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mmu_circTlk1_526
Basic information of circular RNA
PanCircBase ID:
mmu_circTlk1_526
mm39_Chr. Position ID:
chr2|70546955|70552071|-
Gene name:
Tlk1
Transcript:
ENSMUST00000135128.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
21,20,19,18
Exon/intron offsets:
0,1170,4462,4946
Genomic length:
5116
Exon/intron sizes in nt:
1,08,11,21,36,170
Flanking exon/introns:
chr2:70544509-70546955|chr2:70552071-70552250
Splice length:
526
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTTTGTACAGTGCTAGAGTACTGTGAAGGCAATGACTTGGACTTCTACCTGAAGCAGCACAAGTTGATGTCTGAGAAAGAAGCTCGGTCTATTGTGATGCAGATTGTGAATGCCTTACGCTATCTCAATGAAATCAAACCTCCTATTATACATTATGACCTTAAGCCAGGAAATATCCTTCTGGTAGATGGAACAGCATGTGGAGAAATCAAAATCACTGATTTTGGTCTGTCCAAGATTATGGATGACGATAGTTACGGTGTTGATGGGATGGATCTGACTTCCCAGGGGGCAGGCACTTACTGGTATTTACCTCCTGAGTGCTTTGTAGTTGGAAAAGAGCCACCGAAGATCTCCAACAAGGTTGACGTGTGGTCAGTTGGGGTCATCTTCTTCCAGTGCCTCTATGGTAGAAAACCATTTGGTCACAATCAATCTCAACAAGACATTCTACAGGAAAACACAATACTGAAAGCCACAGAAGTCCAGTTCCCTGTAAAACCTGTTGTAAGCAGTGAAGCCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCCACAGAAGTCCAGTTCC
59.6
ACCGAGCTTCTTTCTCAGACA
59.04
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCCACAGAAGTCCAGTTCC
59.6
GACCGAGCTTCTTTCTCAGACA
60.03
142
PCR template sequence:
TCACAATCAATCTCAACAAGACATTCTACAGGAAAACACAATACTGAAAGCCACAGAAGTCCAGTTCCCTGTAAAACCTGTTGTAAGCAGTGAAGCCAAGGTTTTGTACAGTGCTAGAGTACTGTGAAGGCAATGACTTGGACTTCTACCTGAAGCAGCACAAGTTGATGTCTGAGAAAGAAGCTCGGTCTATTGTGATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(1), mmu-miR-101a-3p(1), mmu-miR-467b-5p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CAGTGAAGCCAAGGTTTTGTACAGTG
siRNA sets
CACTGTACAAAACCTTGGC, ACTGTACAAAACCTTGGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTLK1_526_ORF_1
0.9758
0.136394803
0.648335251
486
ORF sequence:
ATGTCTGAGAAAGAAGCTCGGTCTATTGTGATGCAGATTGTGAATGCCTTACGCTATCTCAATGAAATCAAACCTCCTATTATACATTATGACCTTAAGCCAGGAAATATCCTTCTGGTAGATGGAACAGCATGTGGAGAAATCAAAATCACTGATTTTGGTCTGTCCAAGATTATGGATGACGATAGTTACGGTGTTGATGGGATGGATCTGACTTCCCAGGGGGCAGGCACTTACTGGTATTTACCTCCTGAGTGCTTTGTAGTTGGAAAAGAGCCACCGAAGATCTCCAACAAGGTTGACGTGTGGTCAGTTGGGGTCATCTTCTTCCAGTGCCTCTATGGTAGAAAACCATTTGGTCACAATCAATCTCAACAAGACATTCTACAGGAAAACACAATACTGAAAGCCACAGAAGTCCAGTTCCCTGTAAAACCTGTTGTAAGCAGTGAAGCCAAGGTTTTGTACAGTGCTAGAGTACTGTGA
Peptide sequence:
MSEKEARSIVMQIVNALRYLNEIKPPIIHYDLKPGNILLVDGTACGEIKITDFGLSKIMDDDSYGVDGMDLTSQGAGTYWYLPPECFVVGKEPPKISNKVDVWSVGVIFFQCLYGRKPFGHNQSQQDILQENTILKATEVQFPVKPVVSSEAKVLYSARVL
IRESfinder result
IRESfinder score
0.447521039
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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