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mmu_ciPds5a_1328
Basic information of circular RNA
PanCircBase ID:
mmu_ciPds5a_1328
mm39_Chr. Position ID:
chr5|65812282|65813610|-
Gene name:
Pds5a
Transcript:
ENSMUST00000201948.4
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
8
Exon/intron offsets:
0
Genomic length:
1328
Exon/intron sizes in nt:
1328
Flanking exon/introns:
chr5:65812247-65813610
Splice length:
1328
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTATTCTTTAAGGTGTATAGGGAAAAAAAAATCTACTTTGAAGATGTTTTTTCTCTAATTATATGGGAGTGAAATATGAGTTTAGTCTATCTCATTTAGCTCATGTAACATATGAAACATATCCCTAGTTGTTATCTGCTGATAAACAGTGGAAGGAGATGTAAAAGTAGTGTCATCTTTGAAATTTACAATATTCAGTATTAATATTAAAGAACATTTACATATTTAAGTAAATACTAAACTTACTTATTATATAAGTAATGGGTTTAATCATTTTCTTACCAATTTAGTATATTAGGATGCACATTCAGTCATACACTAAATAAATGTAATACTAGAAAAAATAATTGATTAAACTATAAATGTAGAATTTTTATATTTTTGGACTTTTCACTCATTAAGGGATATTTTCAGTTCAACATATTTATATTATCATAATACTTCATTATGACAAATCAACACATTTGTCTGTCAGCAATAACAAACCGTTTTACTCCTGAAGGCAATTTCAGCTTTACTTGAGAAACATGACACCTTACAGTGATGGCGGCAGGGCTTTAGATCAGATTAGTTTTGTTTTAGTAGTTTATAGATGTGAAACCTCACATTACTTGAAGTAATCATGGGTCTGTAAATATAGTCACTCACAAGTAATACAAAATTTTTTATAAAGTCTACTGTTTAATACTTAAGACATTAATTTTTCTTTAAAGAGAGCAAATTGGATTAGTAAATTTTAGACATACTAAATGTTTATAGTGCTGACCATTGTTTTATTTTGGTTGAGAAAAAAGTTTTTAAAGTTTCCATTTTGTTACTACTGTGTGTAAGCCTTACATAATTGTCATTTTCCATTGCTTTATACAAGTGTGCAACTTTTACTCCACTGCCCACAAGCTTTCTGACAGTGATAACTTGAATTTTGAATTCCCATTCTCTAATAGCGTTGTTTTTCACTACTATGTTCTCTAGTCAGTGGAGGGTCATTGCTGGCATTGTATACTAGACCCTTAAGTCATCACTAGTCATGGGGTTCTTTTTTATTTTTCGGGTGCAGCAAATAATTTTTATGAAGGAAACTTAATAGGGTAGGAAGATTGTGTGCTTTTTGTAAAAATTCCTTTAAAATTCTTGAACAAAATGACTATATATAATCAGTGTGCACTTTGCAAATAAGTTGTAAAGTAGGTACGAATTAGTGGTAGGGAAGATATGAGATAAGGTCAGAAAGCCAGGTGATCTAACATGAAATCAGAAAAACATTTCCACAGTAAACACTAGCACGCAATATTTTACATTGTGCATTTTGCAAGTCAAAAGTAAAGGCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCACAGTAAACACTAGCACGC
59.54
AGACTAAACTCATATTTCACTCCCA
57.5
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCACAGTAAACACTAGCACGC
59.54
GACTAAACTCATATTTCACTCCCA
56.2
150
PCR template sequence:
AAGCCAGGTGATCTAACATGAAATCAGAAAAACATTTCCACAGTAAACACTAGCACGCAATATTTTACATTGTGCATTTTGCAAGTCAAAAGTAAAGGCAGTATTCTTTAAGGTGTATAGGGAAAAAAAAATCTACTTTGAAGATGTTTTTTCTCTAATTATATGGGAGTGAAATATGAGTTTAGTCTATCTCATTTAGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-26a-5p(2), mmu-miR-26b-5p(2), mmu-miR-137-3p(1), mmu-miR-20b-5p(1), mmu-miR-17-5p(1), mmu-miR-429-3p(1), mmu-miR-34c-5p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-340-5p(1), mmu-miR-297a-5p(1), mmu-miR-190b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAAAGTAAAGGCAGTATTCTTTAAGG
siRNA sets
AAGAATACTGCCTTTACTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.920028979
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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