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mmu_circKtn1_563
Basic information of circular RNA
PanCircBase ID:
mmu_circKtn1_563
mm39_Chr. Position ID:
chr14|47907581|47914282|+
Gene name:
Ktn1
Transcript:
ENSMUST00000187839.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
4,5,6,7
Exon/intron offsets:
0,2815,4625,6560
Genomic length:
6701
Exon/intron sizes in nt:
1,74,13,11,17,141
Flanking exon/introns:
chr14:47904890-47907581|chr14:47914282-47920839
Splice length:
563
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TTGCAGTCTTGGTAGACGAGCCCCTTATTCATGCAACTACTTACATTCCTTTGGATAATGCTAACTCAAATCTCATGATGGATAAGAGAGAAATTATTGATATGATTAAACCTGATCATGTTGAAGGAATCCAGAAATCTGGAACAAAAAAGCTGAAGATTGAAACTGACAAAGAAAATGCTGAAGTGAAATTTAAAGATTTCCTTCTGTCCTTGAAGACTATGATGTTTTCTGAAGATGAAGCTCTTTGTGTTGTAGACCTGCTGAAGGAAAAGTCTGGTGTGATAAAAGAAGCTTTAAAGAAGTCGAATAAAGGAGAACTGAGTGGTCTTCTGCATCAACTTCAGGAGAAGGAGAGGCTGCTCTCTGCCATGAAGGAAGATGCTGCTGCCTCAAAGGAGCGCTGTAAGCAGTTGACTCAGGAAATGATGACAGAGAAAGAAAGAAGCAGTGTTGTTATAGCAAGAATGAAAGATCGGATTGGAACACTAGAAAAGGAACACAATATATTTCAAAACAAAATGCATGCCAGTTACCAAGAGACTCAGCAGATGCAGATGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGAATGAAAGATCGGATTGGAACAC
59.64
AGTAGTTGCATGAATAAGGGGCT
59.8
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGAATGAAAGATCGGATTGGAACA
58.5
AGTAGTTGCATGAATAAGGGGCT
59.8
140
PCR template sequence:
AAGAATGAAAGATCGGATTGGAACACTAGAAAAGGAACACAATATATTTCAAAACAAAATGCATGCCAGTTACCAAGAGACTCAGCAGATGCAGATGAAGTTGCAGTCTTGGTAGACGAGCCCCTTATTCATGCAACTACTTACATTCCTTTGGATAATGCTAACTCAAATCTCATGATGGATAAGAGAGAAATTATTGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-1a-3p(1), mmu-miR-206-3p(1), mmu-miR-298-5p(1), mmu-miR-709(1), mmu-miR-214-3p(1), mmu-miR-207(1), mmu-miR-335-3p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GATGCAGATGAAGTTGCAGTCTTGGT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKTN1_563_ORF_1
1.1725
0.170203041
0.776247251
504
ORF sequence:
ATGATGGATAAGAGAGAAATTATTGATATGATTAAACCTGATCATGTTGAAGGAATCCAGAAATCTGGAACAAAAAAGCTGAAGATTGAAACTGACAAAGAAAATGCTGAAGTGAAATTTAAAGATTTCCTTCTGTCCTTGAAGACTATGATGTTTTCTGAAGATGAAGCTCTTTGTGTTGTAGACCTGCTGAAGGAAAAGTCTGGTGTGATAAAAGAAGCTTTAAAGAAGTCGAATAAAGGAGAACTGAGTGGTCTTCTGCATCAACTTCAGGAGAAGGAGAGGCTGCTCTCTGCCATGAAGGAAGATGCTGCTGCCTCAAAGGAGCGCTGTAAGCAGTTGACTCAGGAAATGATGACAGAGAAAGAAAGAAGCAGTGTTGTTATAGCAAGAATGAAAGATCGGATTGGAACACTAGAAAAGGAACACAATATATTTCAAAACAAAATGCATGCCAGTTACCAAGAGACTCAGCAGATGCAGATGAAGTTGCAGTCTTGGTAG
Peptide sequence:
MMDKREIIDMIKPDHVEGIQKSGTKKLKIETDKENAEVKFKDFLLSLKTMMFSEDEALCVVDLLKEKSGVIKEALKKSNKGELSGLLHQLQEKERLLSAMKEDAAASKERCKQLTQEMMTEKERSSVVIARMKDRIGTLEKEHNIFQNKMHASYQETQQMQMKLQSW
IRESfinder result
IRESfinder score
0.514195682
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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