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mmu_circKntc1_1350
Basic information of circular RNA
PanCircBase ID:
mmu_circKntc1_1350
mm39_Chr. Position ID:
chr5|123900575|123914703|+
Gene name:
Kntc1
Transcript:
ENSMUST00000031366.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
16
Exon/intron indexes:
9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24
Exon/intron offsets:
0,1282,1602,2484,3399,5257,5406,5779,7100,7340,8575,9573,11424,13190,13880,14026
Genomic length:
14128
Exon/intron sizes in nt:
94,53,11,65,59,94,46,60,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr5:123898779-123900575|chr5:123914703-123916094
Splice length:
1350
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GGAACCGGTAGTTGTGCATTCTCAAAATGGGAACCCGATTCTACCAAGAAAGAAATGTCTCTTAAGAACTTTGTGGGCACAGACATTATTAAAGGTGCAAAGTCATTTCAGCTGATCGACAACCTGCTTTTTGTGCTGGATACTGATAATGTGCTGAGCTTGTGGGATGCTTACACTCTCACTCCTGTGTGGAACTGGCCCTCTCTTCCCGTAGAGCAGTTTGTTCTCACGACAGAAGCGGATTCTCCCTCATCTGTTACCTGGCAAGGAATTACAAATCTCAAATTAGTCACCCTGACAGCAACAGCGAAGGAGAAGATGAGAAGCCTCATCATTTACTCTCTGCCTTCGATGGAAACACTGTACTCTTTGGAAGTATCTAGTGTTTCTTCTTTAGTTCAAACAGGAATCAGCACGGACACTATATATCTTCTGGAAGGAATTCACAAAAATGATCCTAACCTATGTGAAGACTCTGTGTCTGACTTAGTACTTAGGTACCTCACAGAGGTGTTACCAGAAAACAGACTGAGCCGGTTACTTCACAAGCACAGATTTGCCGAAGCCGAGAGCTTTGCCATTCAGTTCGGACTGGATGTTGAGCTTGTTTATAAGGTCAAATCAAATGATATGTTGGAGAAGCTGGCTTTGATTTCCTCGGACAAGAGTGAGCAGTCCAAATGGCAGCAACTTGTAGATGAAGCTAAAGAAAACCTATGCAAAATCCAGGACGATGACTTCGTGGTGAATTTCTGCCTCAAGGCCCAATGGGTAACCTATGAAACCACCCAGGAAATGCTCAGTTATGCCAAAACCAGGCTCATGAAGAAAGAAGACAGAGCTCTACCTGCCTCTTCTGATGCCTTCATGGAGGTGCTAAAAGCTCATGCAAAGTTAACTACATTTTATGGAGCATTTGGACCAGAAAAATTCAGTGGTAGCTCTTGGATTGAGTTCCTGAATAACGAAGATGACCTCAGGGATGTTTTTTTGCAGCTAAGTGAAGGAAACTTCGCTTGTGCTCAGTATCTTTGGCTTAGACATCGGGCTGACTTTGAAAGCAAGTTTGACGTGAAAATGCTGGAGAATTTGCTGAATTCAATATCTACACAATTCCCCTTGGAAAACCTTTGTTCCTGGTTTAAAAATGAAGTGATTCCGTTTGTGAGGAGGATTGTGCCCGAAGGACAAAACATTCTTGCAAAATGGCTAGAACAAGCATCAAGGAACCTAGAGTTAACTGATAAGGCAAACTGGCCAGAAAATGGACTTCAGCTGGCAGAGGTGTTCTTCACTGCAGAAAAAACAGACCGGTTTGGATTCGCATCTTCTTGGCACTGGATTTCCTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTGGCAGAGGTGTTCTTC
59.96
TGTCTGTGCCCACAAAGTTCT
60.06
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGGCAGAGGTGTTCTTCA
60.25
TGTCTGTGCCCACAAAGTTCT
60.06
161
PCR template sequence:
AAACTGGCCAGAAAATGGACTTCAGCTGGCAGAGGTGTTCTTCACTGCAGAAAAAACAGACCGGTTTGGATTCGCATCTTCTTGGCACTGGATTTCCTTGGGAACCGGTAGTTGTGCATTCTCAAAATGGGAACCCGATTCTACCAAGAAAGAAATGTCTCTTAAGAACTTTGTGGGCACAGACATTATTAAAGGTGCAA
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-335-5p(1), mmu-miR-30c-5p(1), mmu-miR-203-3p(1), mmu-miR-185-5p(1), mmu-miR-30b-5p(1), mmu-miR-191-5p(1), mmu-miR-351-5p(1), mmu-miR-676-3p(1), mmu-miR-218-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-207(1), mmu-miR-350-3p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGGATTTCCTTGGGAACCGGTAGTT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKNTC1_1350_ORF_1
0.8183
0.116976445
0.999999861
2646
ORF sequence:
ATGTCTCTTAAGAACTTTGTGGGCACAGACATTATTAAAGGTGCAAAGTCATTTCAGCTGATCGACAACCTGCTTTTTGTGCTGGATACTGATAATGTGCTGAGCTTGTGGGATGCTTACACTCTCACTCCTGTGTGGAACTGGCCCTCTCTTCCCGTAGAGCAGTTTGTTCTCACGACAGAAGCGGATTCTCCCTCATCTGTTACCTGGCAAGGAATTACAAATCTCAAATTAGTCACCCTGACAGCAACAGCGAAGGAGAAGATGAGAAGCCTCATCATTTACTCTCTGCCTTCGATGGAAACACTGTACTCTTTGGAAGTATCTAGTGTTTCTTCTTTAGTTCAAACAGGAATCAGCACGGACACTATATATCTTCTGGAAGGAATTCACAAAAATGATCCTAACCTATGTGAAGACTCTGTGTCTGACTTAGTACTTAGGTACCTCACAGAGGTGTTACCAGAAAACAGACTGAGCCGGTTACTTCACAAGCACAGATTTGCCGAAGCCGAGAGCTTTGCCATTCAGTTCGGACTGGATGTTGAGCTTGTTTATAAGGTCAAATCAAATGATATGTTGGAGAAGCTGGCTTTGATTTCCTCGGACAAGAGTGAGCAGTCCAAATGGCAGCAACTTGTAGATGAAGCTAAAGAAAACCTATGCAAAATCCAGGACGATGACTTCGTGGTGAATTTCTGCCTCAAGGCCCAATGGGTAACCTATGAAACCACCCAGGAAATGCTCAGTTATGCCAAAACCAGGCTCATGAAGAAAGAAGACAGAGCTCTACCTGCCTCTTCTGATGCCTTCATGGAGGTGCTAAAAGCTCATGCAAAGTTAACTACATTTTATGGAGCATTTGGACCAGAAAAATTCAGTGGTAGCTCTTGGATTGAGTTCCTGAATAACGAAGATGACCTCAGGGATGTTTTTTTGCAGCTAAGTGAAGGAAACTTCGCTTGTGCTCAGTATCTTTGGCTTAGACATCGGGCTGACTTTGAAAGCAAGTTTGACGTGAAAATGCTGGAGAATTTGCTGAATTCAATATCTACACAATTCCCCTTGGAAAACCTTTGTTCCTGGTTTAAAAATGAAGTGATTCCGTTTGTGAGGAGGATTGTGCCCGAAGGACAAAACATTCTTGCAAAATGGCTAGAACAAGCATCAAGGAACCTAGAGTTAACTGATAAGGCAAACTGGCCAGAAAATGGACTTCAGCTGGCAGAGGTGTTCTTCACTGCAGAAAAAACAGACCGGTTTGGATTCGCATCTTCTTGGCACTGGATTTCCTTGGGAACCGGTAGTTGTGCATTCTCAAAATGGGAACCCGATTCTACCAAGAAAGAAATGTCTCTTAAGAACTTTGTGGGCACAGACATTATTAAAGGTGCAAAGTCATTTCAGCTGATCGACAACCTGCTTTTTGTGCTGGATACTGATAATGTGCTGAGCTTGTGGGATGCTTACACTCTCACTCCTGTGTGGAACTGGCCCTCTCTTCCCGTAGAGCAGTTTGTTCTCACGACAGAAGCGGATTCTCCCTCATCTGTTACCTGGCAAGGAATTACAAATCTCAAATTAGTCACCCTGACAGCAACAGCGAAGGAGAAGATGAGAAGCCTCATCATTTACTCTCTGCCTTCGATGGAAACACTGTACTCTTTGGAAGTATCTAGTGTTTCTTCTTTAGTTCAAACAGGAATCAGCACGGACACTATATATCTTCTGGAAGGAATTCACAAAAATGATCCTAACCTATGTGAAGACTCTGTGTCTGACTTAGTACTTAGGTACCTCACAGAGGTGTTACCAGAAAACAGACTGAGCCGGTTACTTCACAAGCACAGATTTGCCGAAGCCGAGAGCTTTGCCATTCAGTTCGGACTGGATGTTGAGCTTGTTTATAAGGTCAAATCAAATGATATGTTGGAGAAGCTGGCTTTGATTTCCTCGGACAAGAGTGAGCAGTCCAAATGGCAGCAACTTGTAGATGAAGCTAAAGAAAACCTATGCAAAATCCAGGACGATGACTTCGTGGTGAATTTCTGCCTCAAGGCCCAATGGGTAACCTATGAAACCACCCAGGAAATGCTCAGTTATGCCAAAACCAGGCTCATGAAGAAAGAAGACAGAGCTCTACCTGCCTCTTCTGATGCCTTCATGGAGGTGCTAAAAGCTCATGCAAAGTTAACTACATTTTATGGAGCATTTGGACCAGAAAAATTCAGTGGTAGCTCTTGGATTGAGTTCCTGAATAACGAAGATGACCTCAGGGATGTTTTTTTGCAGCTAAGTGAAGGAAACTTCGCTTGTGCTCAGTATCTTTGGCTTAGACATCGGGCTGACTTTGAAAGCAAGTTTGACGTGAAAATGCTGGAGAATTTGCTGAATTCAATATCTACACAATTCCCCTTGGAAAACCTTTGTTCCTGGTTTAAAAATGAAGTGATTCCGTTTGTGAGGAGGATTGTGCCCGAAGGACAAAACATTCTTGCAAAATGGCTAGAACAAGCATCAAGGAACCTAGAGTTAACTGATAAGGCAAACTGGCCAGAAAATGGACTTCAGCTGGCAGAGGTGTTCTTCACTGCAGAAAAAACAGACCGGTTTGGATTCGCATCTTCTTGGCACTGGATTTCCTTG
Peptide sequence:
MSLKNFVGTDIIKGAKSFQLIDNLLFVLDTDNVLSLWDAYTLTPVWNWPSLPVEQFVLTTEADSPSSVTWQGITNLKLVTLTATAKEKMRSLIIYSLPSMETLYSLEVSSVSSLVQTGISTDTIYLLEGIHKNDPNLCEDSVSDLVLRYLTEVLPENRLSRLLHKHRFAEAESFAIQFGLDVELVYKVKSNDMLEKLALISSDKSEQSKWQQLVDEAKENLCKIQDDDFVVNFCLKAQWVTYETTQEMLSYAKTRLMKKEDRALPASSDAFMEVLKAHAKLTTFYGAFGPEKFSGSSWIEFLNNEDDLRDVFLQLSEGNFACAQYLWLRHRADFESKFDVKMLENLLNSISTQFPLENLCSWFKNEVIPFVRRIVPEGQNILAKWLEQASRNLELTDKANWPENGLQLAEVFFTAEKTDRFGFASSWHWISLGTGSCAFSKWEPDSTKKEMSLKNFVGTDIIKGAKSFQLIDNLLFVLDTDNVLSLWDAYTLTPVWNWPSLPVEQFVLTTEADSPSSVTWQGITNLKLVTLTATAKEKMRSLIIYSLPSMETLYSLEVSSVSSLVQTGISTDTIYLLEGIHKNDPNLCEDSVSDLVLRYLTEVLPENRLSRLLHKHRFAEAESFAIQFGLDVELVYKVKSNDMLEKLALISSDKSEQSKWQQLVDEAKENLCKIQDDDFVVNFCLKAQWVTYETTQEMLSYAKTRLMKKEDRALPASSDAFMEVLKAHAKLTTFYGAFGPEKFSGSSWIEFLNNEDDLRDVFLQLSEGNFACAQYLWLRHRADFESKFDVKMLENLLNSISTQFPLENLCSWFKNEVIPFVRRIVPEGQNILAKWLEQASRNLELTDKANWPENGLQLAEVFFTAEKTDRFGFASSWHWISL
IRESfinder result
IRESfinder score
0.644116503
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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