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mmu_circMark3_1304
Basic information of circular RNA
PanCircBase ID:
mmu_circMark3_1304
mm39_Chr. Position ID:
chr12|111593509|111614162|+
Gene name:
Mark3
Transcript:
ENSMUST00000075281.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
8,9,10,11,12,13,14,15
Exon/intron offsets:
0,403,739,1114,1886,6541,12861,20395
Genomic length:
20653
Exon/intron sizes in nt:
2,37,12,01,00,11,31,54,00,00,00,000
Flanking exon/introns:
chr12:111590977-111593509|chr12:111614162-111621703
Splice length:
1304
Other database IDs:
circAtlas: mmu-Mark3_0019
circBase: hsa_circ_0101357, circAtlas: hsa-MARK3_0033, CIRCpedia: HSA_CIRCpedia_121151
Human Ortholog IDs:
Mature spliced Sequence:
GCTGAAAATCTGTTATTAGATGCGGATATGAACATTAAAATAGCAGATTTTGGTTTTAGCAATGAATTTACTGTTGGCAGTAAACTAGACACGTTTTGTGGTAGTCCTCCATATGCAGCCCCTGAGCTCTTCCAGGGCAAGAAGTATGACGGGCCAGAAGTCGACGTGTGGAGCCTCGGTGTCATTCTCTACACCCTAGTCAGTGGGTCGCTTCCCTTTGATGGTCAAAACCTGAAGGAACTGAGAGAGAGAGTACTCCGCGGGAAGTACAGAATCCCTTTCTACATGTCCACAGACTGCGAGAACCTTCTCAAGCGCTTCCTGGTGCTGAACCCAGTTAAACGGGGCACTCTCGAGCAAATCATGAAGGACAGGTGGATCAATGCAGGCCATGAGGAGGATGAGCTTAAGCCATTTGTTGAACCAGAACTAGACATCTCAGACCAGAAGAGAATAGATATTATGGTGGGAATGGGATATTCCCAAGAAGAAATTCAAGAATCTCTTAGCAAAATGAAATACGATGAAATCACAGCTACTTACTTGCTACTGGGGAGGAAATCTGCAGAGCTGGACGCTAGTGACTCCAGTTCTAGCAGCAACCTTTCACTTGCTAAGGTGCGGCCAAACAGTGACCTCAGCAATAGCACTGGCCAGTCTCCTCATCACAAAGGGCAGAGAAGTGTTTCCTCAAGTCAGAAGCAGAGACGGTACAGTGACCACGCTGGACCAGCTATTCCTTCAGTTGTGGCATATCCAAAGAGGAGTCAGACCAGCACTGCAGATAGTGACCTCAAAGAAGATGGAATTCCCTCCCGAAAATCAAGCAGCAGTGCTGTAGGAGGGAAGGGGATTGCTCCTGCCAGTCCCATGCTTGGGAATGCAGGCAATCCCAATAAAGCCGATATCCCTGAGCGCAAGAAAAGCCCTGCTGTGCCCAGTAGTAACACAGCATCTGGTGGGATGACACGGCGGAACACTTACGTTTGCAGCGAGAGATGTGCAGCAGACAGACATTCTGTGATTCAGAACGGCAAAGAAAACAGCGCTATTCCAGATGAGAGAACTCCAGTTGCTTCAACCCACAGTATTAGCAGTGCGACCACCCCAGATCGCATCCGCTTTCCAAGGGGCACAGCCAGCCGTAGCACTTTCCATGGCCAACCTCGGGAGCGGCGAACCGCAACATATAATGGCCCACCTGCCTCACCCAGCTTGTCCCATGAAGCCACACCGCTGTCTCAGACTCGAAGCCGAGGTTCCACTAATCTTTTTAGTAAATTAACTTCCAAACTCACAAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGTCTCAGACTCGAAGCCG
60.18
ACGTGTCTAGTTTACTGCCAACA
60.18
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCGCTGTCTCAGACTCGAAG
60.18
ACGTGTCTAGTTTACTGCCAACA
60.18
165
PCR template sequence:
CCTCACCCAGCTTGTCCCATGAAGCCACACCGCTGTCTCAGACTCGAAGCCGAGGTTCCACTAATCTTTTTAGTAAATTAACTTCCAAACTCACAAGAAGGCTGAAAATCTGTTATTAGATGCGGATATGAACATTAAAATAGCAGATTTTGGTTTTAGCAATGAATTTACTGTTGGCAGTAAACTAGACACGTTTTGTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-17-5p(1), mmu-miR-429-3p(1), mmu-miR-135a-5p(1), mmu-miR-200c-3p(1), mmu-miR-433-3p(1), mmu-miR-541-5p(1), mmu-miR-129-5p(1), mmu-miR-3065-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
AACTCACAAGAAGGCTGAAAATCTGT
siRNA sets
TTTCAGCCTTCTTGTGAGT, ATTTTCAGCCTTCTTGTGA, TTTTCAGCCTTCTTGTGAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMARK3_1304_ORF_1
0.9808
0.188541196
0.998698716
1296
ORF sequence:
ATGAACATTAAAATAGCAGATTTTGGTTTTAGCAATGAATTTACTGTTGGCAGTAAACTAGACACGTTTTGTGGTAGTCCTCCATATGCAGCCCCTGAGCTCTTCCAGGGCAAGAAGTATGACGGGCCAGAAGTCGACGTGTGGAGCCTCGGTGTCATTCTCTACACCCTAGTCAGTGGGTCGCTTCCCTTTGATGGTCAAAACCTGAAGGAACTGAGAGAGAGAGTACTCCGCGGGAAGTACAGAATCCCTTTCTACATGTCCACAGACTGCGAGAACCTTCTCAAGCGCTTCCTGGTGCTGAACCCAGTTAAACGGGGCACTCTCGAGCAAATCATGAAGGACAGGTGGATCAATGCAGGCCATGAGGAGGATGAGCTTAAGCCATTTGTTGAACCAGAACTAGACATCTCAGACCAGAAGAGAATAGATATTATGGTGGGAATGGGATATTCCCAAGAAGAAATTCAAGAATCTCTTAGCAAAATGAAATACGATGAAATCACAGCTACTTACTTGCTACTGGGGAGGAAATCTGCAGAGCTGGACGCTAGTGACTCCAGTTCTAGCAGCAACCTTTCACTTGCTAAGGTGCGGCCAAACAGTGACCTCAGCAATAGCACTGGCCAGTCTCCTCATCACAAAGGGCAGAGAAGTGTTTCCTCAAGTCAGAAGCAGAGACGGTACAGTGACCACGCTGGACCAGCTATTCCTTCAGTTGTGGCATATCCAAAGAGGAGTCAGACCAGCACTGCAGATAGTGACCTCAAAGAAGATGGAATTCCCTCCCGAAAATCAAGCAGCAGTGCTGTAGGAGGGAAGGGGATTGCTCCTGCCAGTCCCATGCTTGGGAATGCAGGCAATCCCAATAAAGCCGATATCCCTGAGCGCAAGAAAAGCCCTGCTGTGCCCAGTAGTAACACAGCATCTGGTGGGATGACACGGCGGAACACTTACGTTTGCAGCGAGAGATGTGCAGCAGACAGACATTCTGTGATTCAGAACGGCAAAGAAAACAGCGCTATTCCAGATGAGAGAACTCCAGTTGCTTCAACCCACAGTATTAGCAGTGCGACCACCCCAGATCGCATCCGCTTTCCAAGGGGCACAGCCAGCCGTAGCACTTTCCATGGCCAACCTCGGGAGCGGCGAACCGCAACATATAATGGCCCACCTGCCTCACCCAGCTTGTCCCATGAAGCCACACCGCTGTCTCAGACTCGAAGCCGAGGTTCCACTAATCTTTTTAGTAAATTAACTTCCAAACTCACAAGAAGGCTGAAAATCTGTTATTAG
Peptide sequence:
MNIKIADFGFSNEFTVGSKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKRFLVLNPVKRGTLEQIMKDRWINAGHEEDELKPFVEPELDISDQKRIDIMVGMGYSQEEIQESLSKMKYDEITATYLLLGRKSAELDASDSSSSSNLSLAKVRPNSDLSNSTGQSPHHKGQRSVSSSQKQRRYSDHAGPAIPSVVAYPKRSQTSTADSDLKEDGIPSRKSSSSAVGGKGIAPASPMLGNAGNPNKADIPERKKSPAVPSSNTASGGMTRRNTYVCSERCAADRHSVIQNGKENSAIPDERTPVASTHSISSATTPDRIRFPRGTASRSTFHGQPRERRTATYNGPPASPSLSHEATPLSQTRSRGSTNLFSKLTSKLTRRLKICY
IRESfinder result
IRESfinder score
0.432885482
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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