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mmu_circExt1_760
Basic information of circular RNA
PanCircBase ID:
mmu_circExt1_760
mm39_Chr. Position ID:
chr15|52946480|52970967|-
Gene name:
Ext1
Transcript:
ENSMUST00000077273.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
8,7,6,5,4,3,2
Exon/intron offsets:
0,4970,6846,9198,18600,22942,24393
Genomic length:
24487
Exon/intron sizes in nt:
90,96,119,133,120,108,94
Flanking exon/introns:
chr15:52939325-52946480|chr15:52970967-53207797
Splice length:
760
Other database IDs:
circBase: mmu_circ_0005698, CIRCpedia: MMU_CIRCpedia_22514, circAtlas: mmu-Ext1_0011
circAtlas: hsa-EXT1_0015, CIRCpedia: HSA_CIRCpedia_89590
Human Ortholog IDs:
Mature spliced Sequence:
ATATGATTATCGGGAAATGCTGCACAATGCCACTTTCTGTCTGGTTCCTCGTGGTCGCAGGCTTGGGTCCTTCAGATTCCTGGAGGCTTTGCAGGCTGCCTGTGTCCCTGTAATGCTCAGCAACGGATGGGAGTTGCCATTCTCCGAAGTGATTAATTGGAACCAAGCTGCCGTCATAGGCGATGAGAGATTGCTATTACAGATTCCTTCTACAATCAGGTCTATTCATCAGGATAAAATCCTAGCACTTAGACAGCAGACACAGTTCTTGTGGGAGGCTTATTTTTCTTCAGTTGAGAAGATTGTATTAACTACACTAGAGATTATTCAGGACAGAATATTCAAGCACATATCACGTAACAGTTTAATATGGAACAAACATCCTGGAGGATTGTTCGTCCTACCGCAGTATTCATCTTACCTGGGAGATTTCCCTTACTACTATGCTAATTTAGGTTTAAAGCCCCCCTCCAAATTCACTGCAGTCATCCATGCTGTGACTCCCCTGGTCTCTCAGTCCCAGCCAGTGTTGAAGCTTCTTGTGGCTGCAGCCAAATCCCAGTACTGTGCGCAGATCATAGTTCTGTGGAATTGTGACAAGCCTCTACCAGCCAAACATCGCTGGCCTGCCACTGCCGTGCCTGTCATCGTCATTGAAGGAGAAAGCAAGGTTATGAGCAGCCGGTTTCTGCCCTATGACAACATCATCACTGATGCTGTGCTCAGCCTGGATGAGGACACTGTGCTTTCAACTACGGAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGTTATGAGCAGCCGGTTT
59.67
GACCACGAGGAACCAGACAG
60.04
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGGTTATGAGCAGCCGGTT
59.67
GACCACGAGGAACCAGACAG
60.04
149
PCR template sequence:
AGAAAGCAAGGTTATGAGCAGCCGGTTTCTGCCCTATGACAACATCATCACTGATGCTGTGCTCAGCCTGGATGAGGACACTGTGCTTTCAACTACGGAAATATGATTATCGGGAAATGCTGCACAATGCCACTTTCTGTCTGGTTCCTCGTGGTCGCAGGCTTGGGTCCTTCAGATTCCTGGAGGCTTTGCAGGCTGCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-200b-3p(2), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-429-3p(1), mmu-miR-34c-5p(1), mmu-miR-200c-3p(1), mmu-miR-101a-3p(1), mmu-miR-101b-3p(1), mmu-miR-218-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-190b-5p(1), mmu-miR-188-3p(1), mmu-miR-3105-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTCAACTACGGAAATATGATTATCGG
siRNA sets
ATAATCATATTTCCGTAGT, ATCATATTTCCGTAGTTGA, TAATCATATTTCCGTAGTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCEXT1_760_ORF_1
0.7156
0.095815809
0.916622776
825
ORF sequence:
ATGACAACATCATCACTGATGCTGTGCTCAGCCTGGATGAGGACACTGTGCTTTCAACTACGGAAATATGATTATCGGGAAATGCTGCACAATGCCACTTTCTGTCTGGTTCCTCGTGGTCGCAGGCTTGGGTCCTTCAGATTCCTGGAGGCTTTGCAGGCTGCCTGTGTCCCTGTAATGCTCAGCAACGGATGGGAGTTGCCATTCTCCGAAGTGATTAATTGGAACCAAGCTGCCGTCATAGGCGATGAGAGATTGCTATTACAGATTCCTTCTACAATCAGGTCTATTCATCAGGATAAAATCCTAGCACTTAGACAGCAGACACAGTTCTTGTGGGAGGCTTATTTTTCTTCAGTTGAGAAGATTGTATTAACTACACTAGAGATTATTCAGGACAGAATATTCAAGCACATATCACGTAACAGTTTAATATGGAACAAACATCCTGGAGGATTGTTCGTCCTACCGCAGTATTCATCTTACCTGGGAGATTTCCCTTACTACTATGCTAATTTAGGTTTAAAGCCCCCCTCCAAATTCACTGCAGTCATCCATGCTGTGACTCCCCTGGTCTCTCAGTCCCAGCCAGTGTTGAAGCTTCTTGTGGCTGCAGCCAAATCCCAGTACTGTGCGCAGATCATAGTTCTGTGGAATTGTGACAAGCCTCTACCAGCCAAACATCGCTGGCCTGCCACTGCCGTGCCTGTCATCGTCATTGAAGGAGAAAGCAAGGTTATGAGCAGCCGGTTTCTGCCCTATGACAACATCATCACTGATGCTGTGCTCAGCCTGGATGAGGACACTGTGCTTTCAACTACGGAA
Peptide sequence:
MTTSSLMLCSAWMRTLCFQLRKYDYREMLHNATFCLVPRGRRLGSFRFLEALQAACVPVMLSNGWELPFSEVINWNQAAVIGDERLLLQIPSTIRSIHQDKILALRQQTQFLWEAYFSSVEKIVLTTLEIIQDRIFKHISRNSLIWNKHPGGLFVLPQYSSYLGDFPYYYANLGLKPPSKFTAVIHAVTPLVSQSQPVLKLLVAAAKSQYCAQIIVLWNCDKPLPAKHRWPATAVPVIVIEGESKVMSSRFLPYDNIITDAVLSLDEDTVLSTTE
IRESfinder result
IRESfinder score
0.728429698
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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