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mmu_circJmjd6_676
Basic information of circular RNA
PanCircBase ID:
mmu_circJmjd6_676
mm39_Chr. Position ID:
chr11|116731894|116733546|-
Gene name:
Jmjd6
Transcript:
ENSMUST00000141735.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,2
Exon/intron offsets:
0,1263
Genomic length:
1652
Exon/intron sizes in nt:
2,87,389
Flanking exon/introns:
chr11:116731371-116731894|chr11:116733546-116733890
Splice length:
676
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GATAACGTGGAGAGAGCTGATGCCTTACAGCTGTCGGTGAAAGAGTTCGTGGAGCGCTACGAGAGGCCTTACAAGCCCGTGGTTCTGCTCAATGCACAAGAGGGCTGGTCCGCACAGGAGAAATGGACTCTGGAGCGCCTCAAAAGGAAATACCGGAACCAGAAGTTCAAGTGCGGCGAGGATAATGACGGCTACTCGGTTAAGATGAAGATGAAGTACTACATCGAGTACATGGAGAGCACCCGCGATGACAGTCCCCTTTACATCTTCGATAGCAGCTATGGCGAACACCCCAAAAGAAGGAAACTTTTGGAAGACTACAAGGTGCCCAAGTTTTTCACAGATGATCTTTTCCAATACGCGGGGGAGAAACGCAGACCCCCTTACAGGTGGTTTGTGATGGGGCCACCGCGTTCTGGAACTGGGATTCACATCGACCCTCTGGGGACCAGTGCCTGGAATGCCTTAGTTCAGGGTCACAAGCGGTGGTGCCTCTTCCCAACAAACACACCCAGAGAACTCATCAAGGTGACCCGAGAAGAAGGAGGGAACCAACAGGATGAAGCAATTACCTGGTTTAATGTCATCTATCCCCGGACACAGCTTCCAACCTGGCCACCTGAATTCAAACCCCTGGAGATATTACAGAAACCAGGAGAAACTGTCTTTGTACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CATCTATCCCCGGACACAGC
59.97
AGAACCACGGGCTTGTAAGG
59.96
178
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTATCCCCGGACACAGCTTC
59.89
AGAACCACGGGCTTGTAAGG
59.96
175
PCR template sequence:
TTTAATGTCATCTATCCCCGGACACAGCTTCCAACCTGGCCACCTGAATTCAAACCCCTGGAGATATTACAGAAACCAGGAGAAACTGTCTTTGTACCAGGATAACGTGGAGAGAGCTGATGCCTTACAGCTGTCGGTGAAAGAGTTCGTGGAGCGCTACGAGAGGCCTTACAAGCCCGTGGTTCTGCTCAATGCACAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-196a-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-758-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTCTTTGTACCAGGATAACGTGGAGA
siRNA sets
GTTATCCTGGTACAAAGAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCJMJD6_676_ORF_1
0.8793
0.31447607
0.966480706
792
ORF sequence:
ATGAAGCAATTACCTGGTTTAATGTCATCTATCCCCGGACACAGCTTCCAACCTGGCCACCTGAATTCAAACCCCTGGAGATATTACAGAAACCAGGAGAAACTGTCTTTGTACCAGGATAACGTGGAGAGAGCTGATGCCTTACAGCTGTCGGTGAAAGAGTTCGTGGAGCGCTACGAGAGGCCTTACAAGCCCGTGGTTCTGCTCAATGCACAAGAGGGCTGGTCCGCACAGGAGAAATGGACTCTGGAGCGCCTCAAAAGGAAATACCGGAACCAGAAGTTCAAGTGCGGCGAGGATAATGACGGCTACTCGGTTAAGATGAAGATGAAGTACTACATCGAGTACATGGAGAGCACCCGCGATGACAGTCCCCTTTACATCTTCGATAGCAGCTATGGCGAACACCCCAAAAGAAGGAAACTTTTGGAAGACTACAAGGTGCCCAAGTTTTTCACAGATGATCTTTTCCAATACGCGGGGGAGAAACGCAGACCCCCTTACAGGTGGTTTGTGATGGGGCCACCGCGTTCTGGAACTGGGATTCACATCGACCCTCTGGGGACCAGTGCCTGGAATGCCTTAGTTCAGGGTCACAAGCGGTGGTGCCTCTTCCCAACAAACACACCCAGAGAACTCATCAAGGTGACCCGAGAAGAAGGAGGGAACCAACAGGATGAAGCAATTACCTGGTTTAATGTCATCTATCCCCGGACACAGCTTCCAACCTGGCCACCTGAATTCAAACCCCTGGAGATATTACAGAAACCAGGAGAAACTGTCTTTGTACCA
Peptide sequence:
MKQLPGLMSSIPGHSFQPGHLNSNPWRYYRNQEKLSLYQDNVERADALQLSVKEFVERYERPYKPVVLLNAQEGWSAQEKWTLERLKRKYRNQKFKCGEDNDGYSVKMKMKYYIEYMESTRDDSPLYIFDSSYGEHPKRRKLLEDYKVPKFFTDDLFQYAGEKRRPPYRWFVMGPPRSGTGIHIDPLGTSAWNALVQGHKRWCLFPTNTPRELIKVTREEGGNQQDEAITWFNVIYPRTQLPTWPPEFKPLEILQKPGETVFVP
IRESfinder result
IRESfinder score
0.296309672
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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