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mmu_circAlg6_2441
Basic information of circular RNA
PanCircBase ID:
mmu_circAlg6_2441
mm39_Chr. Position ID:
chr4|99636922|99641428|+
Gene name:
Alg6
Transcript:
ENSMUST00000144805.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
11,12,13
Exon/intron offsets:
0,2043,4307
Genomic length:
4506
Exon/intron sizes in nt:
85,2157,199
Flanking exon/introns:
chr4:99634648-99636922|chr4:99641428-99650107
Splice length:
2441
Other database IDs:
circBase: mmu_circ_0011909, CIRCpedia: MMU_CIRCpedia_36192, circAtlas: mmu-Alg6_0005
Human Ortholog IDs:
Mature spliced Sequence:
CTTTTGCTTTACACTTTTGAGCTTGCTTCCTGCATGTATAAAACTGACAGTTCGACCCTCTTGTAAAGGATTCAGATTTACTCTGGTTAGCTGTGCGCTATCATTCTTTCTGTTTTCTTTCCAAGTACATGAAAAGTCCATTCTCTTGGTATCATTGTAAGTAGAAATCTTTGAACTATACATTTATTATAATGTTCATTGTATAAGGATGTTTATAAAAATGTTAATTTAAATGTAAAATAAGACCACACAATAGTTTTGAATATATTTATCTTAGTCATTCTCAGAAGGATAATGCTTTAATTTTACTTTATAAAATACATTTTAAATCAAAACAGTTGACAAAATTATTATTGATATATTCTCATGTTTTCCAGGTCTTCATATTTTCTCTATACTAATCAAATTATACTTCATAATTTCTCTATACATCCTTCAAAGTGGCTTTCTTGCTTCTCCTCTTTGCCTTTTGTATTTCATTCATTTCCACATCGATCCGTTAGCCTTATTCTCTCCATTTACCTTCATGATATCTTTCATATGTTGTGTTCTGTTTTTTGTCCTCTGCTTCCCTACACCACAGTAGATGAAGGTTTCAGATCCTCTTGGTAATCCTTAAAGAGATTGTTTTGTTAAAGAACATTACAGTTTTCCATTTGTCATAGCAAAGAAAAACTGGGTAAAACTGGGGATGTGTTATCCTAATACTATAATATTGTATAAGCTTAGAGTAGCCTGGGATGCTTGGGTCCTCCCAGTTTAGTCCCATTTGTCTGCTGCCTTACGCCATGCCCTACCTGGTGCTTTCAGTGGTTGTGAGAACTCACTGTATAGACCACGCTGGCCTTGAACTCAGAGATCTGTCTTCCTCTGCCTCCTGAGTGTTGGGACTACAGGTGTGTACCACCACTGCCTGGCTCCAAGCTTAAATCTTTATACTGGTTGACATGAAGAAAAAAACCTTTAAGAAACCTTTCCTTTAAGAAAGGGGCTGTGTTAGTTCTGTGGCTGTGATAAAGCACCATGGCCAAGGCGACCAATGGAAGGAAGGCTGTGTCTAGGCATATGGTTCCAAAGGGATGAGCATCCATCCCCATCATGATGGAAGCATGGTGGAAGGCAGGCATGGTGGCTGGAGTATCAAGCTGAGAGCTCACATTTTAATCATAAGCGTGAAGCAGAGAGGGCACGCCTGAATGTCACATTCTTTTAAACGTCAAAGCCCAGCTCCAATGACATACTTCCTCCAGCAATGCTACACACATGTTATAAACCTCTCCAAACAGCGCAACCAAGTAGGGACCAAGTGTAAACACCTGAGTCTATAGGGGGCGCTCTTATCCAAACCATCACAGCGGGAGGATGCTCAAGCTTTTTGGAACCTTTTTAAACAGAAGAGGGGCGAGATTAATAGTAATGGCACCAGTAATTCAACAGCTGTCACTCTTCGAAAACTTTATTTTGTATTGCTAAAAATAAATATTAGGGGATACTTGCAGAGAACAGTGAAATTAATCATTGGCTTGAGTCACACGGCTAAGTGTCAGCTGTGGAGCTAGGACTAAGACCGTCTAACTAGTCAGCTTCTCGTTGAGCATGGATGCAGTCAAATCCAGAAGACCTCAGACAAAGGCTGTGGTAGATACCAGAGACACCAGAAAAGTGGTGGCTCCGTTTATCAGCATCGTGTTCCCAGTTCTCTGTCCTTGCCCTTTCCATGTAGCTTCTAATTATTCATCTTTCATTTTTCTATCAGTTGAATATTTTTAACCTGTCCCTTTATAATTCACCTTTGTTGTCCTTTCTCCATTAACATGGCATCCTGTTCCTCATAACTGTAGTTTGTAACCGGCTGAGGAGCATGGAACATGAAGAAGTTTGAAAATGGTTGCCTCGGGAGTCACTTTGTGCTTGCAGAGTAGAAGGAAATGCTTTCTCTGGTCTTTTCCTCAAGGGACTGTACATGTGGCACACGAAGTGTTTGCTAGTGACCTAGTCAAGTGGCTGTTGGCTAGACGTGTGGAGAAGTTGACACTTCCTGAATAGTCACATGCAGACCTTTTTTCTTTTAAACTAATCTTGAAAATCAGACATGCAGAGTATATTTATTTTTTCCAGGCTCGGAGTAAAATTATATTCTGTAACATTAAAATGCTTTTTCTTGTCATTTTAGACCAGTTTGCTTAGTTTTAACTGAAATTCCTTTCATGTCAACCTGGTTTTTACTAGTTTCAACATTTAGCATGCTGCCTCTTCTATTAAAGGATGAACTCCTGCTGCCCTCGGTTGTGACAGTGATGGCATTTGTAATAGCTTGTGGCACTTTCTTTCCAATGTTGGAGAACACTTCCGAAGAACAACTGCAGTTGAAGTCCTTTGCTGTCTCTGTAAGGAGGCACCTTCCGGGCTTCACATTTTTGCCCAGAATTATGCAGTGTTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCTTCCGGGCTTCACATTT
59.89
GCGCACAGCTAACCAGAGTA
60.11
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CACCTTCCGGGCTTCACATT
60.61
GCGCACAGCTAACCAGAGTA
60.11
143
PCR template sequence:
GAACACTTCCGAAGAACAACTGCAGTTGAAGTCCTTTGCTGTCTCTGTAAGGAGGCACCTTCCGGGCTTCACATTTTTGCCCAGAATTATGCAGTGTTTGCTTTTGCTTTACACTTTTGAGCTTGCTTCCTGCATGTATAAAACTGACAGTTCGACCCTCTTGTAAAGGATTCAGATTTACTCTGGTTAGCTGTGCGCTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
26
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-16-5p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-106a-5p(1), mmu-miR-20a-5p(1), mmu-miR-7b-5p(1), mmu-miR-223-3p(1), mmu-miR-30e-5p(1), mmu-let-7c-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-146a-5p(1), mmu-miR-18a-5p(1), mmu-miR-298-5p(1), mmu-miR-7a-5p(1), mmu-miR-184-3p(1), mmu-miR-709(1), mmu-miR-185-5p(1), mmu-miR-433-3p(1), mmu-miR-340-5p(1), mmu-miR-1187(1), mmu-miR-539-5p(1), mmu-miR-697(1), mmu-miR-146b-5p(1), mmu-miR-339-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TATGCAGTGTTTGCTTTTGCTTTACA
siRNA sets
TAAAGCAAAAGCAAACACT, AAAGCAAAAGCAAACACTG, TGTAAAGCAAAAGCAAACA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCALG6_2441_ORF_1
0.9091
-0.160016081
0.103779531
300
ORF sequence:
ATGTCAACCTGGTTTTTACTAGTTTCAACATTTAGCATGCTGCCTCTTCTATTAAAGGATGAACTCCTGCTGCCCTCGGTTGTGACAGTGATGGCATTTGTAATAGCTTGTGGCACTTTCTTTCCAATGTTGGAGAACACTTCCGAAGAACAACTGCAGTTGAAGTCCTTTGCTGTCTCTGTAAGGAGGCACCTTCCGGGCTTCACATTTTTGCCCAGAATTATGCAGTGTTTGCTTTTGCTTTACACTTTTGAGCTTGCTTCCTGCATGTATAAAACTGACAGTTCGACCCTCTTGTAA
Peptide sequence:
MSTWFLLVSTFSMLPLLLKDELLLPSVVTVMAFVIACGTFFPMLENTSEEQLQLKSFAVSVRRHLPGFTFLPRIMQCLLLLYTFELASCMYKTDSSTLL
IRESfinder result
IRESfinder score
0.883575767
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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