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mmu_circPdss1_445
Basic information of circular RNA
PanCircBase ID:
mmu_circPdss1_445
mm39_Chr. Position ID:
chr2|22802611|22819632|+
Gene name:
Pdss1
Transcript:
ENSMUST00000053729.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,6,7,8
Exon/intron offsets:
0,2602,2815,16940
Genomic length:
17021
Exon/intron sizes in nt:
142,112,110,81
Flanking exon/introns:
chr2:22796937-22802611|chr2:22819632-22819755
Splice length:
445
Other database IDs:
circAtlas: hsa-PDSS1_0038
Human Ortholog IDs:
Mature spliced Sequence:
AGAGATGCAAGCCAGCCAGCGCTCCATAGCCTTAGTTGCAGAAATGATCCACACTGCTACTCTGGTTCATGATGACGTTATTGATGATGCAAGTTCTCGAAGAGGAAAACATACAGTTAATAAAATCTGGGGTGAGAAAAAGGCTGTTCTTGCTGGAGATTTAATTCTTTCTGCAGCGTCTGTAGCTCTGGCACGGATTGGAAACACAGCTGTTGTATCTATGTTAGCCCAAGTTATTGAAGATTTGGTGCGTGGTGAATTTCTTCAGCTAGGGTCAAAAGAAAATGAGAATGAAAGGTTTGCCCACTACCTTGAGAAGACCTTCAAGAAGACAGCCAGCCTGATAGCCAACAGTTGTAAAGCAGTCTCTGTCCTGGGTTGCCCTGACCCAGTGGTGCATGAGATAGCCTATCAGTATGGGAAAAATGTTGGAATAGCTTTTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGTCTCTGTCCTGGGTTGC
60.32
TGAACCAGAGTAGCAGTGTGG
59.66
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGTCTCTGTCCTGGGTTG
60.32
TGAACCAGAGTAGCAGTGTGG
59.66
153
PCR template sequence:
AGCCAACAGTTGTAAAGCAGTCTCTGTCCTGGGTTGCCCTGACCCAGTGGTGCATGAGATAGCCTATCAGTATGGGAAAAATGTTGGAATAGCTTTTCAGAGAGATGCAAGCCAGCCAGCGCTCCATAGCCTTAGTTGCAGAAATGATCCACACTGCTACTCTGGTTCATGATGACGTTATTGATGATGCAAGTTCTCGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-501-3p(1), mmu-miR-297a-5p(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AATAGCTTTTCAGAGAGATGCAAGCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDSS1_445_ORF_1
1.0103
0.052252126
0.629599321
513
ORF sequence:
ATGCAAGCCAGCCAGCGCTCCATAGCCTTAGTTGCAGAAATGATCCACACTGCTACTCTGGTTCATGATGACGTTATTGATGATGCAAGTTCTCGAAGAGGAAAACATACAGTTAATAAAATCTGGGGTGAGAAAAAGGCTGTTCTTGCTGGAGATTTAATTCTTTCTGCAGCGTCTGTAGCTCTGGCACGGATTGGAAACACAGCTGTTGTATCTATGTTAGCCCAAGTTATTGAAGATTTGGTGCGTGGTGAATTTCTTCAGCTAGGGTCAAAAGAAAATGAGAATGAAAGGTTTGCCCACTACCTTGAGAAGACCTTCAAGAAGACAGCCAGCCTGATAGCCAACAGTTGTAAAGCAGTCTCTGTCCTGGGTTGCCCTGACCCAGTGGTGCATGAGATAGCCTATCAGTATGGGAAAAATGTTGGAATAGCTTTTCAGAGAGATGCAAGCCAGCCAGCGCTCCATAGCCTTAGTTGCAGAAATGATCCACACTGCTACTCTGGTTCATGA
Peptide sequence:
MQASQRSIALVAEMIHTATLVHDDVIDDASSRRGKHTVNKIWGEKKAVLAGDLILSAASVALARIGNTAVVSMLAQVIEDLVRGEFLQLGSKENENERFAHYLEKTFKKTASLIANSCKAVSVLGCPDPVVHEIAYQYGKNVGIAFQRDASQPALHSLSCRNDPHCYSGS
IRESfinder result
IRESfinder score
0.63634317
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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