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mmu_circPds5a_1152
Basic information of circular RNA
PanCircBase ID:
mmu_circPds5a_1152
mm39_Chr. Position ID:
chr5|65776286|65787398|-
Gene name:
Pds5a
Transcript:
ENSMUST00000201948.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
31,30,29,28,27,26,25,24,23
Exon/intron offsets:
0,676,1606,4036,4976,8141,8616,9055,10975
Genomic length:
11112
Exon/intron sizes in nt:
1,09,14,66,31,20,13,31,00,00,00,00,000
Flanking exon/introns:
chr5:65772947-65776286|chr5:65787398-65789055
Splice length:
1152
Other database IDs:
circBase: hsa_circ_0126288, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_137254
Human Ortholog IDs:
Mature spliced Sequence:
GTACAGGCAATTAAACTTCTGGTAAGGTGGCTGTTGGGTATGAAAAACAACCAGTCTAAATCTGCCAACTCAACTCTTCGGTTATTATCAGCCATGCTGGTTAGTGAGGGCGACCTGACAGAGCAAAAGAGGATCAGTAAATCTGATATGTCTCGCTTGCGATTAGCTGCTGGTAGTGCCATAATGAAGCTTGCTCAGGAACCTTGCTACCATGAAATTATTACCCCAGAACAGTTTCAGCTCTGTGCACTGGTTATTAATGATGAGTGCTACCAAGTAAGGCAGATATTTGCCCAGAAGCTTCATAAGGCACTTGTGAAGTTGCTTCTCCCACTGGAGTATATGGCCATCTTTGCTTTGTGTGCCAAAGACCCTGTGAAAGAAAGGAGAGCACACGCTCGGCAGTGTTTGTTAAAGAACATCAGCATCCGCAGGGAGTACATCAAACAGAACCCCATGGCCACTGAGAAATTATTGTCACTGCTGCCTGAATATGTGGTTCCATACATGATTCACCTCCTAGCCCATGATCCTGATTTCACACGGTCACAAGATGTTGATCAACTTCGTGATATAAAAGAGTGCCTGTGGTTTATGCTTGAAGTCTTAATGACAAAGAATGAAAACAACAGCCATGCATTCATGAAAAAGATGGCAGAGAATATCAAGCTAACCAGAGACGCCCAGTCTCCCGATGAATCCAAGACAAATGAAAAACTTTATACGGTTTGTGACGTGGCTCTGTGTGTTATAAATAGTAAAAGTGCTTTGTGCAATGCAGACTCACCAAAGGACCCAGTCCTCCCAATGAAGTTCTTTACACAGCCTGAAAAGGACTTCTGTAATGACAAAAGCTATATTTCAGAAGAGACAAGAGTTCTTCTGTTAACAGGAAAGCCAAAGCCTACTGGAGTATTAGGTACAGTGAACAAGCCTTTATCAGCAACGGGAAGGAAGCCTTATGTTAGAAGCGCCGGCACAGAGACTGGAAGCAATATTAACGCCAATTCAGAGCTGAGTCCTTCAGCCGGAAGTCGTTCAAGGGAACAGAGTTCAGAGGCATCAGAAACTGGAGTTAGTGAAAATGAGGAGAATCCTGTGAGAATAATTTCTGTCACACCTGTAAAGAATATTGATACTGTAAAGAATAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGAGGCATCAGAAACTGGAGT
60.03
ACCGAAGAGTTGAGTTGGCA
59.53
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGAGGCATCAGAAACTGGAGT
58.74
ACCGAAGAGTTGAGTTGGCA
59.53
179
PCR template sequence:
TTCAGAGGCATCAGAAACTGGAGTTAGTGAAAATGAGGAGAATCCTGTGAGAATAATTTCTGTCACACCTGTAAAGAATATTGATACTGTAAAGAATAAGGTACAGGCAATTAAACTTCTGGTAAGGTGGCTGTTGGGTATGAAAAACAACCAGTCTAAATCTGCCAACTCAACTCTTCGGTTATTATCAGCCATGCTGG
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
TGTAAAGAATAAGGTACAGGCAATTA
siRNA sets
AATTGCCTGTACCTTATTC, ATTGCCTGTACCTTATTCT, TAATTGCCTGTACCTTATT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDS5A_1152_ORF_1
0.9941
0.119592696
0.999998463
2265
ORF sequence:
ATGAAAAACAACCAGTCTAAATCTGCCAACTCAACTCTTCGGTTATTATCAGCCATGCTGGTTAGTGAGGGCGACCTGACAGAGCAAAAGAGGATCAGTAAATCTGATATGTCTCGCTTGCGATTAGCTGCTGGTAGTGCCATAATGAAGCTTGCTCAGGAACCTTGCTACCATGAAATTATTACCCCAGAACAGTTTCAGCTCTGTGCACTGGTTATTAATGATGAGTGCTACCAAGTAAGGCAGATATTTGCCCAGAAGCTTCATAAGGCACTTGTGAAGTTGCTTCTCCCACTGGAGTATATGGCCATCTTTGCTTTGTGTGCCAAAGACCCTGTGAAAGAAAGGAGAGCACACGCTCGGCAGTGTTTGTTAAAGAACATCAGCATCCGCAGGGAGTACATCAAACAGAACCCCATGGCCACTGAGAAATTATTGTCACTGCTGCCTGAATATGTGGTTCCATACATGATTCACCTCCTAGCCCATGATCCTGATTTCACACGGTCACAAGATGTTGATCAACTTCGTGATATAAAAGAGTGCCTGTGGTTTATGCTTGAAGTCTTAATGACAAAGAATGAAAACAACAGCCATGCATTCATGAAAAAGATGGCAGAGAATATCAAGCTAACCAGAGACGCCCAGTCTCCCGATGAATCCAAGACAAATGAAAAACTTTATACGGTTTGTGACGTGGCTCTGTGTGTTATAAATAGTAAAAGTGCTTTGTGCAATGCAGACTCACCAAAGGACCCAGTCCTCCCAATGAAGTTCTTTACACAGCCTGAAAAGGACTTCTGTAATGACAAAAGCTATATTTCAGAAGAGACAAGAGTTCTTCTGTTAACAGGAAAGCCAAAGCCTACTGGAGTATTAGGTACAGTGAACAAGCCTTTATCAGCAACGGGAAGGAAGCCTTATGTTAGAAGCGCCGGCACAGAGACTGGAAGCAATATTAACGCCAATTCAGAGCTGAGTCCTTCAGCCGGAAGTCGTTCAAGGGAACAGAGTTCAGAGGCATCAGAAACTGGAGTTAGTGAAAATGAGGAGAATCCTGTGAGAATAATTTCTGTCACACCTGTAAAGAATATTGATACTGTAAAGAATAAGGTACAGGCAATTAAACTTCTGGTAAGGTGGCTGTTGGGTATGAAAAACAACCAGTCTAAATCTGCCAACTCAACTCTTCGGTTATTATCAGCCATGCTGGTTAGTGAGGGCGACCTGACAGAGCAAAAGAGGATCAGTAAATCTGATATGTCTCGCTTGCGATTAGCTGCTGGTAGTGCCATAATGAAGCTTGCTCAGGAACCTTGCTACCATGAAATTATTACCCCAGAACAGTTTCAGCTCTGTGCACTGGTTATTAATGATGAGTGCTACCAAGTAAGGCAGATATTTGCCCAGAAGCTTCATAAGGCACTTGTGAAGTTGCTTCTCCCACTGGAGTATATGGCCATCTTTGCTTTGTGTGCCAAAGACCCTGTGAAAGAAAGGAGAGCACACGCTCGGCAGTGTTTGTTAAAGAACATCAGCATCCGCAGGGAGTACATCAAACAGAACCCCATGGCCACTGAGAAATTATTGTCACTGCTGCCTGAATATGTGGTTCCATACATGATTCACCTCCTAGCCCATGATCCTGATTTCACACGGTCACAAGATGTTGATCAACTTCGTGATATAAAAGAGTGCCTGTGGTTTATGCTTGAAGTCTTAATGACAAAGAATGAAAACAACAGCCATGCATTCATGAAAAAGATGGCAGAGAATATCAAGCTAACCAGAGACGCCCAGTCTCCCGATGAATCCAAGACAAATGAAAAACTTTATACGGTTTGTGACGTGGCTCTGTGTGTTATAAATAGTAAAAGTGCTTTGTGCAATGCAGACTCACCAAAGGACCCAGTCCTCCCAATGAAGTTCTTTACACAGCCTGAAAAGGACTTCTGTAATGACAAAAGCTATATTTCAGAAGAGACAAGAGTTCTTCTGTTAACAGGAAAGCCAAAGCCTACTGGAGTATTAGGTACAGTGAACAAGCCTTTATCAGCAACGGGAAGGAAGCCTTATGTTAGAAGCGCCGGCACAGAGACTGGAAGCAATATTAACGCCAATTCAGAGCTGAGTCCTTCAGCCGGAAGTCGTTCAAGGGAACAGAGTTCAGAGGCATCAGAAACTGGAGTTAGTGAAAATGAGGAGAATCCTGTGAGAATAATTTCTGTCACACCTGTAAAGAATATTGATACTGTAAAGAATAAG
Peptide sequence:
MKNNQSKSANSTLRLLSAMLVSEGDLTEQKRISKSDMSRLRLAAGSAIMKLAQEPCYHEIITPEQFQLCALVINDECYQVRQIFAQKLHKALVKLLLPLEYMAIFALCAKDPVKERRAHARQCLLKNISIRREYIKQNPMATEKLLSLLPEYVVPYMIHLLAHDPDFTRSQDVDQLRDIKECLWFMLEVLMTKNENNSHAFMKKMAENIKLTRDAQSPDESKTNEKLYTVCDVALCVINSKSALCNADSPKDPVLPMKFFTQPEKDFCNDKSYISEETRVLLLTGKPKPTGVLGTVNKPLSATGRKPYVRSAGTETGSNINANSELSPSAGSRSREQSSEASETGVSENEENPVRIISVTPVKNIDTVKNKVQAIKLLVRWLLGMKNNQSKSANSTLRLLSAMLVSEGDLTEQKRISKSDMSRLRLAAGSAIMKLAQEPCYHEIITPEQFQLCALVINDECYQVRQIFAQKLHKALVKLLLPLEYMAIFALCAKDPVKERRAHARQCLLKNISIRREYIKQNPMATEKLLSLLPEYVVPYMIHLLAHDPDFTRSQDVDQLRDIKECLWFMLEVLMTKNENNSHAFMKKMAENIKLTRDAQSPDESKTNEKLYTVCDVALCVINSKSALCNADSPKDPVLPMKFFTQPEKDFCNDKSYISEETRVLLLTGKPKPTGVLGTVNKPLSATGRKPYVRSAGTETGSNINANSELSPSAGSRSREQSSEASETGVSENEENPVRIISVTPVKNIDTVKNK
IRESfinder result
IRESfinder score
0.586776553
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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