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mmu_circVps50_1035
Basic information of circular RNA
PanCircBase ID:
mmu_circVps50_1035
mm39_Chr. Position ID:
chr6|3545509|3578915|+
Gene name:
Vps50
Transcript:
ENSMUST00000001412.17
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
13,14,15,16,17,18,19,20,21
Exon/intron offsets:
0,5503,9486,9858,16758,20006,22225,25492,33284
Genomic length:
33406
Exon/intron sizes in nt:
133,92,95,99,91,177,119,107,122
Flanking exon/introns:
chr6:3536972-3545509|chr6:3578915-3588005
Splice length:
1035
Other database IDs:
circBase: mmu_circ_0001436, CIRCpedia: MMU_CIRCpedia_17750, circAtlas: mmu-Ccdc132_0014
circBase: hsa_circ_0081045, circAtlas: hsa-VPS50_0020, CIRCpedia: HSA_CIRCpedia_59332
Human Ortholog IDs:
Mature spliced Sequence:
CATGTGACACCAGACAGCTATATTCCATGCCTGGCAGACCTGTGCAAAGCACTGTGGGAAGTCATGCTCAGCTACTACAGAACCATGGAGTGGCACGAGAAACATGACAATGAGGAAACAGCTGCAGCTGCTGAAGGAAGCAATGTGATGAGTACTGAGGAGGCCACTTTTGACCGTGGCTATGTAAAGAAGAAGTTAGAGCACGGCCTTACCCGGATATGGCAGGATGTTCAACTAAAAGTAAAAACCTACTTGCTTGGAACTGATTTATCTATATTCAAATATGATGATTTCATCTTTGTTCTGGATATTGTCAGCAGGTTGATGCAAGTTGGAGAAGAATTTTGTGGTAGCAAGTCTGAAGTTTTGCAGGAGTCCATTAGAAAACAAAGTGTCAATTACTTCAAGAACCACCATAGGATACGACTTGATGAACTGAGAATGTTCTTAGAGAATGAGACATGGGAGCTTTGCCCTGTTAAGTCAAATTTTAGCATCTTGCAGCTTCATGAGTTTAAATTCCTGGAACAGTCTCGCTCCCCATCAGTTTCACCTAGTAAGCAGCCATCAGCAACTTCTTCAAAGCCTGTGACTTTGTTTGAGCAGTACTGCAGTGGTGGGAATCCATTTGAAATACAAGCCGACCACAAAGATGAAGAAACTGAAGATGTCTTAGCCTCTAATGGGTATGAGTCTGATGAGCAAGAGAAGAGCGCCTATCAGGACTATGACAGTGACAGCGACGTCCCTGAGGAGCTGAAGCGGGATTACGTGGACGAGCAGACCGGCGACGTGCCCGTGAAGAGTGTTTCCCGAGAGACCCTGAAGAGCAGGAAGAAGTCGGATTACAGTCTAAACAAAGTGAATGCACCCATCTTAACAAACACAACACTGAATGTAATAAGGCTTGTTGGAAAGTACATGCAGATGATGAACATCCTTAAGCCAATCGCCTTCGATGTGATCCATTTCATGTCTCAGCTCTTTGACTATTACTTGTATGCCATATATACCTTTTTTGGTCGGAATGATTCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTTAAGCCAATCGCCTTCG
59.34
AGCTGAGCATGACTTCCCAC
60.04
170
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCGCCTTCGATGTGATCCAT
59.25
AGCTGAGCATGACTTCCCAC
60.04
159
PCR template sequence:
CATCCTTAAGCCAATCGCCTTCGATGTGATCCATTTCATGTCTCAGCTCTTTGACTATTACTTGTATGCCATATATACCTTTTTTGGTCGGAATGATTCACATGTGACACCAGACAGCTATATTCCATGCCTGGCAGACCTGTGCAAAGCACTGTGGGAAGTCATGCTCAGCTACTACAGAACCATGGAGTGGCACGAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-miR-181a-5p(1), mmu-miR-23a-3p(1), mmu-miR-181b-5p(1), mmu-miR-153-3p(1), mmu-miR-127-5p(1), mmu-miR-382-5p(1), mmu-miR-697(1), mmu-miR-3105-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCGGAATGATTCACATGTGACACCAG
siRNA sets
TCACATGTGAATCATTCCG, GTCACATGTGAATCATTCC, TGTCACATGTGAATCATTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVPS50_1035_ORF_1
1.0135
0.242546872
0.99999426
2007
ORF sequence:
ATGCTCAGCTACTACAGAACCATGGAGTGGCACGAGAAACATGACAATGAGGAAACAGCTGCAGCTGCTGAAGGAAGCAATGTGATGAGTACTGAGGAGGCCACTTTTGACCGTGGCTATGTAAAGAAGAAGTTAGAGCACGGCCTTACCCGGATATGGCAGGATGTTCAACTAAAAGTAAAAACCTACTTGCTTGGAACTGATTTATCTATATTCAAATATGATGATTTCATCTTTGTTCTGGATATTGTCAGCAGGTTGATGCAAGTTGGAGAAGAATTTTGTGGTAGCAAGTCTGAAGTTTTGCAGGAGTCCATTAGAAAACAAAGTGTCAATTACTTCAAGAACCACCATAGGATACGACTTGATGAACTGAGAATGTTCTTAGAGAATGAGACATGGGAGCTTTGCCCTGTTAAGTCAAATTTTAGCATCTTGCAGCTTCATGAGTTTAAATTCCTGGAACAGTCTCGCTCCCCATCAGTTTCACCTAGTAAGCAGCCATCAGCAACTTCTTCAAAGCCTGTGACTTTGTTTGAGCAGTACTGCAGTGGTGGGAATCCATTTGAAATACAAGCCGACCACAAAGATGAAGAAACTGAAGATGTCTTAGCCTCTAATGGGTATGAGTCTGATGAGCAAGAGAAGAGCGCCTATCAGGACTATGACAGTGACAGCGACGTCCCTGAGGAGCTGAAGCGGGATTACGTGGACGAGCAGACCGGCGACGTGCCCGTGAAGAGTGTTTCCCGAGAGACCCTGAAGAGCAGGAAGAAGTCGGATTACAGTCTAAACAAAGTGAATGCACCCATCTTAACAAACACAACACTGAATGTAATAAGGCTTGTTGGAAAGTACATGCAGATGATGAACATCCTTAAGCCAATCGCCTTCGATGTGATCCATTTCATGTCTCAGCTCTTTGACTATTACTTGTATGCCATATATACCTTTTTTGGTCGGAATGATTCACATGTGACACCAGACAGCTATATTCCATGCCTGGCAGACCTGTGCAAAGCACTGTGGGAAGTCATGCTCAGCTACTACAGAACCATGGAGTGGCACGAGAAACATGACAATGAGGAAACAGCTGCAGCTGCTGAAGGAAGCAATGTGATGAGTACTGAGGAGGCCACTTTTGACCGTGGCTATGTAAAGAAGAAGTTAGAGCACGGCCTTACCCGGATATGGCAGGATGTTCAACTAAAAGTAAAAACCTACTTGCTTGGAACTGATTTATCTATATTCAAATATGATGATTTCATCTTTGTTCTGGATATTGTCAGCAGGTTGATGCAAGTTGGAGAAGAATTTTGTGGTAGCAAGTCTGAAGTTTTGCAGGAGTCCATTAGAAAACAAAGTGTCAATTACTTCAAGAACCACCATAGGATACGACTTGATGAACTGAGAATGTTCTTAGAGAATGAGACATGGGAGCTTTGCCCTGTTAAGTCAAATTTTAGCATCTTGCAGCTTCATGAGTTTAAATTCCTGGAACAGTCTCGCTCCCCATCAGTTTCACCTAGTAAGCAGCCATCAGCAACTTCTTCAAAGCCTGTGACTTTGTTTGAGCAGTACTGCAGTGGTGGGAATCCATTTGAAATACAAGCCGACCACAAAGATGAAGAAACTGAAGATGTCTTAGCCTCTAATGGGTATGAGTCTGATGAGCAAGAGAAGAGCGCCTATCAGGACTATGACAGTGACAGCGACGTCCCTGAGGAGCTGAAGCGGGATTACGTGGACGAGCAGACCGGCGACGTGCCCGTGAAGAGTGTTTCCCGAGAGACCCTGAAGAGCAGGAAGAAGTCGGATTACAGTCTAAACAAAGTGAATGCACCCATCTTAACAAACACAACACTGAATGTAATAAGGCTTGTTGGAAAGTACATGCAGATGATGAACATCCTTAAGCCAATCGCCTTCGATGTGATCCATTTCATGTCTCAGCTCTTTGACTATTACTTGTATGCCATATATACCTTTTTTGGTCGGAATGATTCA
Peptide sequence:
MLSYYRTMEWHEKHDNEETAAAAEGSNVMSTEEATFDRGYVKKKLEHGLTRIWQDVQLKVKTYLLGTDLSIFKYDDFIFVLDIVSRLMQVGEEFCGSKSEVLQESIRKQSVNYFKNHHRIRLDELRMFLENETWELCPVKSNFSILQLHEFKFLEQSRSPSVSPSKQPSATSSKPVTLFEQYCSGGNPFEIQADHKDEETEDVLASNGYESDEQEKSAYQDYDSDSDVPEELKRDYVDEQTGDVPVKSVSRETLKSRKKSDYSLNKVNAPILTNTTLNVIRLVGKYMQMMNILKPIAFDVIHFMSQLFDYYLYAIYTFFGRNDSHVTPDSYIPCLADLCKALWEVMLSYYRTMEWHEKHDNEETAAAAEGSNVMSTEEATFDRGYVKKKLEHGLTRIWQDVQLKVKTYLLGTDLSIFKYDDFIFVLDIVSRLMQVGEEFCGSKSEVLQESIRKQSVNYFKNHHRIRLDELRMFLENETWELCPVKSNFSILQLHEFKFLEQSRSPSVSPSKQPSATSSKPVTLFEQYCSGGNPFEIQADHKDEETEDVLASNGYESDEQEKSAYQDYDSDSDVPEELKRDYVDEQTGDVPVKSVSRETLKSRKKSDYSLNKVNAPILTNTTLNVIRLVGKYMQMMNILKPIAFDVIHFMSQLFDYYLYAIYTFFGRNDS
IRESfinder result
IRESfinder score
0.507105649
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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