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mmu_circTrak2_633
Basic information of circular RNA
PanCircBase ID:
mmu_circTrak2_633
mm39_Chr. Position ID:
chr1|58954844|58961048|-
Gene name:
Trak2
Transcript:
ENSMUST00000027186.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
10,9,8,7,6
Exon/intron offsets:
0,3086,3535,5388,5994
Genomic length:
6204
Exon/intron sizes in nt:
13,87,51,31,79,210
Flanking exon/introns:
chr1:58951421-58954844|chr1:58961048-58962680
Splice length:
633
Other database IDs:
circAtlas: mmu-Trak2_0019
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_146396
Human Ortholog IDs:
Mature spliced Sequence:
GTTAATCAGCTGCAGCACGAGCTCTCCAAGAAAGACGAGCTGCTCCGAATCGTCTCTATTGCCTCCGAGGAGAGTGAAACGGATTCTAGCTGCTCCACGCCCCTTCGGTTCAATGAGTCCTTCAGCTTATCTCAGGGGCTGCTGCAGCTGGACATGCTGCATGAGAAGCTCAGGGAGCTGGAAGAAGAGAACATGGCCCTACGATCCAAGGCTTGTCATATCAAGACAGAAACATTTACCTATGAAGAGAAGGAACAACAGCTCGTCAATGACTGTGTTAAAGAACTTCGTGAGACCAATGCACAGATGTCCAGAATGACTGAAGAGCTGTCGGGAAAGAGCGACGAGCTGCTCCGGTACCAAGAGGAGATCTCCTCCCTGCTGTCTCAGATCGTAGACCTTCAGCACAAACTGAAAGAGCATGTGATCGAGAAGGAAGAACTAAGACTTCACCTGCAGGCTTCCAAAGATGCCCAGCGACAGCTGACAATGGAGCTTCATGAGTTACAGGACAGGAACATGGAATGCCTGGGAATGTTACATGAGTCCCAAGAAGAAATAAAAGAGCTTCGTAGCAAGTCCGGCCCTTCTGCTCATCTCTGCTTCTCCCAGTCTTACGGCGTTTTTACAGGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCCCTTCTGCTCATCTCTG
60.18
GTGGAGCAGCTAGAATCCGT
59.54
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCCCTTCTGCTCATCTCTG
60.18
CGTGGAGCAGCTAGAATCCG
60.6
150
PCR template sequence:
AATGTTACATGAGTCCCAAGAAGAAATAAAAGAGCTTCGTAGCAAGTCCGGCCCTTCTGCTCATCTCTGCTTCTCCCAGTCTTACGGCGTTTTTACAGGGGTTAATCAGCTGCAGCACGAGCTCTCCAAGAAAGACGAGCTGCTCCGAATCGTCTCTATTGCCTCCGAGGAGAGTGAAACGGATTCTAGCTGCTCCACGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-103-3p(1), mmu-miR-709(1), mmu-miR-125b-5p(1), mmu-miR-107-3p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CGTTTTTACAGGGGTTAATCAGCTGC
siRNA sets
ATTAACCCCTGTAAAAACG, GATTAACCCCTGTAAAAAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTRAK2_633_ORF_1
1.1856
0.407268419
0.998680274
1113
ORF sequence:
ATGCTGCATGAGAAGCTCAGGGAGCTGGAAGAAGAGAACATGGCCCTACGATCCAAGGCTTGTCATATCAAGACAGAAACATTTACCTATGAAGAGAAGGAACAACAGCTCGTCAATGACTGTGTTAAAGAACTTCGTGAGACCAATGCACAGATGTCCAGAATGACTGAAGAGCTGTCGGGAAAGAGCGACGAGCTGCTCCGGTACCAAGAGGAGATCTCCTCCCTGCTGTCTCAGATCGTAGACCTTCAGCACAAACTGAAAGAGCATGTGATCGAGAAGGAAGAACTAAGACTTCACCTGCAGGCTTCCAAAGATGCCCAGCGACAGCTGACAATGGAGCTTCATGAGTTACAGGACAGGAACATGGAATGCCTGGGAATGTTACATGAGTCCCAAGAAGAAATAAAAGAGCTTCGTAGCAAGTCCGGCCCTTCTGCTCATCTCTGCTTCTCCCAGTCTTACGGCGTTTTTACAGGGGTTAATCAGCTGCAGCACGAGCTCTCCAAGAAAGACGAGCTGCTCCGAATCGTCTCTATTGCCTCCGAGGAGAGTGAAACGGATTCTAGCTGCTCCACGCCCCTTCGGTTCAATGAGTCCTTCAGCTTATCTCAGGGGCTGCTGCAGCTGGACATGCTGCATGAGAAGCTCAGGGAGCTGGAAGAAGAGAACATGGCCCTACGATCCAAGGCTTGTCATATCAAGACAGAAACATTTACCTATGAAGAGAAGGAACAACAGCTCGTCAATGACTGTGTTAAAGAACTTCGTGAGACCAATGCACAGATGTCCAGAATGACTGAAGAGCTGTCGGGAAAGAGCGACGAGCTGCTCCGGTACCAAGAGGAGATCTCCTCCCTGCTGTCTCAGATCGTAGACCTTCAGCACAAACTGAAAGAGCATGTGATCGAGAAGGAAGAACTAAGACTTCACCTGCAGGCTTCCAAAGATGCCCAGCGACAGCTGACAATGGAGCTTCATGAGTTACAGGACAGGAACATGGAATGCCTGGGAATGTTACATGAGTCCCAAGAAGAAATAAAAGAGCTTCGTAGCAAGTCCGGCCCTTCTGCTCATCTCTGCTTCTCCCAGTCTTACGGCGTTTTTACAGGG
Peptide sequence:
MLHEKLRELEEENMALRSKACHIKTETFTYEEKEQQLVNDCVKELRETNAQMSRMTEELSGKSDELLRYQEEISSLLSQIVDLQHKLKEHVIEKEELRLHLQASKDAQRQLTMELHELQDRNMECLGMLHESQEEIKELRSKSGPSAHLCFSQSYGVFTGVNQLQHELSKKDELLRIVSIASEESETDSSCSTPLRFNESFSLSQGLLQLDMLHEKLRELEEENMALRSKACHIKTETFTYEEKEQQLVNDCVKELRETNAQMSRMTEELSGKSDELLRYQEEISSLLSQIVDLQHKLKEHVIEKEELRLHLQASKDAQRQLTMELHELQDRNMECLGMLHESQEEIKELRSKSGPSAHLCFSQSYGVFTG
IRESfinder result
IRESfinder score
0.331117251
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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