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mmu_circKsr1_584
Basic information of circular RNA
PanCircBase ID:
mmu_circKsr1_584
mm39_Chr. Position ID:
chr11|78919300|78931763|-
Gene name:
Ksr1
Transcript:
ENSMUST00000018478.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
12,11,10,9,8,7,6
Exon/intron offsets:
0,554,4743,8020,8212,9677,12402
Genomic length:
12463
Exon/intron sizes in nt:
49,55,166,107,62,84,61
Flanking exon/introns:
chr11:78918625-78919300|chr11:78931763-78934021
Splice length:
584
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AACTCCCTCATGGATCCCCACAGCTGGTACGAAGGGATATCGGGCTCTCGGTGACGCACAGGTTCTCCACAAAGTCATGGTTGTCACAGGTGTGCAACGTGTGCCAGAAGAGCATGATTTTTGGCGTGAAGTGCAAACACTGCAGGTTAAAATGCCATAACAAGTGCACAAAGGAAGCTCCCGCCTGCAGGATCACCTTCCTCCCACTGGCCAGGCTTCGGAGGACAGAGTCTGTCCCGTCAGATATCAACAACCCAGTGGACAGAGCAGCAGAGCCCCATTTTGGAACCCTTCCCAAGGCCCTGACAAAGAAGGAGCACCCTCCAGCCATGAACCTGGACTCCAGCAGCAACCCATCCTCCACCACGTCCTCCACACCCTCATCGCCGGCACCTTTCCTGACCTCATCTAATCCCTCCAGTGCCACCACGCCTCCCAACCCGTCACCTGGCCAGCGGGACAGCAGGTTCAGCTTCCCAGACATTTCAGCCTGTTCTCAGGCAGCCCCGCTGTCCAGCACAGCCGACAGTACACGGCTCGACGACCAGCCCAAAACAGATGTGCTAGGTGTTCACGAAGCAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCACAGCCGACAGTACAC
60.01
TTTGTGGAGAACCTGTGCGT
60.11
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCACAGCCGACAGTACA
60.01
TTTGTGGAGAACCTGTGCGT
60.11
143
PCR template sequence:
TTCAGCCTGTTCTCAGGCAGCCCCGCTGTCCAGCACAGCCGACAGTACACGGCTCGACGACCAGCCCAAAACAGATGTGCTAGGTGTTCACGAAGCAGAGAACTCCCTCATGGATCCCCACAGCTGGTACGAAGGGATATCGGGCTCTCGGTGACGCACAGGTTCTCCACAAAGTCATGGTTGTCACAGGTGTGCAACGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-705(2), mmu-miR-203-3p(1), mmu-miR-541-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCACGAAGCAGAGAACTCCCTCATGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKSR1_584_ORF_1
0.7297
0.267924118
0.725226066
525
ORF sequence:
ATGATTTTTGGCGTGAAGTGCAAACACTGCAGGTTAAAATGCCATAACAAGTGCACAAAGGAAGCTCCCGCCTGCAGGATCACCTTCCTCCCACTGGCCAGGCTTCGGAGGACAGAGTCTGTCCCGTCAGATATCAACAACCCAGTGGACAGAGCAGCAGAGCCCCATTTTGGAACCCTTCCCAAGGCCCTGACAAAGAAGGAGCACCCTCCAGCCATGAACCTGGACTCCAGCAGCAACCCATCCTCCACCACGTCCTCCACACCCTCATCGCCGGCACCTTTCCTGACCTCATCTAATCCCTCCAGTGCCACCACGCCTCCCAACCCGTCACCTGGCCAGCGGGACAGCAGGTTCAGCTTCCCAGACATTTCAGCCTGTTCTCAGGCAGCCCCGCTGTCCAGCACAGCCGACAGTACACGGCTCGACGACCAGCCCAAAACAGATGTGCTAGGTGTTCACGAAGCAGAGAACTCCCTCATGGATCCCCACAGCTGGTACGAAGGGATATCGGGCTCTCGGTGA
Peptide sequence:
MIFGVKCKHCRLKCHNKCTKEAPACRITFLPLARLRRTESVPSDINNPVDRAAEPHFGTLPKALTKKEHPPAMNLDSSSNPSSTTSSTPSSPAPFLTSSNPSSATTPPNPSPGQRDSRFSFPDISACSQAAPLSSTADSTRLDDQPKTDVLGVHEAENSLMDPHSWYEGISGSR
IRESfinder result
IRESfinder score
0.468101242
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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