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mmu_circPds5a_1748
Basic information of circular RNA
PanCircBase ID:
mmu_circPds5a_1748
mm39_Chr. Position ID:
chr5|65801362|65823654|-
Gene name:
Pds5a
Transcript:
ENSMUST00000201948.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
15
Exon/intron indexes:
17,16,15,14,13,12,11,10,9,8,7,6,5,4,3
Exon/intron offsets:
0,2313,3068,3904,6373,7125,8368,9985,10769,12248,14327,15587,19836,20408,22088
Genomic length:
22292
Exon/intron sizes in nt:
11,61,40,49,82,11,41,50,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr5:65796005-65801362|chr5:65823654-65854105
Splice length:
1748
Other database IDs:
CIRCpedia: MMU_CIRCpedia_220877, circAtlas: mmu-Pds5a_0013
circBase: hsa_circ_0126316, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_147462
Human Ortholog IDs:
Mature spliced Sequence:
ATGGTAGTGAAAACTTTTATGGATATGGATCAGGATTCAGAAGATGAAAAGCAACAGTATCTCCCACTAGCCTTGCATCTCGCATCTGAATTCTTTCTCAGGAACCCTAATAAAGATGTGCGCCTTCTCGTAGCATGTTGTTTGGCTGATATATTTCGAATCTATGCCCCAGAAGCTCCATATACTTCCCATGATAAACTTAAGGACATATTTCTCTTTATTACCAGACAGTTAAAAGGTTTGGAGGATACAAAGAGTCCACAGTTTAATAGATATTTTTATTTATTAGAGAATTTAGCTTGGGTTAAATCATATAACATCTGCTTTGAGTTGGAAGATTGCAATGAAATTTTTATTCAGCTTTTTAGAACTCTCTTCTCGGTAATCAACAATAGCCACAATACGAAAGTACAAATGCACATGTTAGACTTGATGAGTTCTATCATCATGGAAGGTGATGGAGTTACTCAAGAATTATTGGATTCCATTCTTATCAACCTCATCCCTGCACACAAGAACTTAAATAAACAGTCCTTCGACCTTGCAAAAGTCCTACTGAAAAGGACAGTCCAGACTATTGAAGCATGTATTGCCAATTTTTTCAATCAAGTCCTGGTGCTGGGCAGATCATCAGTCAGCGACCTGTCTGAACACGTATTTGATCTGATTCAGGAACTTTTTGCTATCGATCCTCAGTTACTGTTATCTGTCATGCCACAGCTTGAATTCAAACTGAAGAGCAACGATGGTGAAGAACGCCTAGCTGTGGTTCGACTCCTCGCAAAATTGTTCGGCTCTAAAGATTCAGATTTAGCAACACAGAATCGGCCTCTCTGGCAGTGCTTTCTTGGGCGATTTAATGACATTCATGTTCCTGTGAGGTTAGAAAGTGTGAAGTTTGCCAGCCACTGTTTGATGAATCACCCAGACTTAGCGAAGGATCTGACAGAATATTTGAAAGTTAGGTCACATGATCCAGAAGAAGCCATTCGTCATGATGTTATTGTTACTATAATAACAGCTGCCAAAAGAGACCTTGCCTTAGTAAATGATCAGTTGCTTGGCTTTGTCAGGGAAAGGACACTGGATAAACGGTGGCGAGTAAGAAAAGAAGCCATGATGGGTCTGGCTCAGCTCTATAAGAAATACTGTCTTCATGGGGAAGCAGGAAAGGAAGCCGCGGAGAAAGTCAGCTGGATAAAGGACAAGCTGCTGCATATCTACTATCAGAACAGCATTGATGACAAACTATTGGTAGAGAAAATCTTTGCTCAGTATCTTGTTCCCCACAACCTGGAAACAGAAGAGAGAATGAAATGCTTATATTATTTATATGCTAGCTTGGATCCAAATGCTGTAAAAGCTCTCAATGAAATGTGGAAATGTCAGAACATGCTTCGAAGTCATGTGCGTGAACTATTGGACTTACACAAGCAGCCTACATCAGAAGCGAACTGTTCTGCCATGTTTGGGAAACTGATGACCATAGCAAAGAATTTGCCTGACCCTGGAAAAGCACAAGATTTTGTAAAGAAATTTAACCAGGTTCTTGGTGATGATGAGAAACTGAGGTCTCAGTTGGAATTATTAATCAGCCCAACCTGTTCATGCAAGCAGGCTGACGTTTGTGTGAGGGAAATAGCTCGGAAACTTGCAAATCCTAAGCAGCCAACCAACCCTTTTCTAGAGATGGTCAAATTTCTTTTGGAAAGAATTGCTCCTGTGCACATCGATTCAGAAGCCATAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TAAGCAGCCAACCAACCCTT
59.81
CGAGATGCAAGGCTAGTGGG
60.53
169
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGCCAACCAACCCTTTTC
60.25
CGAGATGCAAGGCTAGTGGG
60.53
166
PCR template sequence:
AACTTGCAAATCCTAAGCAGCCAACCAACCCTTTTCTAGAGATGGTCAAATTTCTTTTGGAAAGAATTGCTCCTGTGCACATCGATTCAGAAGCCATAAGATGGTAGTGAAAACTTTTATGGATATGGATCAGGATTCAGAAGATGAAAAGCAACAGTATCTCCCACTAGCCTTGCATCTCGCATCTGAATTCTTTCTCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(3), mmu-miR-223-3p(1), mmu-miR-320-3p(1), mmu-miR-136-5p(1), mmu-miR-194-5p(1), mmu-miR-324-3p(1), mmu-miR-705(1), mmu-miR-802-5p(1), mmu-miR-342-3p(1), mmu-miR-377-3p(1), mmu-miR-539-5p(1), mmu-miR-335-3p(1), mmu-miR-669d-5p(1), mmu-miR-3105-3p(1), mmu-miR-296-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CAGAAGCCATAAGATGGTAGTGAAAA
siRNA sets
TTTTCACTACCATCTTATG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDS5A_1748_ORF_1
0.904
0.054968185
0.999903484
1755
ORF sequence:
ATGGTAGTGAAAACTTTTATGGATATGGATCAGGATTCAGAAGATGAAAAGCAACAGTATCTCCCACTAGCCTTGCATCTCGCATCTGAATTCTTTCTCAGGAACCCTAATAAAGATGTGCGCCTTCTCGTAGCATGTTGTTTGGCTGATATATTTCGAATCTATGCCCCAGAAGCTCCATATACTTCCCATGATAAACTTAAGGACATATTTCTCTTTATTACCAGACAGTTAAAAGGTTTGGAGGATACAAAGAGTCCACAGTTTAATAGATATTTTTATTTATTAGAGAATTTAGCTTGGGTTAAATCATATAACATCTGCTTTGAGTTGGAAGATTGCAATGAAATTTTTATTCAGCTTTTTAGAACTCTCTTCTCGGTAATCAACAATAGCCACAATACGAAAGTACAAATGCACATGTTAGACTTGATGAGTTCTATCATCATGGAAGGTGATGGAGTTACTCAAGAATTATTGGATTCCATTCTTATCAACCTCATCCCTGCACACAAGAACTTAAATAAACAGTCCTTCGACCTTGCAAAAGTCCTACTGAAAAGGACAGTCCAGACTATTGAAGCATGTATTGCCAATTTTTTCAATCAAGTCCTGGTGCTGGGCAGATCATCAGTCAGCGACCTGTCTGAACACGTATTTGATCTGATTCAGGAACTTTTTGCTATCGATCCTCAGTTACTGTTATCTGTCATGCCACAGCTTGAATTCAAACTGAAGAGCAACGATGGTGAAGAACGCCTAGCTGTGGTTCGACTCCTCGCAAAATTGTTCGGCTCTAAAGATTCAGATTTAGCAACACAGAATCGGCCTCTCTGGCAGTGCTTTCTTGGGCGATTTAATGACATTCATGTTCCTGTGAGGTTAGAAAGTGTGAAGTTTGCCAGCCACTGTTTGATGAATCACCCAGACTTAGCGAAGGATCTGACAGAATATTTGAAAGTTAGGTCACATGATCCAGAAGAAGCCATTCGTCATGATGTTATTGTTACTATAATAACAGCTGCCAAAAGAGACCTTGCCTTAGTAAATGATCAGTTGCTTGGCTTTGTCAGGGAAAGGACACTGGATAAACGGTGGCGAGTAAGAAAAGAAGCCATGATGGGTCTGGCTCAGCTCTATAAGAAATACTGTCTTCATGGGGAAGCAGGAAAGGAAGCCGCGGAGAAAGTCAGCTGGATAAAGGACAAGCTGCTGCATATCTACTATCAGAACAGCATTGATGACAAACTATTGGTAGAGAAAATCTTTGCTCAGTATCTTGTTCCCCACAACCTGGAAACAGAAGAGAGAATGAAATGCTTATATTATTTATATGCTAGCTTGGATCCAAATGCTGTAAAAGCTCTCAATGAAATGTGGAAATGTCAGAACATGCTTCGAAGTCATGTGCGTGAACTATTGGACTTACACAAGCAGCCTACATCAGAAGCGAACTGTTCTGCCATGTTTGGGAAACTGATGACCATAGCAAAGAATTTGCCTGACCCTGGAAAAGCACAAGATTTTGTAAAGAAATTTAACCAGGTTCTTGGTGATGATGAGAAACTGAGGTCTCAGTTGGAATTATTAATCAGCCCAACCTGTTCATGCAAGCAGGCTGACGTTTGTGTGAGGGAAATAGCTCGGAAACTTGCAAATCCTAAGCAGCCAACCAACCCTTTTCTAGAGATGGTCAAATTTCTTTTGGAAAGAATTGCTCCTGTGCACATCGATTCAGAAGCCATAAGATGGTAG
Peptide sequence:
MVVKTFMDMDQDSEDEKQQYLPLALHLASEFFLRNPNKDVRLLVACCLADIFRIYAPEAPYTSHDKLKDIFLFITRQLKGLEDTKSPQFNRYFYLLENLAWVKSYNICFELEDCNEIFIQLFRTLFSVINNSHNTKVQMHMLDLMSSIIMEGDGVTQELLDSILINLIPAHKNLNKQSFDLAKVLLKRTVQTIEACIANFFNQVLVLGRSSVSDLSEHVFDLIQELFAIDPQLLLSVMPQLEFKLKSNDGEERLAVVRLLAKLFGSKDSDLATQNRPLWQCFLGRFNDIHVPVRLESVKFASHCLMNHPDLAKDLTEYLKVRSHDPEEAIRHDVIVTIITAAKRDLALVNDQLLGFVRERTLDKRWRVRKEAMMGLAQLYKKYCLHGEAGKEAAEKVSWIKDKLLHIYYQNSIDDKLLVEKIFAQYLVPHNLETEERMKCLYYLYASLDPNAVKALNEMWKCQNMLRSHVRELLDLHKQPTSEANCSAMFGKLMTIAKNLPDPGKAQDFVKKFNQVLGDDEKLRSQLELLISPTCSCKQADVCVREIARKLANPKQPTNPFLEMVKFLLERIAPVHIDSEAIRW
IRESfinder result
IRESfinder score
0.690861317
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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