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mmu_circGm42878_812
Basic information of circular RNA
PanCircBase ID:
mmu_circGm42878_812
mm39_Chr. Position ID:
chr5|121669595|121678638|-
Gene name:
Gm42878
Transcript:
ENSMUST00000125946.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
9,8,7,6,5,4,3,2
Exon/intron offsets:
0,1776,2802,4321,5575,6860,7639,8969
Genomic length:
9043
Exon/intron sizes in nt:
188,81,96,86,113,98,76,74
Flanking exon/introns:
chr5:121667053-121669595|chr5:121678638-121683227
Splice length:
812
Other database IDs:
circAtlas: mmu-Mapkapk5_0003
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GAGACCTCCATTTTAGAAGAATATAGTATCAATTGGACTCAGAAACTGGGAGCCGGAATTAGTGGTCCAGTTAGAGTCTGTGTGAAGAAATCCACTCAAGAACGGTTTGCACTGAAAATTCTTCTTGATCGTCCAAAAGCTAGAAATGAGGTGCGCCTGCACATGATGTGTGCCACACACCCCAACATAGTTCAGATTATTGAAGTGTTTGCTAACAGTGTACAGTTCCCTCATGAGTCCAGCCCCAGGGCTCGACTCTTAATTGTAATGGAGATGATGGAAGGGGGAGAGCTATTTCACAGAATCAGCCAGCACCGGCACTTTACAGAGAAGCAAGCCAGCCAAGTAACAAAGCAGGCAACCCTGGCTCTACAGCACTGTCACTTGCTAAACATTGCGCACAGAGACCTCAAGCCTGAAAATCTGCTTTTCAAGGATAACTCTCTGGACGCCCCTGTGAAATTATGTGACTTTGGGTTTGCTAAAGTTGACCAAGGTGATTTGATGACACCCCAGTTTACCCCTTACTATGTAGCACCTCAGGTACTGGAAGCGCAGAGACGGCACCAGAAGGAGAAGTCTGGCATCATACCTACCTCGCCAACACCCTACACTTACAACAAGAGCTGTGACTTGTGGTCCCTAGGGGTGATAATTTATGTGATGCTGTGCGGATATCCTCCTTTTTACTCCAAACACCATAGTCGGACTATCCCAAAGGATATGCGGAAAAAGATCATGACAGGAAGTTTCGAGTTCCCAGAAGAAGAGTGGAGCCAGATCTCAGAGATGGCTAAAGATGTTGTGAGGAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACAGGAAGTTTCGAGTTCCCA
59.23
ACTGGACCACTAATTCCGGC
59.75
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGGAAGTTTCGAGTTCCCAGA
59.96
ACTGGACCACTAATTCCGGC
59.75
141
PCR template sequence:
TCCCAAAGGATATGCGGAAAAAGATCATGACAGGAAGTTTCGAGTTCCCAGAAGAAGAGTGGAGCCAGATCTCAGAGATGGCTAAAGATGTTGTGAGGAAGAGACCTCCATTTTAGAAGAATATAGTATCAATTGGACTCAGAAACTGGGAGCCGGAATTAGTGGTCCAGTTAGAGTCTGTGTGAAGAAATCCACTCAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-let-7a-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-17-5p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-221-3p(1), mmu-let-7c-5p(1), mmu-miR-106b-5p(1), mmu-miR-152-3p(1), mmu-let-7d-5p(1), mmu-miR-149-5p(1), mmu-miR-362-5p(1), mmu-miR-98-5p(1), mmu-miR-377-3p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATGTTGTGAGGAAGAGACCTCCATTT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGM42878_812_ORF_1
1.0411
0.156496807
0.890993767
666
ORF sequence:
ATGATGTGTGCCACACACCCCAACATAGTTCAGATTATTGAAGTGTTTGCTAACAGTGTACAGTTCCCTCATGAGTCCAGCCCCAGGGCTCGACTCTTAATTGTAATGGAGATGATGGAAGGGGGAGAGCTATTTCACAGAATCAGCCAGCACCGGCACTTTACAGAGAAGCAAGCCAGCCAAGTAACAAAGCAGGCAACCCTGGCTCTACAGCACTGTCACTTGCTAAACATTGCGCACAGAGACCTCAAGCCTGAAAATCTGCTTTTCAAGGATAACTCTCTGGACGCCCCTGTGAAATTATGTGACTTTGGGTTTGCTAAAGTTGACCAAGGTGATTTGATGACACCCCAGTTTACCCCTTACTATGTAGCACCTCAGGTACTGGAAGCGCAGAGACGGCACCAGAAGGAGAAGTCTGGCATCATACCTACCTCGCCAACACCCTACACTTACAACAAGAGCTGTGACTTGTGGTCCCTAGGGGTGATAATTTATGTGATGCTGTGCGGATATCCTCCTTTTTACTCCAAACACCATAGTCGGACTATCCCAAAGGATATGCGGAAAAAGATCATGACAGGAAGTTTCGAGTTCCCAGAAGAAGAGTGGAGCCAGATCTCAGAGATGGCTAAAGATGTTGTGAGGAAGAGACCTCCATTTTAG
Peptide sequence:
MMCATHPNIVQIIEVFANSVQFPHESSPRARLLIVMEMMEGGELFHRISQHRHFTEKQASQVTKQATLALQHCHLLNIAHRDLKPENLLFKDNSLDAPVKLCDFGFAKVDQGDLMTPQFTPYYVAPQVLEAQRRHQKEKSGIIPTSPTPYTYNKSCDLWSLGVIIYVMLCGYPPFYSKHHSRTIPKDMRKKIMTGSFEFPEEEWSQISEMAKDVVRKRPPF
IRESfinder result
IRESfinder score
0.531523353
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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