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mmu_circPcsk2_920
Basic information of circular RNA
PanCircBase ID:
mmu_circPcsk2_920
mm39_Chr. Position ID:
chr2|143529483|143637964|+
Gene name:
Pcsk2
Transcript:
ENSMUST00000028905.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
3,4,5,6,7,8,9,10
Exon/intron offsets:
0,2763,9093,61561,86337,96964,105525,108380
Genomic length:
108481
Exon/intron sizes in nt:
11,41,09,38,77,89,17,60,00,000
Flanking exon/introns:
chr2:143415467-143529483|chr2:143637964-143642923
Splice length:
920
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATAAAGATGGCGCTGCAACAAGAAGGATTTGACCGTAAAAAGAGAGGGTACAGGGACATCAATGAGATTGACATCAACATGAATGATCCTCTCTTTACAAAGCAATGGTACCTGTTCAACACTGGGCAAGCCGATGGAACTCCTGGGCTAGACTTGAACGTGGCCGAAGCCTGGGAGCTGGGATACACAGGAAAAGGAGTGACCATTGGAATTATGGATGATGGAATTGACTATCTCCACCCAGACCTGGCCTACAACTACAACGCTGATGCAAGTTATGACTTCAGCAGCAATGACCCCTACCCATACCCTCGATACACAGATGACTGGTTCAACAGCCATGGAACTAGGTGTGCAGGAGAAGTTTCTGCTGCAGCCAGCAACAATATCTGTGGAGTCGGCGTAGCATACAACTCCAAGGTGGCAGGGATCCGGATGCTGGACCAGCCCTTTATGACAGACATCATCGAAGCCTCCTCCATCAGCCACATGCCTCAACTGATCGACATCTACAGTGCAAGCTGGGGCCCCACAGACAATGGGAAGACGGTTGATGGGCCCCGAGAGCTCACACTCCAGGCCATGGCTGATGGCGTGAACAAGGGCCGTGGGGGCAAAGGCAGCATCTATGTGTGGGCCTCTGGGGACGGTGGCAGCTACGATGACTGCAACTGTGACGGCTATGCTTCAAGCATGTGGACCATCTCCATCAACTCAGCCATCAATGATGGCAGGACTGCCTTGTATGATGAGAGTTGCTCTTCCACCTTAGCATCCACCTTCAGCAATGGGAGGAAGAGGAATCCTGAGGCTGGTGTGGCTACCACAGACTTGTATGGCAACTGTACTCTGAGACACTCTGGGACATCTGCAGCTGCTCCGGAGGCAGCTGGCGTGTTTGCATTAGCTTTGGAGGCTAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGCAACTGTACTCTGAGACAC
59.96
TGATGTCCCTGTACCCTCTCT
59.35
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCACAGACTTGTATGGCAACT
59.89
TGATGTCCCTGTACCCTCTCT
59.35
159
PCR template sequence:
CTACCACAGACTTGTATGGCAACTGTACTCTGAGACACTCTGGGACATCTGCAGCTGCTCCGGAGGCAGCTGGCGTGTTTGCATTAGCTTTGGAGGCTAAATAAAGATGGCGCTGCAACAAGAAGGATTTGACCGTAAAAAGAGAGGGTACAGGGACATCAATGAGATTGACATCAACATGAATGATCCTCTCTTTACAA
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-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-199a-5p(1), mmu-miR-122-5p(1), mmu-miR-381-3p(1), mmu-let-7d-5p(1), mmu-miR-434-3p(1), mmu-miR-127-3p(1), mmu-miR-362-5p(1), mmu-miR-98-5p(1), mmu-miR-129-5p(1), mmu-miR-207(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTTTGGAGGCTAAATAAAGATGGCGC
siRNA sets
CCATCTTTATTTAGCCTCC, CATCTTTATTTAGCCTCCA, ATCTTTATTTAGCCTCCAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPCSK2_920_ORF_1
0.9894
0.367023131
0.990797105
918
ORF sequence:
ATGGCGCTGCAACAAGAAGGATTTGACCGTAAAAAGAGAGGGTACAGGGACATCAATGAGATTGACATCAACATGAATGATCCTCTCTTTACAAAGCAATGGTACCTGTTCAACACTGGGCAAGCCGATGGAACTCCTGGGCTAGACTTGAACGTGGCCGAAGCCTGGGAGCTGGGATACACAGGAAAAGGAGTGACCATTGGAATTATGGATGATGGAATTGACTATCTCCACCCAGACCTGGCCTACAACTACAACGCTGATGCAAGTTATGACTTCAGCAGCAATGACCCCTACCCATACCCTCGATACACAGATGACTGGTTCAACAGCCATGGAACTAGGTGTGCAGGAGAAGTTTCTGCTGCAGCCAGCAACAATATCTGTGGAGTCGGCGTAGCATACAACTCCAAGGTGGCAGGGATCCGGATGCTGGACCAGCCCTTTATGACAGACATCATCGAAGCCTCCTCCATCAGCCACATGCCTCAACTGATCGACATCTACAGTGCAAGCTGGGGCCCCACAGACAATGGGAAGACGGTTGATGGGCCCCGAGAGCTCACACTCCAGGCCATGGCTGATGGCGTGAACAAGGGCCGTGGGGGCAAAGGCAGCATCTATGTGTGGGCCTCTGGGGACGGTGGCAGCTACGATGACTGCAACTGTGACGGCTATGCTTCAAGCATGTGGACCATCTCCATCAACTCAGCCATCAATGATGGCAGGACTGCCTTGTATGATGAGAGTTGCTCTTCCACCTTAGCATCCACCTTCAGCAATGGGAGGAAGAGGAATCCTGAGGCTGGTGTGGCTACCACAGACTTGTATGGCAACTGTACTCTGAGACACTCTGGGACATCTGCAGCTGCTCCGGAGGCAGCTGGCGTGTTTGCATTAGCTTTGGAGGCTAAATAA
Peptide sequence:
MALQQEGFDRKKRGYRDINEIDINMNDPLFTKQWYLFNTGQADGTPGLDLNVAEAWELGYTGKGVTIGIMDDGIDYLHPDLAYNYNADASYDFSSNDPYPYPRYTDDWFNSHGTRCAGEVSAAASNNICGVGVAYNSKVAGIRMLDQPFMTDIIEASSISHMPQLIDIYSASWGPTDNGKTVDGPRELTLQAMADGVNKGRGGKGSIYVWASGDGGSYDDCNCDGYASSMWTISINSAINDGRTALYDESCSSTLASTFSNGRKRNPEAGVATTDLYGNCTLRHSGTSAAAPEAAGVFALALEAK
IRESfinder result
IRESfinder score
0.246377305
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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