top of page
mmu_circCog6_987
Basic information of circular RNA
PanCircBase ID:
mmu_circCog6_987
mm39_Chr. Position ID:
chr3|52903428|52921307|-
Gene name:
Cog6
Transcript:
ENSMUST00000036665.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
13,12,11,10,9,8,7,6,5,4,3
Exon/intron offsets:
0,2249,4473,6238,6405,11238,13045,13465,14568,16898,17807
Genomic length:
17879
Exon/intron sizes in nt:
118,92,65,92,129,94,71,83,112,59,72
Flanking exon/introns:
chr3:52900992-52903428|chr3:52921307-52922889
Splice length:
987
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GAGCTTGAAAGCATCAATGAAGATGTACAGGCCATGAGCAGCTGTTGTCAGGATATGACAAGTCGCTTACAGGCAGCAAAAGAACAGACTCAAGATTTAATAGTAAAGACCACTAAGCTGCAAGCGGAAAACCAAAGACTAGAGATTAGAGCACAGGTTGTGGATGCCTTTTTGGCCAAGTTCCAGCTGACTTCGGATGAAATGAGTCTCCTCCGCGGTACAAGAGGAGGCCCCGTTACTGAGGACTTTTTCAAGGCATTGGGAAGAGTGAAACAGATTCATAATGACGTCAAGGTTCTTTTGCGAACCAACCAGCAGACGGCAGGTTTGGAGATTATGGAACAGATGGCCTTGCTTCAAGAAACTGCTTATGAAAGACTTTACCGGTGGGCTCAAAGCGAGTGCAGAGCACTGACTCAAGAGTCCTGTGATGTGTCTGCGGTGTTATCCCAGGCCATGGAAGCCCTGCAGGACAGGCCTGTCTTATACAAGTATACCTTAGATGAATTTGGAACGGCCCGACGAAGCACTGTTGTTCGTGGGTTTATTGATGCTCTTACAAGAGGAGGGCCAGGAGGTACACCTAGGCCCATTGAAATGCACTCCCATGACCCGCTGAGGTATGTGGGAGACATGCTGGCATGGCTCCATCAAGCTACTGCCTCTGAGAAGGAACATCTGGAAGCTCTCTTAAAGCATGTAACTGCTCAGGGTGTTAAAGAAAATATCCAAGAAGTCGTTGGGCATATCACCGAGGGTGTGTGTCGGCCTCTAAAGGTTCGAATTGAACAAGTAATACTTGCTGAACCTGGGGCAGTGTTGTTATATAAAATTTCTAACCTCCTCAAGTTTTACCACCACACCATCAGTGGCATCGTTGGAAATAGTGCAGCTACTCTACTGACAACAATTGAGGAAATGCACCTGCTAAGCAAAAAAATCTTCTTCACTAGCTTGAGTCTCCATGCGAATAAACTGATGGACAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGAAATGCACCTGCTAAGCA
58.82
TTGCTGCCTGTAAGCGACTT
60.25
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAAATGCACCTGCTAAGCA
58.82
TTTGCTGCCTGTAAGCGACT
60.25
153
PCR template sequence:
TGCAGCTACTCTACTGACAACAATTGAGGAAATGCACCTGCTAAGCAAAAAAATCTTCTTCACTAGCTTGAGTCTCCATGCGAATAAACTGATGGACAAGGAGCTTGAAAGCATCAATGAAGATGTACAGGCCATGAGCAGCTGTTGTCAGGATATGACAAGTCGCTTACAGGCAGCAAAAGAACAGACTCAAGATTTAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
19
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-let-7a-5p(1), mmu-miR-141-3p(1), mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-328-3p(1), mmu-miR-709(1), mmu-miR-125b-5p(1), mmu-miR-339-5p(1), mmu-let-7d-5p(1), mmu-miR-431-5p(1), mmu-miR-351-5p(1), mmu-miR-324-3p(1), mmu-miR-802-5p(1), mmu-miR-410-3p(1), mmu-miR-344d-3p(1), mmu-miR-532-5p(1), mmu-miR-188-3p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTGATGGACAAGGAGCTTGAAAGCA
siRNA sets
CTTTCAAGCTCCTTGTCCA, TTTCAAGCTCCTTGTCCAT, TCAAGCTCCTTGTCCATCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCOG6_987_ORF_1
1.0425
0.149402062
0.999987214
1941
ORF sequence:
ATGAGCAGCTGTTGTCAGGATATGACAAGTCGCTTACAGGCAGCAAAAGAACAGACTCAAGATTTAATAGTAAAGACCACTAAGCTGCAAGCGGAAAACCAAAGACTAGAGATTAGAGCACAGGTTGTGGATGCCTTTTTGGCCAAGTTCCAGCTGACTTCGGATGAAATGAGTCTCCTCCGCGGTACAAGAGGAGGCCCCGTTACTGAGGACTTTTTCAAGGCATTGGGAAGAGTGAAACAGATTCATAATGACGTCAAGGTTCTTTTGCGAACCAACCAGCAGACGGCAGGTTTGGAGATTATGGAACAGATGGCCTTGCTTCAAGAAACTGCTTATGAAAGACTTTACCGGTGGGCTCAAAGCGAGTGCAGAGCACTGACTCAAGAGTCCTGTGATGTGTCTGCGGTGTTATCCCAGGCCATGGAAGCCCTGCAGGACAGGCCTGTCTTATACAAGTATACCTTAGATGAATTTGGAACGGCCCGACGAAGCACTGTTGTTCGTGGGTTTATTGATGCTCTTACAAGAGGAGGGCCAGGAGGTACACCTAGGCCCATTGAAATGCACTCCCATGACCCGCTGAGGTATGTGGGAGACATGCTGGCATGGCTCCATCAAGCTACTGCCTCTGAGAAGGAACATCTGGAAGCTCTCTTAAAGCATGTAACTGCTCAGGGTGTTAAAGAAAATATCCAAGAAGTCGTTGGGCATATCACCGAGGGTGTGTGTCGGCCTCTAAAGGTTCGAATTGAACAAGTAATACTTGCTGAACCTGGGGCAGTGTTGTTATATAAAATTTCTAACCTCCTCAAGTTTTACCACCACACCATCAGTGGCATCGTTGGAAATAGTGCAGCTACTCTACTGACAACAATTGAGGAAATGCACCTGCTAAGCAAAAAAATCTTCTTCACTAGCTTGAGTCTCCATGCGAATAAACTGATGGACAAGGAGCTTGAAAGCATCAATGAAGATGTACAGGCCATGAGCAGCTGTTGTCAGGATATGACAAGTCGCTTACAGGCAGCAAAAGAACAGACTCAAGATTTAATAGTAAAGACCACTAAGCTGCAAGCGGAAAACCAAAGACTAGAGATTAGAGCACAGGTTGTGGATGCCTTTTTGGCCAAGTTCCAGCTGACTTCGGATGAAATGAGTCTCCTCCGCGGTACAAGAGGAGGCCCCGTTACTGAGGACTTTTTCAAGGCATTGGGAAGAGTGAAACAGATTCATAATGACGTCAAGGTTCTTTTGCGAACCAACCAGCAGACGGCAGGTTTGGAGATTATGGAACAGATGGCCTTGCTTCAAGAAACTGCTTATGAAAGACTTTACCGGTGGGCTCAAAGCGAGTGCAGAGCACTGACTCAAGAGTCCTGTGATGTGTCTGCGGTGTTATCCCAGGCCATGGAAGCCCTGCAGGACAGGCCTGTCTTATACAAGTATACCTTAGATGAATTTGGAACGGCCCGACGAAGCACTGTTGTTCGTGGGTTTATTGATGCTCTTACAAGAGGAGGGCCAGGAGGTACACCTAGGCCCATTGAAATGCACTCCCATGACCCGCTGAGGTATGTGGGAGACATGCTGGCATGGCTCCATCAAGCTACTGCCTCTGAGAAGGAACATCTGGAAGCTCTCTTAAAGCATGTAACTGCTCAGGGTGTTAAAGAAAATATCCAAGAAGTCGTTGGGCATATCACCGAGGGTGTGTGTCGGCCTCTAAAGGTTCGAATTGAACAAGTAATACTTGCTGAACCTGGGGCAGTGTTGTTATATAAAATTTCTAACCTCCTCAAGTTTTACCACCACACCATCAGTGGCATCGTTGGAAATAGTGCAGCTACTCTACTGACAACAATTGAGGAAATGCACCTGCTAAGCAAAAAAATCTTCTTCACTAGCTTGAGTCTCCATGCGAATAAACTGATGGACAAG
Peptide sequence:
MSSCCQDMTSRLQAAKEQTQDLIVKTTKLQAENQRLEIRAQVVDAFLAKFQLTSDEMSLLRGTRGGPVTEDFFKALGRVKQIHNDVKVLLRTNQQTAGLEIMEQMALLQETAYERLYRWAQSECRALTQESCDVSAVLSQAMEALQDRPVLYKYTLDEFGTARRSTVVRGFIDALTRGGPGGTPRPIEMHSHDPLRYVGDMLAWLHQATASEKEHLEALLKHVTAQGVKENIQEVVGHITEGVCRPLKVRIEQVILAEPGAVLLYKISNLLKFYHHTISGIVGNSAATLLTTIEEMHLLSKKIFFTSLSLHANKLMDKELESINEDVQAMSSCCQDMTSRLQAAKEQTQDLIVKTTKLQAENQRLEIRAQVVDAFLAKFQLTSDEMSLLRGTRGGPVTEDFFKALGRVKQIHNDVKVLLRTNQQTAGLEIMEQMALLQETAYERLYRWAQSECRALTQESCDVSAVLSQAMEALQDRPVLYKYTLDEFGTARRSTVVRGFIDALTRGGPGGTPRPIEMHSHDPLRYVGDMLAWLHQATASEKEHLEALLKHVTAQGVKENIQEVVGHITEGVCRPLKVRIEQVILAEPGAVLLYKISNLLKFYHHTISGIVGNSAATLLTTIEEMHLLSKKIFFTSLSLHANKLMDK
IRESfinder result
IRESfinder score
0.409655064
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page