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mmu_circDepdc5_656
Basic information of circular RNA
PanCircBase ID:
mmu_circDepdc5_656
mm39_Chr. Position ID:
chr5|33075268|33085283|+
Gene name:
Depdc5
Transcript:
ENSMUST00000049780.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
21,22,23,24
Exon/intron offsets:
0,6237,8965,9920
Genomic length:
10015
Exon/intron sizes in nt:
221,204,136,95
Flanking exon/introns:
chr5:33070564-33075268|chr5:33085283-33091293
Splice length:
656
Other database IDs:
circAtlas: mmu-Depdc5_0052
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_36465
Human Ortholog IDs:
Mature spliced Sequence:
GTCTGTGAGAGAACAGGAGAATCACAGTCGCAAAAGTGCAAGCTCCTGTGATGTCTCATCCAGCCCTTCCCTGCCAAGCCGTGCACTGCCCACTGAGGAAGTGAGGAGCCAGGCTTCTGATGACAGCTCCCTGGGCAAGAGCACCAACATCCTGATGATCCCTAACCCCCACCTGCACCAGTATGAAGTCAGCAGCTCACTGGGCTACACCAGCACCCGAGATGTCCTGGAGAACATGATAGAACCCCCACAGAGGGACTCCAGTGCACCAGGAAGGTTCCATGTGGGTAGTGCAGAGTCCATGCTCCATGTCCGACCTGGAGGATACACGCCTCAGAGAGCGCTGATTAACCCCTTCGCCCCCTCGAGGATGCCCATGAAGCTCACCTCCAACAGAAGGCGCTGGATGCACACTTTTCCTGTAGGCCCATCTGGAGAGGCCATCCAGATCCATCATCAGACCCGGCAAAACATGGCAGAGCTGCAGGGCAGCAGGCAGAGGGACCCTACCCACTCCTCTGCAGAGCTGTTGGAGTTGGCATACCATGAAGCTGCCGGGAGGCACAGCACTTCCCGCCAGCCTGGTGACAGCATGTCCTTGAACTTCAGTGGAACGGAAGAGCTTTCTGTCAGCCTGCTTAGCAACAGCAGTACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGAGGCACAGCACTTCCC
60.36
ACATCACAGGAGCTTGCACT
59.6
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGAGGCACAGCACTTCC
60.36
ACATCACAGGAGCTTGCACT
59.6
154
PCR template sequence:
GGGAGGCACAGCACTTCCCGCCAGCCTGGTGACAGCATGTCCTTGAACTTCAGTGGAACGGAAGAGCTTTCTGTCAGCCTGCTTAGCAACAGCAGTACAGGTCTGTGAGAGAACAGGAGAATCACAGTCGCAAAAGTGCAAGCTCCTGTGATGTCTCATCCAGCCCTTCCCTGCCAAGCCGTGCACTGCCCACTGAGGAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-298-5p(1), mmu-miR-138-5p(1), mmu-miR-149-5p(1), mmu-miR-370-3p(1), mmu-miR-541-5p(1), mmu-miR-3061-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AACAGCAGTACAGGTCTGTGAGAGAA
siRNA sets
TTCTCTCACAGACCTGTAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDEPDC5_656_ORF_1
0.8288
0.283546366
0.751587419
510
ORF sequence:
ATGATCCCTAACCCCCACCTGCACCAGTATGAAGTCAGCAGCTCACTGGGCTACACCAGCACCCGAGATGTCCTGGAGAACATGATAGAACCCCCACAGAGGGACTCCAGTGCACCAGGAAGGTTCCATGTGGGTAGTGCAGAGTCCATGCTCCATGTCCGACCTGGAGGATACACGCCTCAGAGAGCGCTGATTAACCCCTTCGCCCCCTCGAGGATGCCCATGAAGCTCACCTCCAACAGAAGGCGCTGGATGCACACTTTTCCTGTAGGCCCATCTGGAGAGGCCATCCAGATCCATCATCAGACCCGGCAAAACATGGCAGAGCTGCAGGGCAGCAGGCAGAGGGACCCTACCCACTCCTCTGCAGAGCTGTTGGAGTTGGCATACCATGAAGCTGCCGGGAGGCACAGCACTTCCCGCCAGCCTGGTGACAGCATGTCCTTGAACTTCAGTGGAACGGAAGAGCTTTCTGTCAGCCTGCTTAGCAACAGCAGTACAGGTCTGTGA
Peptide sequence:
MIPNPHLHQYEVSSSLGYTSTRDVLENMIEPPQRDSSAPGRFHVGSAESMLHVRPGGYTPQRALINPFAPSRMPMKLTSNRRRWMHTFPVGPSGEAIQIHHQTRQNMAELQGSRQRDPTHSSAELLELAYHEAAGRHSTSRQPGDSMSLNFSGTEELSVSLLSNSSTGL
IRESfinder result
IRESfinder score
0.339398168
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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