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mmu_ciPknox1_2619
Basic information of circular RNA
PanCircBase ID:
mmu_ciPknox1_2619
mm39_Chr. Position ID:
chr17|31815867|31818486|+
Gene name:
Pknox1
Transcript:
ENSMUST00000097352.11
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
7
Exon/intron offsets:
0
Genomic length:
2619
Exon/intron sizes in nt:
2619
Flanking exon/introns:
chr17:31815867-31818488
Splice length:
2619
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGTGTGCCACCTTCTAGATGGACTTGTTATGAGTGCTGCCTGGGTAGGGAGCAGTGGAGCGAGCTAAGCTGTCCTTGTGACTGTCATTTATTGTCAAGTAGCCTCTGGTTGGTTTGTTTCTTTTCATGCTTTATCTGCCTTATTGGGGAAATCTGCAAATTTCAGAACAGTCTGAGACTCCAGGGAGGTTATTCATGGCCCTGGAAGCAGCCATGCCCAGTGGCAAGGCTGGTTTATGGGAGTGTTCGCTGTGTGCGCTCACCAAGACTCCAAGTCCAGGCGGAACAGCCAGGTAGAATTTTCAGAAGCAGAGCCCAGACTGTACCCCTAGCCTGAGGCAGCATCCCAAGTGCTGGAGGCACCCCGGGCCTCTGTCTGACATCCTTGGCATGATTGGGGTCCTGTGTTGAAGCCAGGCTCTCATCTTTAGGCGTTTGGCTTCCAGAACAAGAGGTGACCTGTGACTTACCATGGCCATGGTCATTCTACAGTCTTCCTATTCCATTGTAGTAAAATGTAGATATTGGATCTTCCTGGCTGGAAGACCCTCTAAGTTCTGGAAACATGACTTTTTTTTTAATAATTTAAGACAAGGTTTAAAATATAGTTCTTTCTTTGTGCACATGGCTTCACTCTGTGAGGTCTCTGTCCATGTCTCATCACGGATTCTCATGCCTAGCCCTGGGTGTGGTCCAAGTGGGCTGCAGTGACTCAGTGGTCTGGGTAGTCTGGAGCTGCCATCTTGGCTACAGAGGTTTGGGAGCCACACTGGAGAAGAAGACTCAGGTGTCACTGACATAGGCGGCAGCTTGAGAGCTGACCTGAGCTTCGTGACTGCTCAGGCCCAGGCGTAGAGGAGAACCAGATCTCACCAATGCTGCCTCTATCGCCACACCAGCCCCCTTCCCTTGTGTTTTCCCATTTAAAATGTTTGCAACAACAGTTTTTCCATGTCCACTCACTGCATAGTTTTTTTAGGATTGAATTATGCTTCCTCTAGGCAGAAGACATTTTAAGTCAAATAGTGAGCTAGTACTGTCGCATATACTCATTTATTTTGTTGGAAAAGAAAGTGGTTTTTTGTTTGCTTTAGGGAACTTGGGACAGGATTTCACTTTATACCTTGCCTGGCCTGGAAATCTCTGTGATCTTTCTGCTCAGCCTCCCAAATGAGAAGAGTCTTCCGTGTAGCTGAGTTTTCTGAGGAGCAAAGGTTGCTCGCTTCAAATAGCAAGCATGCCGAGTCTAAGCACCTCAGGACGTGCTTTCTGACCCTCGGTCCCACAGTTTCCCACTGTCACTCGGGTGTCAGCCTTGGTCGGTTACACTGACCTGGCAACAGCAGACTAGAGCTGGGACTTGTGGGAGATGCCCACTGAGAAGTCTTTCTCCCGCTCGCATGCACCCATGTAAAGATGGTTTTGAGGGTGAGGAGAGGGCAAGAGGGAGGTTTTCATGAATTAGTAGCTGGCCTTAGCCTCTATAACAAAGGATAACCCTGGACTTGTCACCATCTGCTTCTGCCTTCTGAGTGTTAGGATGCCAGCATGTGTCATGGAACCCGATTACTTCCATAGCTGCAGCCCCACCTGCCTGGCACCCGTTCTTAACCACTGGTACTCAAAGAGTGTCAGGTTTTTCACTCCCTGCCCTCTCACCCTTACTTGGGATGTTTTTATGAGGTGGAGTGTGTCACAGCTTAGCCCTCAGGCACCGTAGGTAGGCCACAGATCTGAACAGTTCTCCGATCCCCCCAGGTCCCCTCCAAATCCTTGATCCATTTATTCCACTACTCCCATGTGTTTCAAAAGGAAAGCTTGCCTCTGTTGAATGTCCTTGAAACGTGCTCGCCTGCCTTTCCCTGCTGCAGGACTCCACTCTGACCCCTGGCACACCGTCTGTCTCCAGTTGCGCCATGCCAGCTGCATGGTGACCCCTAGCTCAGCCCTTCTGCGCCCTCAGCAGCGGCTCTGCACTGCAGTGGCTCAAATGCTGCTTTCTTTTTGTGTGTGCAAGGTTTTCAGTATGTAAGTGCCCAGAGCACCAGGTGACACATCAGTGCTGCCTGTCCTGCCAGAGCCAGCTGCTTCAGGGCTGTCTTCCTCCCTGTGCCCGTTGTGCTGGTCCTTCTCGTGAAGGCCATTGCAGAGGATGCAGATGGAAACAGGAAGAGAGTGGGGTGTGAGAGCTCCCAGGTTCCTCTCTAGCATGCCACCCTCTAGGAGCTTGGAAGCTTCATGACATAGTAGGGTGGATGAACCCACACTGACAGTTCGTGATCACCCTAAACTTCTTAGCCCCTTGGTGCACTGCAGAGGTTAGGATCTGTGAGCAGTCCCTGCCTGGAGACGTAGGTCAGCCGTCAGTGTATAGGAAGACATCCCTTTGCAGAGTCTAAGAGTTGTAGGGCTTGCATGCTGAGAAGGTGGGAAGGAAGACCAAATATTATTGTTGACAGTGTCAGGTGTGCCCTTAGTCCGTACAGGGTTTCAGCACATGCCTCTTTACTGTAAATAAGCCCAGGAGAGGGCCTTGGTAAGGCCTCCATCTGAAGTTGTAAGCTACTTGATGTGCTGGCATTTCAAGGCCTTTCTGACGTTATTTATCAATTGTGTGAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGGAGAGGGCCTTGGTAAG
59.46
ACCCAGGCAGCACTCATAAC
60.04
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGGAGAGGGCCTTGGTAAG
59.46
CCCAGGCAGCACTCATAACA
60.04
143
PCR template sequence:
CCCAGGAGAGGGCCTTGGTAAGGCCTCCATCTGAAGTTGTAAGCTACTTGATGTGCTGGCATTTCAAGGCCTTTCTGACGTTATTTATCAATTGTGTGAAGTGTGTGCCACCTTCTAGATGGACTTGTTATGAGTGCTGCCTGGGTAGGGAGCAGTGGAGCGAGCTAAGCTGTCCTTGTGACTGTCATTTATTGTCAAGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
34
Interacting miRNAs (#binding sites)
mmu-miR-7b-5p(2), mmu-miR-103-3p(2), mmu-miR-7a-5p(2), mmu-miR-107-3p(2), mmu-miR-540-3p(2), mmu-miR-7a-2-3p(2), mmu-miR-181a-5p(1), mmu-miR-150-5p(1), mmu-miR-101a-3p(1), mmu-miR-322-5p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-298-5p(1), mmu-miR-184-3p(1), mmu-miR-709(1), mmu-miR-203-3p(1), mmu-miR-326-3p(1), mmu-miR-138-5p(1), mmu-miR-10b-5p(1), mmu-miR-214-3p(1), mmu-miR-676-3p(1), mmu-miR-127-5p(1), mmu-miR-182-5p(1), mmu-miR-192-5p(1), mmu-miR-215-5p(1), mmu-miR-342-5p(1), mmu-miR-27a-5p(1), mmu-miR-680(1), mmu-miR-207(1), mmu-miR-300-3p(1), mmu-miR-3065-5p(1), mmu-miR-1199-5p(1), mmu-miR-466b-3p(1), mmu-miR-490-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCAATTGTGTGAAGTGTGTGCCACCT
siRNA sets
ACACACTTCACACAATTGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIPKNOX1_2619_ORF_1
0.6478
-0.226553221
0.091587746
387
ORF sequence:
ATGTGCTGGCATTTCAAGGCCTTTCTGACGTTATTTATCAATTGTGTGAAGTGTGTGCCACCTTCTAGATGGACTTGTTATGAGTGCTGCCTGGGTAGGGAGCAGTGGAGCGAGCTAAGCTGTCCTTGTGACTGTCATTTATTGTCAAGTAGCCTCTGGTTGGTTTGTTTCTTTTCATGCTTTATCTGCCTTATTGGGGAAATCTGCAAATTTCAGAACAGTCTGAGACTCCAGGGAGGTTATTCATGGCCCTGGAAGCAGCCATGCCCAGTGGCAAGGCTGGTTTATGGGAGTGTTCGCTGTGTGCGCTCACCAAGACTCCAAGTCCAGGCGGAACAGCCAGGTAGAATTTTCAGAAGCAGAGCCCAGACTGTACCCCTAGCCTGA
Peptide sequence:
MCWHFKAFLTLFINCVKCVPPSRWTCYECCLGREQWSELSCPCDCHLLSSSLWLVCFFSCFICLIGEICKFQNSLRLQGGYSWPWKQPCPVARLVYGSVRCVRSPRLQVQAEQPGRIFRSRAQTVPLA
IRESfinder result
IRESfinder score
0.720540926
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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