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDEPDC5_655_ORF_1
0.9606
0.121397882
0.221129062
240
ORF sequence:
ATGTCTGTGGTGATCACGCCGGGGGTGGGTGTCTTTGAAGTGGACCGCCTACTCATGATCTTGACCAAGCAGCGGATGATTGATAATGGAATTGGTGTGGACTTAGTGTGCATGGGAGAGCAGCCACTACATGCTGTGCCATTATTCAAGCTACATAACCGGAGTGTTCCGAGGGATTCTCGACTGGGTGATGATTATAATATTCCTCACTGGATAAACCATAGGGGATCTGTACTTTGA
Peptide sequence:
MSVVITPGVGVFEVDRLLMILTKQRMIDNGIGVDLVCMGEQPLHAVPLFKLHNRSVPRDSRLGDDYNIPHWINHRGSVL
IRESfinder result
IRESfinder score
0.666462269
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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