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mmu_circTrpm7_340
Basic information of circular RNA
PanCircBase ID:
mmu_circTrpm7_340
mm39_Chr. Position ID:
chr2|126641088|126649299|-
Gene name:
Trpm7
Transcript:
ENSMUST00000103224.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
33,32,31,30,29,28
Exon/intron offsets:
0,144,1954,3417,5848,8120
Genomic length:
8211
Exon/intron sizes in nt:
66,51,26,35,71,91
Flanking exon/introns:
chr2:126639865-126641088|chr2:126649299-126652082
Splice length:
340
Other database IDs:
circAtlas: mmu-Trpm7_0084
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_130650
Human Ortholog IDs:
Mature spliced Sequence:
AATGATACTCCTGAAAACACTCTGAAACATGTGGGTGCTGCTGGATATAGTGAATGTTGTAAGACTTCTACTTCTCTTCACTCGGTGCAAGCAGAAAGCTGTAGTAGAAGAGCGTCGACGGAAGACTCTCCAGAAGTCGATTCTAAAGCAGCTTTGTTACCGGATTGGTTACGAGATAGACCATCAAACAGAGAAATGCCATCTGAAGGAGGAACATTAAATGGTCTTGCTTCTCCATTTAAGCCCGTTTTGGATACAAATTACTATTATTCAGCTGTGGAAAGAAATAACCTGATGAGGTTGTCACAGAGTATTCCCTTCGTTCCTGTACCTCCACGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTGATGAGGTTGTCACAGAGT
59.7
TTCTGCTTGCACCGAGTGAA
60.18
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTGATGAGGTTGTCACAGAGT
59.7
TTTCTGCTTGCACCGAGTGA
60.18
147
PCR template sequence:
AAGCCCGTTTTGGATACAAATTACTATTATTCAGCTGTGGAAAGAAATAACCTGATGAGGTTGTCACAGAGTATTCCCTTCGTTCCTGTACCTCCACGAGAATGATACTCCTGAAAACACTCTGAAACATGTGGGTGCTGCTGGATATAGTGAATGTTGTAAGACTTCTACTTCTCTTCACTCGGTGCAAGCAGAAAGCT
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-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-320-3p(1), mmu-miR-181b-5p(1), mmu-miR-1904(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GTACCTCCACGAGAATGATACTCCTG
siRNA sets
GAGTATCATTCTCGTGGAG, AGGAGTATCATTCTCGTGG, AGTATCATTCTCGTGGAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTRPM7_340_ORF_3
0.7888
-0.120317802
0.039105258
150
ORF sequence:
ATGCCATCTGAAGGAGGAACATTAAATGGTCTTGCTTCTCCATTTAAGCCCGTTTTGGATACAAATTACTATTATTCAGCTGTGGAAAGAAATAACCTGATGAGGTTGTCACAGAGTATTCCCTTCGTTCCTGTACCTCCACGAGAATGA
Peptide sequence:
MPSEGGTLNGLASPFKPVLDTNYYYSAVERNNLMRLSQSIPFVPVPPRE
IRESfinder result
IRESfinder score
0.556045735
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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