top of page
mmu_circPpp1cb_540
Basic information of circular RNA
PanCircBase ID:
mmu_circPpp1cb_540
mm39_Chr. Position ID:
chr5|32635409|32642674|+
Gene name:
Ppp1cb
Transcript:
ENSMUST00000015100.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
2,3,4,5
Exon/intron offsets:
0,2624,5294,7193
Genomic length:
7265
Exon/intron sizes in nt:
132,231,105,72
Flanking exon/introns:
chr5:32616751-32635409|chr5:32642674-32643224
Splice length:
540
Other database IDs:
CIRCpedia: MMU_CIRCpedia_16529, circAtlas: mmu-Ppp1cb_0004
circBase: hsa_circ_0003905, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_40655
Human Ortholog IDs:
Mature spliced Sequence:
TACGAGGATGTCGTCCAGGAAAGATTGTACAAATGACTGAAGCAGAAGTCCGAGGGTTGTGTATCAAGTCTCGTGAAATCTTTCTCAGCCAGCCTATTCTTTTGGAATTGGAAGCACCACTGAAGATTTGTGGAGACATTCATGGACAATATACAGACTTACTAAGATTATTTGAATATGGAGGTTTTCCACCAGAAGCCAACTATCTTTTCTTAGGAGATTATGTGGACAGAGGAAAGCAGTCTTTGGAAACCATCTGTTTGCTATTGGCTTACAAAATCAAATACCCGGAGAACTTCTTTCTTCTAAGAGGAAACCATGAGTGTGCTAGCATCAATCGCATTTATGGATTCTACGATGAGTGTAAACGAAGATTTAATATTAAATTGTGGAAGACATTCACTGATTGTTTTAACTGTCTGCCTATAGCTGCTATTGTTGATGAGAAAATCTTCTGTTGTCATGGAGGACTGTCACCAGACCTACAATCTATGGAACAGATTCGGAGAATTATGAGACCCACTGACGTACCTGATACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTCATGGAGGACTGTCACCA
59.02
CAACCCTCGGACTTCTGCTT
59.96
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCATGGAGGACTGTCACC
59.02
CAACCCTCGGACTTCTGCTT
59.96
141
PCR template sequence:
GATGAGAAAATCTTCTGTTGTCATGGAGGACTGTCACCAGACCTACAATCTATGGAACAGATTCGGAGAATTATGAGACCCACTGACGTACCTGATACAGTACGAGGATGTCGTCCAGGAAAGATTGTACAAATGACTGAAGCAGAAGTCCGAGGGTTGTGTATCAAGTCTCGTGAAATCTTTCTCAGCCAGCCTATTCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GTACCTGATACAGTACGAGGATGTCG
siRNA sets
ACATCCTCGTACTGTATCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPPP1CB_540_ORF_1
0.6712
0.008484583
0.972615189
1047
ORF sequence:
ATGACTGAAGCAGAAGTCCGAGGGTTGTGTATCAAGTCTCGTGAAATCTTTCTCAGCCAGCCTATTCTTTTGGAATTGGAAGCACCACTGAAGATTTGTGGAGACATTCATGGACAATATACAGACTTACTAAGATTATTTGAATATGGAGGTTTTCCACCAGAAGCCAACTATCTTTTCTTAGGAGATTATGTGGACAGAGGAAAGCAGTCTTTGGAAACCATCTGTTTGCTATTGGCTTACAAAATCAAATACCCGGAGAACTTCTTTCTTCTAAGAGGAAACCATGAGTGTGCTAGCATCAATCGCATTTATGGATTCTACGATGAGTGTAAACGAAGATTTAATATTAAATTGTGGAAGACATTCACTGATTGTTTTAACTGTCTGCCTATAGCTGCTATTGTTGATGAGAAAATCTTCTGTTGTCATGGAGGACTGTCACCAGACCTACAATCTATGGAACAGATTCGGAGAATTATGAGACCCACTGACGTACCTGATACAGTACGAGGATGTCGTCCAGGAAAGATTGTACAAATGACTGAAGCAGAAGTCCGAGGGTTGTGTATCAAGTCTCGTGAAATCTTTCTCAGCCAGCCTATTCTTTTGGAATTGGAAGCACCACTGAAGATTTGTGGAGACATTCATGGACAATATACAGACTTACTAAGATTATTTGAATATGGAGGTTTTCCACCAGAAGCCAACTATCTTTTCTTAGGAGATTATGTGGACAGAGGAAAGCAGTCTTTGGAAACCATCTGTTTGCTATTGGCTTACAAAATCAAATACCCGGAGAACTTCTTTCTTCTAAGAGGAAACCATGAGTGTGCTAGCATCAATCGCATTTATGGATTCTACGATGAGTGTAAACGAAGATTTAATATTAAATTGTGGAAGACATTCACTGATTGTTTTAACTGTCTGCCTATAGCTGCTATTGTTGATGAGAAAATCTTCTGTTGTCATGGAGGACTGTCACCAGACCTACAATCTATGGAACAGATTCGGAGAATTATGAGACCCACTGACGTACCTGATACA
Peptide sequence:
MTEAEVRGLCIKSREIFLSQPILLELEAPLKICGDIHGQYTDLLRLFEYGGFPPEANYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRFNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDTVRGCRPGKIVQMTEAEVRGLCIKSREIFLSQPILLELEAPLKICGDIHGQYTDLLRLFEYGGFPPEANYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRFNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDT
IRESfinder result
IRESfinder score
0.741787084
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page