top of page
mmu_circPds5a_498
Basic information of circular RNA
PanCircBase ID:
mmu_circPds5a_498
mm39_Chr. Position ID:
chr5|65809730|65813751|-
Gene name:
Pds5a
Transcript:
ENSMUST00000201948.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
11,10,9,8
Exon/intron offsets:
0,1617,2401,3880
Genomic length:
4021
Exon/intron sizes in nt:
14,69,51,16,141
Flanking exon/introns:
chr5:65808639-65809730|chr5:65813751-65815689
Splice length:
498
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
TTTTTCAATCAAGTCCTGGTGCTGGGCAGATCATCAGTCAGCGACCTGTCTGAACACGTATTTGATCTGATTCAGGAACTTTTTGCTATCGATCCTCAGTTACTGTTATCTGTCATGCCACAGCTTGAATTCAAACTGAAGAGCAACGATGGTGAAGAACGCCTAGCTGTGGTTCGACTCCTCGCAAAATTGTTCGGCTCTAAAGATTCAGATTTAGCAACACAGAATCGGCCTCTCTGGCAGTGCTTTCTTGGGCGATTTAATGACATTCATGTTCCTGTGAGGTTAGAAAGTGTGAAGTTTGCCAGCCACTGTTTGATGAATCACCCAGACTTAGCGAAGGATCTGACAGAATATTTGAAAGTTAGGTCACATGATCCAGAAGAAGCCATTCGTCATGATGTTATTGTTACTATAATAACAGCTGCCAAAAGAGACCTTGCCTTAGTAAATGATCAGTTGCTTGGCTTTGTCAGGGAAAGGACACTGGATAAACGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AATAACAGCTGCCAAAAGAGACC
59.49
CGTGTTCAGACAGGTCGCT
60.01
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TAATAACAGCTGCCAAAAGAGACC
59.3
GTGTTCAGACAGGTCGCTGA
59.97
140
PCR template sequence:
TGATGTTATTGTTACTATAATAACAGCTGCCAAAAGAGACCTTGCCTTAGTAAATGATCAGTTGCTTGGCTTTGTCAGGGAAAGGACACTGGATAAACGGTTTTTCAATCAAGTCCTGGTGCTGGGCAGATCATCAGTCAGCGACCTGTCTGAACACGTATTTGATCTGATTCAGGAACTTTTTGCTATCGATCCTCAGT
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-135a-5p(1), mmu-miR-194-5p(1), mmu-miR-324-3p(1), mmu-miR-802-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTGGATAAACGGTTTTTCAATCAAG
siRNA sets
ATTGAAAAACCGTTTATCC, TTGAAAAACCGTTTATCCA, TGAAAAACCGTTTATCCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDS5A_498_ORF_1
1.0527
0.090672723
0.968531176
882
ORF sequence:
ATGCCACAGCTTGAATTCAAACTGAAGAGCAACGATGGTGAAGAACGCCTAGCTGTGGTTCGACTCCTCGCAAAATTGTTCGGCTCTAAAGATTCAGATTTAGCAACACAGAATCGGCCTCTCTGGCAGTGCTTTCTTGGGCGATTTAATGACATTCATGTTCCTGTGAGGTTAGAAAGTGTGAAGTTTGCCAGCCACTGTTTGATGAATCACCCAGACTTAGCGAAGGATCTGACAGAATATTTGAAAGTTAGGTCACATGATCCAGAAGAAGCCATTCGTCATGATGTTATTGTTACTATAATAACAGCTGCCAAAAGAGACCTTGCCTTAGTAAATGATCAGTTGCTTGGCTTTGTCAGGGAAAGGACACTGGATAAACGGTTTTTCAATCAAGTCCTGGTGCTGGGCAGATCATCAGTCAGCGACCTGTCTGAACACGTATTTGATCTGATTCAGGAACTTTTTGCTATCGATCCTCAGTTACTGTTATCTGTCATGCCACAGCTTGAATTCAAACTGAAGAGCAACGATGGTGAAGAACGCCTAGCTGTGGTTCGACTCCTCGCAAAATTGTTCGGCTCTAAAGATTCAGATTTAGCAACACAGAATCGGCCTCTCTGGCAGTGCTTTCTTGGGCGATTTAATGACATTCATGTTCCTGTGAGGTTAGAAAGTGTGAAGTTTGCCAGCCACTGTTTGATGAATCACCCAGACTTAGCGAAGGATCTGACAGAATATTTGAAAGTTAGGTCACATGATCCAGAAGAAGCCATTCGTCATGATGTTATTGTTACTATAATAACAGCTGCCAAAAGAGACCTTGCCTTAGTAAATGATCAGTTGCTTGGCTTTGTCAGGGAAAGGACACTGGATAAACGG
Peptide sequence:
MPQLEFKLKSNDGEERLAVVRLLAKLFGSKDSDLATQNRPLWQCFLGRFNDIHVPVRLESVKFASHCLMNHPDLAKDLTEYLKVRSHDPEEAIRHDVIVTIITAAKRDLALVNDQLLGFVRERTLDKRFFNQVLVLGRSSVSDLSEHVFDLIQELFAIDPQLLLSVMPQLEFKLKSNDGEERLAVVRLLAKLFGSKDSDLATQNRPLWQCFLGRFNDIHVPVRLESVKFASHCLMNHPDLAKDLTEYLKVRSHDPEEAIRHDVIVTIITAAKRDLALVNDQLLGFVRERTLDKR
IRESfinder result
IRESfinder score
0.627522582
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page