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mmu_circPak2_635
Basic information of circular RNA
PanCircBase ID:
mmu_circPak2_635
mm39_Chr. Position ID:
chr16|31853712|31863399|-
Gene name:
Pak2
Transcript:
ENSMUST00000023467.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
9,8,7,6,5,4,3
Exon/intron offsets:
0,2350,4904,6573,8251,8958,9586
Genomic length:
9687
Exon/intron sizes in nt:
4,96,41,33,10,83,21,48,000
Flanking exon/introns:
chr16:31852717-31853712|chr16:31863399-31870993
Splice length:
635
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GAAGTAAAAAGAAAGAAAAAGAACGGCCAGAGATTTCTCCCCCATCTGATTTTGAGCACACCATCCATGTTGGCTTTGATGCTGTTACGGGAGAGTTCACTGGCATGCCAGAACAGTGGGCGCGGCTGTTGCAGACCTCCAACATTACCAAACTCGAGCAGAAGAAGAACCCTCAGGCAGTGCTGGATGTCTTGAAGTTCTACGACTCCAACACTGTGAAACAGAAGTACCTGAGTTTCACTCCTCCTGAGAAAGATGGCTTCCCTTCTGGAACACCAGCACTGAACACCAAGGGGTCAGAGACATCAGCTGTAGTGACAGAGGAAGATGATGATGATGAAGACGCTGCTCCTCCCGTCATTGCCCCTCGGCCAGATCATACAAAATCAATTTACACACGGTCTGTCATCGACCCCATTCCTGCTCCAGTTGGTGATTCTAATGTTGACAGTGGTGCCAAGTCTTCAGACAAACAGAAAAAGAAAGCCAAGATGACCGATGAAGAGATTATGGAGAAATTAAGAACTATTGTGAGCATAGGGGACCCAAAGAAAAAATACACAAGATATGAAAAAATTGGGCAAGGGGCTTCTGGAACAGTTTTTACTGCCACTGATGTGGCCCTGGGGCAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAATTGGGCAAGGGGCTTCT
60.18
CCCGTAACAGCATCAAAGCC
59.55
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAAATTGGGCAAGGGGCTTC
59.31
CCCGTAACAGCATCAAAGCC
59.55
154
PCR template sequence:
CATAGGGGACCCAAAGAAAAAATACACAAGATATGAAAAAATTGGGCAAGGGGCTTCTGGAACAGTTTTTACTGCCACTGATGTGGCCCTGGGGCAAGAGGAAGTAAAAAGAAAGAAAAAGAACGGCCAGAGATTTCTCCCCCATCTGATTTTGAGCACACCATCCATGTTGGCTTTGATGCTGTTACGGGAGAGTTCAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(1), mmu-miR-181a-5p(1), mmu-miR-138-5p(1), mmu-miR-181b-5p(1), mmu-miR-96-5p(1), mmu-miR-194-5p(1), mmu-miR-324-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCTGGGGCAAGAGGAAGTAAAAAGAA
siRNA sets
TTTTTACTTCCTCTTGCCC, TTTTACTTCCTCTTGCCCC, CTTTTTACTTCCTCTTGCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPAK2_635_ORF_1
0.8546
0.208162788
0.917327681
726
ORF sequence:
ATGCCAGAACAGTGGGCGCGGCTGTTGCAGACCTCCAACATTACCAAACTCGAGCAGAAGAAGAACCCTCAGGCAGTGCTGGATGTCTTGAAGTTCTACGACTCCAACACTGTGAAACAGAAGTACCTGAGTTTCACTCCTCCTGAGAAAGATGGCTTCCCTTCTGGAACACCAGCACTGAACACCAAGGGGTCAGAGACATCAGCTGTAGTGACAGAGGAAGATGATGATGATGAAGACGCTGCTCCTCCCGTCATTGCCCCTCGGCCAGATCATACAAAATCAATTTACACACGGTCTGTCATCGACCCCATTCCTGCTCCAGTTGGTGATTCTAATGTTGACAGTGGTGCCAAGTCTTCAGACAAACAGAAAAAGAAAGCCAAGATGACCGATGAAGAGATTATGGAGAAATTAAGAACTATTGTGAGCATAGGGGACCCAAAGAAAAAATACACAAGATATGAAAAAATTGGGCAAGGGGCTTCTGGAACAGTTTTTACTGCCACTGATGTGGCCCTGGGGCAAGAGGAAGTAAAAAGAAAGAAAAAGAACGGCCAGAGATTTCTCCCCCATCTGATTTTGAGCACACCATCCATGTTGGCTTTGATGCTGTTACGGGAGAGTTCACTGGCATGCCAGAACAGTGGGCGCGGCTGTTGCAGACCTCCAACATTACCAAACTCGAGCAGAAGAAGAACCCTCAGGCAGTGCTGGATGTCTTGA
Peptide sequence:
MPEQWARLLQTSNITKLEQKKNPQAVLDVLKFYDSNTVKQKYLSFTPPEKDGFPSGTPALNTKGSETSAVVTEEDDDDEDAAPPVIAPRPDHTKSIYTRSVIDPIPAPVGDSNVDSGAKSSDKQKKKAKMTDEEIMEKLRTIVSIGDPKKKYTRYEKIGQGASGTVFTATDVALGQEEVKRKKKNGQRFLPHLILSTPSMLALMLLRESSLACQNSGRGCCRPPTLPNSSRRRTLRQCWMS
IRESfinder result
IRESfinder score
0.419063958
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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