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mmu_circArfgef1_1095
Basic information of circular RNA
PanCircBase ID:
mmu_circArfgef1_1095
mm39_Chr. Position ID:
chr1|10222025|10230253|-
Gene name:
Arfgef1
Transcript:
ENSMUST00000088615.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
32,31,30,29,28,27,26,25
Exon/intron offsets:
0,1585,1806,2480,5113,6099,7767,8076
Genomic length:
8228
Exon/intron sizes in nt:
73,13,91,36,13,01,31,10,00,00,000
Flanking exon/introns:
chr1:10217760-10222025|chr1:10230253-10230925
Splice length:
1095
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTGGTTGCAATCCTAATGAAGATGTAGCCATATTTGCAGTAGACTCTCTGAGGCAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACGACCTTTTGAACATATAATGAAACGAAACAGGTCTCCAACAATTCGAGATATGGTTGTACGGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCATCTAGCTGCATCAGACCAAGATGAAAGCATAGTAGAACTTGCATTTCAGACAACAGGGCACATTGTCACTCTTGTATTTGAAAAACACTTTCCGGCCACCATTGATTCTTTCCAGGATGCAGTGAAGTGTTTGTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGCCCTTTATGCAATATGTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTGGTTATTCTGAATGGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AATTCCTCACGCGCTTCTGA
60.04
TGCCTCAGAGAGTCTACTGCA
60.27
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AATTCCTCACGCGCTTCTGA
60.04
AGCTGCCTCAGAGAGTCTACT
59.72
144
PCR template sequence:
TATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGTTGGTTGCAATCCTAATGAAGATGTAGCCATATTTGCAGTAGACTCTCTGAGGCAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-320-3p(2), mmu-miR-381-3p(2), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-221-3p(1), mmu-miR-135a-5p(1), mmu-miR-200c-3p(1), mmu-miR-217-5p(1), mmu-miR-222-3p(1), mmu-miR-203-3p(1), mmu-miR-339-5p(1), mmu-miR-382-5p(1), mmu-miR-673-5p(1), mmu-miR-335-3p(1), mmu-miR-542-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGAAAAGCCGTTGGTTGGTTGCAATC
siRNA sets
GATTGCAACCAACCAACGG, ATTGCAACCAACCAACGGC, TTGCAACCAACCAACGGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARFGEF1_1095_ORF_1
0.7863
0.038191317
0.999991481
2127
ORF sequence:
ATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACGACCTTTTGAACATATAATGAAACGAAACAGGTCTCCAACAATTCGAGATATGGTTGTACGGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCATCTAGCTGCATCAGACCAAGATGAAAGCATAGTAGAACTTGCATTTCAGACAACAGGGCACATTGTCACTCTTGTATTTGAAAAACACTTTCCGGCCACCATTGATTCTTTCCAGGATGCAGTGAAGTGTTTGTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGCCCTTTATGCAATATGTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTGGTTATTCTGAATGGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGTTGGTTGCAATCCTAATGAAGATGTAGCCATATTTGCAGTAGACTCTCTGAGGCAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACGACCTTTTGAACATATAATGAAACGAAACAGGTCTCCAACAATTCGAGATATGGTTGTACGGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCATCTAGCTGCATCAGACCAAGATGAAAGCATAGTAGAACTTGCATTTCAGACAACAGGGCACATTGTCACTCTTGTATTTGAAAAACACTTTCCGGCCACCATTGATTCTTTCCAGGATGCAGTGAAGTGTTTGTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGCCCTTTATGCAATATGTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTGGTTATTCTGAATGGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTG
Peptide sequence:
MKFLEKGELANFRFQKDFLRPFEHIMKRNRSPTIRDMVVRCIAQMVNSQAANIRSGWKNIFSVFHLAASDQDESIVELAFQTTGHIVTLVFEKHFPATIDSFQDAVKCLSEFACNAAFPDTSMEAIRLIRHCAKYVSDRPQAFKEYTSDDMSVAPEDRVWVRGWFPILFELSCIINRCKLDVRTRGLTVMFEIMKTYGHTYEKHWWQDLFRIVFRIFDNMKLPEQQTEKAEWMTTTCNHALYAICDVFTQYLEVLSDVLLDDIFAQLYWCVQQDNEQLARSGTNCLENVVILNGEKFTLEIWDKTCNCTLDIFKTTIPHALLTWRPTSGEAEPPSPSAVSEKPLVGCNPNEDVAIFAVDSLRQLSMKFLEKGELANFRFQKDFLRPFEHIMKRNRSPTIRDMVVRCIAQMVNSQAANIRSGWKNIFSVFHLAASDQDESIVELAFQTTGHIVTLVFEKHFPATIDSFQDAVKCLSEFACNAAFPDTSMEAIRLIRHCAKYVSDRPQAFKEYTSDDMSVAPEDRVWVRGWFPILFELSCIINRCKLDVRTRGLTVMFEIMKTYGHTYEKHWWQDLFRIVFRIFDNMKLPEQQTEKAEWMTTTCNHALYAICDVFTQYLEVLSDVLLDDIFAQLYWCVQQDNEQLARSGTNCLENVVILNGEKFTLEIWDKTCNCTLDIFKTTIPHALLTWRPTSGEAEPPSPSAVSEKPL
IRESfinder result
IRESfinder score
0.645231395
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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