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mmu_circPds5a_1544
Basic information of circular RNA
PanCircBase ID:
mmu_circPds5a_1544
mm39_Chr. Position ID:
chr5|65801362|65821857|-
Gene name:
Pds5a
Transcript:
ENSMUST00000201948.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
14
Exon/intron indexes:
17,16,15,14,13,12,11,10,9,8,7,6,5,4
Exon/intron offsets:
0,2313,3068,3904,6373,7125,8368,9985,10769,12248,14327,15587,19836,20408
Genomic length:
20495
Exon/intron sizes in nt:
116,140,49,82,114,152,146,95,116,141,81,127,98,87
Flanking exon/introns:
chr5:65796005-65801362|chr5:65821857-65823450
Splice length:
1544
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GACATATTTCTCTTTATTACCAGACAGTTAAAAGGTTTGGAGGATACAAAGAGTCCACAGTTTAATAGATATTTTTATTTATTAGAGAATTTAGCTTGGGTTAAATCATATAACATCTGCTTTGAGTTGGAAGATTGCAATGAAATTTTTATTCAGCTTTTTAGAACTCTCTTCTCGGTAATCAACAATAGCCACAATACGAAAGTACAAATGCACATGTTAGACTTGATGAGTTCTATCATCATGGAAGGTGATGGAGTTACTCAAGAATTATTGGATTCCATTCTTATCAACCTCATCCCTGCACACAAGAACTTAAATAAACAGTCCTTCGACCTTGCAAAAGTCCTACTGAAAAGGACAGTCCAGACTATTGAAGCATGTATTGCCAATTTTTTCAATCAAGTCCTGGTGCTGGGCAGATCATCAGTCAGCGACCTGTCTGAACACGTATTTGATCTGATTCAGGAACTTTTTGCTATCGATCCTCAGTTACTGTTATCTGTCATGCCACAGCTTGAATTCAAACTGAAGAGCAACGATGGTGAAGAACGCCTAGCTGTGGTTCGACTCCTCGCAAAATTGTTCGGCTCTAAAGATTCAGATTTAGCAACACAGAATCGGCCTCTCTGGCAGTGCTTTCTTGGGCGATTTAATGACATTCATGTTCCTGTGAGGTTAGAAAGTGTGAAGTTTGCCAGCCACTGTTTGATGAATCACCCAGACTTAGCGAAGGATCTGACAGAATATTTGAAAGTTAGGTCACATGATCCAGAAGAAGCCATTCGTCATGATGTTATTGTTACTATAATAACAGCTGCCAAAAGAGACCTTGCCTTAGTAAATGATCAGTTGCTTGGCTTTGTCAGGGAAAGGACACTGGATAAACGGTGGCGAGTAAGAAAAGAAGCCATGATGGGTCTGGCTCAGCTCTATAAGAAATACTGTCTTCATGGGGAAGCAGGAAAGGAAGCCGCGGAGAAAGTCAGCTGGATAAAGGACAAGCTGCTGCATATCTACTATCAGAACAGCATTGATGACAAACTATTGGTAGAGAAAATCTTTGCTCAGTATCTTGTTCCCCACAACCTGGAAACAGAAGAGAGAATGAAATGCTTATATTATTTATATGCTAGCTTGGATCCAAATGCTGTAAAAGCTCTCAATGAAATGTGGAAATGTCAGAACATGCTTCGAAGTCATGTGCGTGAACTATTGGACTTACACAAGCAGCCTACATCAGAAGCGAACTGTTCTGCCATGTTTGGGAAACTGATGACCATAGCAAAGAATTTGCCTGACCCTGGAAAAGCACAAGATTTTGTAAAGAAATTTAACCAGGTTCTTGGTGATGATGAGAAACTGAGGTCTCAGTTGGAATTATTAATCAGCCCAACCTGTTCATGCAAGCAGGCTGACGTTTGTGTGAGGGAAATAGCTCGGAAACTTGCAAATCCTAAGCAGCCAACCAACCCTTTTCTAGAGATGGTCAAATTTCTTTTGGAAAGAATTGCTCCTGTGCACATCGATTCAGAAGCCATAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TAAGCAGCCAACCAACCCTT
59.81
CTGTGGACTCTTTGTATCCTCCA
59.48
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TAAGCAGCCAACCAACCCTT
59.81
ACTGTGGACTCTTTGTATCCTCC
59.48
148
PCR template sequence:
AACTTGCAAATCCTAAGCAGCCAACCAACCCTTTTCTAGAGATGGTCAAATTTCTTTTGGAAAGAATTGCTCCTGTGCACATCGATTCAGAAGCCATAAGGACATATTTCTCTTTATTACCAGACAGTTAAAAGGTTTGGAGGATACAAAGAGTCCACAGTTTAATAGATATTTTTATTTATTAGAGAATTTAGCTTGGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
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-802-5p(1), mmu-miR-342-3p(1), mmu-miR-377-3p(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
CAGAAGCCATAAGGACATATTTCTCT
siRNA sets
AGAAATATGTCCTTATGGC, GAAATATGTCCTTATGGCT, ATATGTCCTTATGGCTTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDS5A_1544_ORF_1
0.9458
0.083280852
0.998687312
1365
ORF sequence:
ATGCACATGTTAGACTTGATGAGTTCTATCATCATGGAAGGTGATGGAGTTACTCAAGAATTATTGGATTCCATTCTTATCAACCTCATCCCTGCACACAAGAACTTAAATAAACAGTCCTTCGACCTTGCAAAAGTCCTACTGAAAAGGACAGTCCAGACTATTGAAGCATGTATTGCCAATTTTTTCAATCAAGTCCTGGTGCTGGGCAGATCATCAGTCAGCGACCTGTCTGAACACGTATTTGATCTGATTCAGGAACTTTTTGCTATCGATCCTCAGTTACTGTTATCTGTCATGCCACAGCTTGAATTCAAACTGAAGAGCAACGATGGTGAAGAACGCCTAGCTGTGGTTCGACTCCTCGCAAAATTGTTCGGCTCTAAAGATTCAGATTTAGCAACACAGAATCGGCCTCTCTGGCAGTGCTTTCTTGGGCGATTTAATGACATTCATGTTCCTGTGAGGTTAGAAAGTGTGAAGTTTGCCAGCCACTGTTTGATGAATCACCCAGACTTAGCGAAGGATCTGACAGAATATTTGAAAGTTAGGTCACATGATCCAGAAGAAGCCATTCGTCATGATGTTATTGTTACTATAATAACAGCTGCCAAAAGAGACCTTGCCTTAGTAAATGATCAGTTGCTTGGCTTTGTCAGGGAAAGGACACTGGATAAACGGTGGCGAGTAAGAAAAGAAGCCATGATGGGTCTGGCTCAGCTCTATAAGAAATACTGTCTTCATGGGGAAGCAGGAAAGGAAGCCGCGGAGAAAGTCAGCTGGATAAAGGACAAGCTGCTGCATATCTACTATCAGAACAGCATTGATGACAAACTATTGGTAGAGAAAATCTTTGCTCAGTATCTTGTTCCCCACAACCTGGAAACAGAAGAGAGAATGAAATGCTTATATTATTTATATGCTAGCTTGGATCCAAATGCTGTAAAAGCTCTCAATGAAATGTGGAAATGTCAGAACATGCTTCGAAGTCATGTGCGTGAACTATTGGACTTACACAAGCAGCCTACATCAGAAGCGAACTGTTCTGCCATGTTTGGGAAACTGATGACCATAGCAAAGAATTTGCCTGACCCTGGAAAAGCACAAGATTTTGTAAAGAAATTTAACCAGGTTCTTGGTGATGATGAGAAACTGAGGTCTCAGTTGGAATTATTAATCAGCCCAACCTGTTCATGCAAGCAGGCTGACGTTTGTGTGAGGGAAATAGCTCGGAAACTTGCAAATCCTAAGCAGCCAACCAACCCTTTTCTAGAGATGGTCAAATTTCTTTTGGAAAGAATTGCTCCTGTGCACATCGATTCAGAAGCCATAAGGACATATTTCTCTTTATTACCAGACAGTTAA
Peptide sequence:
MHMLDLMSSIIMEGDGVTQELLDSILINLIPAHKNLNKQSFDLAKVLLKRTVQTIEACIANFFNQVLVLGRSSVSDLSEHVFDLIQELFAIDPQLLLSVMPQLEFKLKSNDGEERLAVVRLLAKLFGSKDSDLATQNRPLWQCFLGRFNDIHVPVRLESVKFASHCLMNHPDLAKDLTEYLKVRSHDPEEAIRHDVIVTIITAAKRDLALVNDQLLGFVRERTLDKRWRVRKEAMMGLAQLYKKYCLHGEAGKEAAEKVSWIKDKLLHIYYQNSIDDKLLVEKIFAQYLVPHNLETEERMKCLYYLYASLDPNAVKALNEMWKCQNMLRSHVRELLDLHKQPTSEANCSAMFGKLMTIAKNLPDPGKAQDFVKKFNQVLGDDEKLRSQLELLISPTCSCKQADVCVREIARKLANPKQPTNPFLEMVKFLLERIAPVHIDSEAIRTYFSLLPDS
IRESfinder result
IRESfinder score
0.682878114
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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