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mmu_circPds5a_834
Basic information of circular RNA
PanCircBase ID:
mmu_circPds5a_834
mm39_Chr. Position ID:
chr5|65780322|65787398|-
Gene name:
Pds5a
Transcript:
ENSMUST00000201948.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
28,27,26,25,24,23
Exon/intron offsets:
0,940,4105,4580,5019,6939
Genomic length:
7076
Exon/intron sizes in nt:
1,20,13,31,15,20,51,24,000
Flanking exon/introns:
chr5:65777955-65780322|chr5:65787398-65789055
Splice length:
834
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_164789
Human Ortholog IDs:
Mature spliced Sequence:
GTACAGGCAATTAAACTTCTGGTAAGGTGGCTGTTGGGTATGAAAAACAACCAGTCTAAATCTGCCAACTCAACTCTTCGGTTATTATCAGCCATGCTGGTTAGTGAGGGCGACCTGACAGAGCAAAAGAGGATCAGTAAATCTGATATGTCTCGCTTGCGATTAGCTGCTGGTAGTGCCATAATGAAGCTTGCTCAGGAACCTTGCTACCATGAAATTATTACCCCAGAACAGTTTCAGCTCTGTGCACTGGTTATTAATGATGAGTGCTACCAAGTAAGGCAGATATTTGCCCAGAAGCTTCATAAGGCACTTGTGAAGTTGCTTCTCCCACTGGAGTATATGGCCATCTTTGCTTTGTGTGCCAAAGACCCTGTGAAAGAAAGGAGAGCACACGCTCGGCAGTGTTTGTTAAAGAACATCAGCATCCGCAGGGAGTACATCAAACAGAACCCCATGGCCACTGAGAAATTATTGTCACTGCTGCCTGAATATGTGGTTCCATACATGATTCACCTCCTAGCCCATGATCCTGATTTCACACGGTCACAAGATGTTGATCAACTTCGTGATATAAAAGAGTGCCTGTGGTTTATGCTTGAAGTCTTAATGACAAAGAATGAAAACAACAGCCATGCATTCATGAAAAAGATGGCAGAGAATATCAAGCTAACCAGAGACGCCCAGTCTCCCGATGAATCCAAGACAAATGAAAAACTTTATACGGTTTGTGACGTGGCTCTGTGTGTTATAAATAGTAAAAGTGCTTTGTGCAATGCAGACTCACCAAAGGACCCAGTCCTCCCAATGAAGTTCTTTACACAGCCTGAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCAGACTCACCAAAGGACC
59.89
ACCGAAGAGTTGAGTTGGCA
59.53
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGCAATGCAGACTCACCA
60.18
ACCGAAGAGTTGAGTTGGCA
59.53
147
PCR template sequence:
CGTGGCTCTGTGTGTTATAAATAGTAAAAGTGCTTTGTGCAATGCAGACTCACCAAAGGACCCAGTCCTCCCAATGAAGTTCTTTACACAGCCTGAAAAGGTACAGGCAATTAAACTTCTGGTAAGGTGGCTGTTGGGTATGAAAAACAACCAGTCTAAATCTGCCAACTCAACTCTTCGGTTATTATCAGCCATGCTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-335-3p(3), mmu-miR-9-5p(2), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-199a-5p(1), mmu-miR-33-5p(1), mmu-miR-152-3p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-495-3p(1), mmu-miR-183-5p(1), mmu-miR-499-5p(1), mmu-miR-410-3p(1), mmu-miR-350-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACAGCCTGAAAAGGTACAGGCAATTA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDS5A_834_ORF_1
1.0486
0.146516455
0.999879335
1629
ORF sequence:
ATGAAAAACAACCAGTCTAAATCTGCCAACTCAACTCTTCGGTTATTATCAGCCATGCTGGTTAGTGAGGGCGACCTGACAGAGCAAAAGAGGATCAGTAAATCTGATATGTCTCGCTTGCGATTAGCTGCTGGTAGTGCCATAATGAAGCTTGCTCAGGAACCTTGCTACCATGAAATTATTACCCCAGAACAGTTTCAGCTCTGTGCACTGGTTATTAATGATGAGTGCTACCAAGTAAGGCAGATATTTGCCCAGAAGCTTCATAAGGCACTTGTGAAGTTGCTTCTCCCACTGGAGTATATGGCCATCTTTGCTTTGTGTGCCAAAGACCCTGTGAAAGAAAGGAGAGCACACGCTCGGCAGTGTTTGTTAAAGAACATCAGCATCCGCAGGGAGTACATCAAACAGAACCCCATGGCCACTGAGAAATTATTGTCACTGCTGCCTGAATATGTGGTTCCATACATGATTCACCTCCTAGCCCATGATCCTGATTTCACACGGTCACAAGATGTTGATCAACTTCGTGATATAAAAGAGTGCCTGTGGTTTATGCTTGAAGTCTTAATGACAAAGAATGAAAACAACAGCCATGCATTCATGAAAAAGATGGCAGAGAATATCAAGCTAACCAGAGACGCCCAGTCTCCCGATGAATCCAAGACAAATGAAAAACTTTATACGGTTTGTGACGTGGCTCTGTGTGTTATAAATAGTAAAAGTGCTTTGTGCAATGCAGACTCACCAAAGGACCCAGTCCTCCCAATGAAGTTCTTTACACAGCCTGAAAAGGTACAGGCAATTAAACTTCTGGTAAGGTGGCTGTTGGGTATGAAAAACAACCAGTCTAAATCTGCCAACTCAACTCTTCGGTTATTATCAGCCATGCTGGTTAGTGAGGGCGACCTGACAGAGCAAAAGAGGATCAGTAAATCTGATATGTCTCGCTTGCGATTAGCTGCTGGTAGTGCCATAATGAAGCTTGCTCAGGAACCTTGCTACCATGAAATTATTACCCCAGAACAGTTTCAGCTCTGTGCACTGGTTATTAATGATGAGTGCTACCAAGTAAGGCAGATATTTGCCCAGAAGCTTCATAAGGCACTTGTGAAGTTGCTTCTCCCACTGGAGTATATGGCCATCTTTGCTTTGTGTGCCAAAGACCCTGTGAAAGAAAGGAGAGCACACGCTCGGCAGTGTTTGTTAAAGAACATCAGCATCCGCAGGGAGTACATCAAACAGAACCCCATGGCCACTGAGAAATTATTGTCACTGCTGCCTGAATATGTGGTTCCATACATGATTCACCTCCTAGCCCATGATCCTGATTTCACACGGTCACAAGATGTTGATCAACTTCGTGATATAAAAGAGTGCCTGTGGTTTATGCTTGAAGTCTTAATGACAAAGAATGAAAACAACAGCCATGCATTCATGAAAAAGATGGCAGAGAATATCAAGCTAACCAGAGACGCCCAGTCTCCCGATGAATCCAAGACAAATGAAAAACTTTATACGGTTTGTGACGTGGCTCTGTGTGTTATAAATAGTAAAAGTGCTTTGTGCAATGCAGACTCACCAAAGGACCCAGTCCTCCCAATGAAGTTCTTTACACAGCCTGAAAAG
Peptide sequence:
MKNNQSKSANSTLRLLSAMLVSEGDLTEQKRISKSDMSRLRLAAGSAIMKLAQEPCYHEIITPEQFQLCALVINDECYQVRQIFAQKLHKALVKLLLPLEYMAIFALCAKDPVKERRAHARQCLLKNISIRREYIKQNPMATEKLLSLLPEYVVPYMIHLLAHDPDFTRSQDVDQLRDIKECLWFMLEVLMTKNENNSHAFMKKMAENIKLTRDAQSPDESKTNEKLYTVCDVALCVINSKSALCNADSPKDPVLPMKFFTQPEKVQAIKLLVRWLLGMKNNQSKSANSTLRLLSAMLVSEGDLTEQKRISKSDMSRLRLAAGSAIMKLAQEPCYHEIITPEQFQLCALVINDECYQVRQIFAQKLHKALVKLLLPLEYMAIFALCAKDPVKERRAHARQCLLKNISIRREYIKQNPMATEKLLSLLPEYVVPYMIHLLAHDPDFTRSQDVDQLRDIKECLWFMLEVLMTKNENNSHAFMKKMAENIKLTRDAQSPDESKTNEKLYTVCDVALCVINSKSALCNADSPKDPVLPMKFFTQPEK
IRESfinder result
IRESfinder score
0.596095216
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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