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mmu_circNtrk2_234
Basic information of circular RNA
PanCircBase ID:
mmu_circNtrk2_234
mm39_Chr. Position ID:
chr13|59019549|59026076|+
Gene name:
Ntrk2
Transcript:
ENSMUST00000225488.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
10,11,12
Exon/intron offsets:
0,2592,6427
Genomic length:
6527
Exon/intron sizes in nt:
36,98,100
Flanking exon/introns:
chr13:59009369-59019549|chr13:59026076-59133615
Splice length:
234
Other database IDs:
CIRCpedia: MMU_CIRCpedia_24300, circAtlas: mmu-Ntrk2_0001
circBase: hsa_circ_0087378, circAtlas: hsa-NTRK2_0001, CIRCpedia: HSA_CIRCpedia_64550
Human Ortholog IDs:
Mature spliced Sequence:
AGACAAACCCAAATTACCCTGAAGTCCTCTATGAAGACTGGACCACGCCAACTGACATTGGGGATACTACGAACAAAAGTAATGAAATCCCCTCCACGGATGTTGCTGACCAAAGCAATCGGGAGCATCTCTCGGTCTATGCCGTGGTGGTGATTGCATCTGTGGTGGGATTCTGCCTGCTGGTGATGTTGCTCCTGCTCAAGTTGGCGAGACATTCCAAGTTTGGCATGAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTCTATGCCGTGGTGGTGAT
59.82
CAATGTCAGTTGGCGTGGTC
59.76
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGTGGTGGTGATTGCATCTG
59.55
CAATGTCAGTTGGCGTGGTC
59.76
152
PCR template sequence:
GTCTATGCCGTGGTGGTGATTGCATCTGTGGTGGGATTCTGCCTGCTGGTGATGTTGCTCCTGCTCAAGTTGGCGAGACATTCCAAGTTTGGCATGAAAGAGACAAACCCAAATTACCCTGAAGTCCTCTATGAAGACTGGACCACGCCAACTGACATTGGGGATACTACGAACAAAAGTAATGAAATCCCCTCCACGGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-214-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTGGCATGAAAGAGACAAACCCAAA
siRNA sets
GTTTGTCTCTTTCATGCCA, TTTGGGTTTGTCTCTTTCA, TTTGTCTCTTTCATGCCAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNTRK2_234_ORF_1
1.2473
0.330851499
0.611399515
282
ORF sequence:
ATGTTGCTCCTGCTCAAGTTGGCGAGACATTCCAAGTTTGGCATGAAAGAGACAAACCCAAATTACCCTGAAGTCCTCTATGAAGACTGGACCACGCCAACTGACATTGGGGATACTACGAACAAAAGTAATGAAATCCCCTCCACGGATGTTGCTGACCAAAGCAATCGGGAGCATCTCTCGGTCTATGCCGTGGTGGTGATTGCATCTGTGGTGGGATTCTGCCTGCTGGTGATGTTGCTCCTGCTCAAGTTGGCGAGACATTCCAAGTTTGGCATGAAA
Peptide sequence:
MLLLLKLARHSKFGMKETNPNYPEVLYEDWTTPTDIGDTTNKSNEIPSTDVADQSNREHLSVYAVVVIASVVGFCLLVMLLLLKLARHSKFGMK
IRESfinder result
IRESfinder score
0.421562238
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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