top of page
mmu_circPcca_475
Basic information of circular RNA
PanCircBase ID:
mmu_circPcca_475
mm39_Chr. Position ID:
chr14|122922293|122938577|+
Gene name:
Pcca
Transcript:
ENSMUST00000038374.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
13,14,15,16,17
Exon/intron offsets:
0,1221,5217,7298,16173
Genomic length:
16284
Exon/intron sizes in nt:
1,44,75,69,76,111
Flanking exon/introns:
chr14:122906083-122922293|chr14:122938577-122951434
Splice length:
475
Other database IDs:
circBase: mmu_circ_0005018, CIRCpedia: MMU_CIRCpedia_5866, circAtlas: mmu-Pcca_0020
circBase: hsa_circ_0002880, circAtlas: hsa-PCCA_0024, CIRCpedia: HSA_CIRCpedia_9972
Human Ortholog IDs:
Mature spliced Sequence:
GTCGAACATCCTGTCACAGAGTGCATTACTGGCCTGGACTTAGTCCAAGAAATGATCCTTGTTGCTAAGGGTTACCCACTCAGGCACAAGCAAGAGGATATTCCCATCAGTGGCTGGGCAGTTGAATGTCGGGTTTATGCTGAGGACCCCTACAAGTCTTTCGGTTTACCGTCTATTGGGAGGCTGTCCCAGTACCAAGAGCCGATACATCTACCTGGTGTCCGAGTTGACAGTGGCATCCAACCAGGAAGTGACATCAGCATCTATTATGATCCTATGATTTCAAAGCTAGTCACATATGGGTCTGACAGAGCAGAAGCCCTGAAGAGGATGGAAGACGCACTGGACAATTATGTGATCCGGGGTGTTACACACAACATCCCATTGCTCCGGGAGGTGATAATCAACACACGTTTTGTGAAAGGAGACATCAGCACTAAGTTTCTCTCTGATGTGTATCCTGATGGCTTCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AACATCCCATTGCTCCGGG
60.08
AGTCCAGGCCAGTAATGCAC
60.04
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AACATCCCATTGCTCCGGG
60.08
AAGTCCAGGCCAGTAATGCA
59.3
141
PCR template sequence:
AACATCCCATTGCTCCGGGAGGTGATAATCAACACACGTTTTGTGAAAGGAGACATCAGCACTAAGTTTCTCTCTGATGTGTATCCTGATGGCTTCAAAGGTCGAACATCCTGTCACAGAGTGCATTACTGGCCTGGACTTAGTCCAAGAAATGATCCTTGTTGCTAAGGGTTACCCACTCAGGCACAAGCAAGAGGATA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-181a-5p(1), mmu-miR-322-5p(1), mmu-miR-181b-5p(1), mmu-miR-3470b(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GATGGCTTCAAAGGTCGAACATCCTG
siRNA sets
ATGTTCGACCTTTGAAGCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPCCA_475_ORF_1
1.093
0.226868007
0.783905067
498
ORF sequence:
ATGTGTATCCTGATGGCTTCAAAGGTCGAACATCCTGTCACAGAGTGCATTACTGGCCTGGACTTAGTCCAAGAAATGATCCTTGTTGCTAAGGGTTACCCACTCAGGCACAAGCAAGAGGATATTCCCATCAGTGGCTGGGCAGTTGAATGTCGGGTTTATGCTGAGGACCCCTACAAGTCTTTCGGTTTACCGTCTATTGGGAGGCTGTCCCAGTACCAAGAGCCGATACATCTACCTGGTGTCCGAGTTGACAGTGGCATCCAACCAGGAAGTGACATCAGCATCTATTATGATCCTATGATTTCAAAGCTAGTCACATATGGGTCTGACAGAGCAGAAGCCCTGAAGAGGATGGAAGACGCACTGGACAATTATGTGATCCGGGGTGTTACACACAACATCCCATTGCTCCGGGAGGTGATAATCAACACACGTTTTGTGAAAGGAGACATCAGCACTAAGTTTCTCTCTGATGTGTATCCTGATGGCTTCAAA
Peptide sequence:
MCILMASKVEHPVTECITGLDLVQEMILVAKGYPLRHKQEDIPISGWAVECRVYAEDPYKSFGLPSIGRLSQYQEPIHLPGVRVDSGIQPGSDISIYYDPMISKLVTYGSDRAEALKRMEDALDNYVIRGVTHNIPLLREVIINTRFVKGDISTKFLSDVYPDGFK
IRESfinder result
IRESfinder score
0.59786143
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page