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mmu_circVps13d_1672
Basic information of circular RNA
PanCircBase ID:
mmu_circVps13d_1672
mm39_Chr. Position ID:
chr4|144887154|144899728|-
Gene name:
Vps13d
Transcript:
ENSMUST00000036579.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
18,17,16,15,14,13,12,11,10,9,8,7
Exon/intron offsets:
0,1413,2591,3171,3971,6806,7531,7891,9651,11060,11493,12469
Genomic length:
12574
Exon/intron sizes in nt:
133,131,171,76,131,180,202,102,169,101,171,105
Flanking exon/introns:
chr4:144883352-144887154|chr4:144899728-144901378
Splice length:
1672
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTACAGAAACTAATGCGAAAGAAGCGATTAGACGTGGCTGAGTTTAGTATTTATTGGGATGTCAACTGCACTTTACTGGGGGACTTGCCTCAAGCGGAGTTACAGGAGGCCATGGCCAGAAGCATGGAGAGTCGCAGTCATCACTACATCTTGGAGCCTGTGTGCGCTTCTGCCCTCTTGAAAAGGAACTGCTCCAAGGAGCCTCTGAGGTCGAGGCACAGCCCGAGGATTGAATGTGATATTCAGCTGGAGACCATTCCCTTGAAGCTGTCTCAGCTGCAGTACCGGCAGATCATGGCATTCCTCAAGGAGCTGGAACGAAAGGAGAGGCAGCTGAAATTCCGGAAGTGGAAACCAAAAGTGGCCGTGTCCAAGAACTGTCGGGAATGGTGGTATTTTGCCCTGAACGCTAACTTGTATGAGATCAGAGAGCAGAGGAAGTGTTGGACCTGGGATTTCTTGTTGCATCGTGCCCGAGATGCTGTGTTTTACACTGACAGATATTTCAACAAGTTAAAAGGAGGCGTGCTGTCTGCAGATGACAAGGAGGAGATGTGTCGCATTGAGGAGGAGCAGAGCTTTGAGGAATTGAAGATTCTGCGCGAACTCGTTCATGATAGATTTTATAAGCAGGAGGAGCTAGCAGAGAGTCTTCGAGAACCGCAGTTTGATTCTCCGGGAACCTCACCTGGTGATCCAGATGGCAGCGGAGGCAGCGGGATGCTGCAGTACCTGCAGTCCTGGTTTCCAGGGTGGGGCGGCTGGTATGGACAGCAGAGCCCTGAAGGGAAAGTGGTAGAAGGACTGACAGCGGAGTCACATGAGCACTGGACACCGGAAGAGATCTTGGGTACGGAGGAGTTCTTTGACCCCACTGCAGATGCTTCATGTATGAATACCTATACAAAGCGAGATCACGTCTTTGCCAAGCTGAATGTGCAGCTACAGCGGGGTACTGTGACTCTCCTGCACAAGGAGCAGGGCACTGCTCATGCCAACGAGAGTGCATTCATGCAGCTCGAGTTCTCAGATGTAAAACTTCTAGCAGAGTCTCTTCCCCGAAGAAACTCCTCCTTGCTTTTGGTCCGGTTGGGTGGACTGTTCCTCCGAGACCTGGCTACAGAAGGAACCATGTTTCCTCTCCTGGTCTTCCCTAATCCGCAGAAAGAAGTAGGCAGAGTCTCACAGTCTTTTGGTCTTCAAACTGCATCAGAAGACAGAAGTGATCAATACTCTGCTGCGGACCCAGACAACCCAGTCTTTGAGATGCTCTATGAGAGAAACCCAGTGCACAGCCACTTTGAGAGGCGGTTGCATGTCAGCACAAGGCCCTTGAACATCATCTACAACCCACAGGCTATTAAAAAAGTGGCAGACTTTTTCTACAAGGGAAAGGTTCATACCTCAGGCTTTGGCTATCAGTCTGAGCTGGAGTTAAGGGTAGCTGAAGCAGCCCGAAGACAATATGACAAGCTGAAGGTGCAGACCAAGGCTGAGATCCGACAGACCCTTGACCGTTTGCTTGTGGGAGATTTTATTGAGGAAAGTAAGCGGTGGACTGTTCGCCTGGACATCTCTGCCCCTCAAGTGATATTTCCAGATGATTTCACCTTCAAGAATCCCGTGTTGGTTGTTGTGGACCTTGGAAGAATGCTTTTGACCAACACCCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCGTGTTGGTTGTTGTGGAC
59.9
GGCAAGTCCCCCAGTAAAGT
59.6
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGTGTTGGTTGTTGTGGACC
59.9
TGAGGCAAGTCCCCCAGTAA
60.47
142
PCR template sequence:
ATCTCTGCCCCTCAAGTGATATTTCCAGATGATTTCACCTTCAAGAATCCCGTGTTGGTTGTTGTGGACCTTGGAAGAATGCTTTTGACCAACACCCAAGGTACAGAAACTAATGCGAAAGAAGCGATTAGACGTGGCTGAGTTTAGTATTTATTGGGATGTCAACTGCACTTTACTGGGGGACTTGCCTCAAGCGGAGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-miR-93-5p(1), mmu-miR-199a-5p(1), mmu-miR-181a-5p(1), mmu-miR-101a-3p(1), mmu-miR-106b-5p(1), mmu-miR-146a-5p(1), mmu-miR-7a-5p(1), mmu-miR-132-3p(1), mmu-miR-181b-5p(1), mmu-miR-212-3p(1), mmu-miR-182-5p(1), mmu-miR-188-3p(1), mmu-miR-3470b(1), mmu-miR-3105-3p(1), mmu-miR-146b-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACCAACACCCAAGGTACAGAAACTAA
siRNA sets
TTAGTTTCTGTACCTTGGG, GTTTCTGTACCTTGGGTGT, TCTGTACCTTGGGTGTTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVPS13D_1672_ORF_1
1.0062
0.279977002
0.999953201
1701
ORF sequence:
ATGCGAAAGAAGCGATTAGACGTGGCTGAGTTTAGTATTTATTGGGATGTCAACTGCACTTTACTGGGGGACTTGCCTCAAGCGGAGTTACAGGAGGCCATGGCCAGAAGCATGGAGAGTCGCAGTCATCACTACATCTTGGAGCCTGTGTGCGCTTCTGCCCTCTTGAAAAGGAACTGCTCCAAGGAGCCTCTGAGGTCGAGGCACAGCCCGAGGATTGAATGTGATATTCAGCTGGAGACCATTCCCTTGAAGCTGTCTCAGCTGCAGTACCGGCAGATCATGGCATTCCTCAAGGAGCTGGAACGAAAGGAGAGGCAGCTGAAATTCCGGAAGTGGAAACCAAAAGTGGCCGTGTCCAAGAACTGTCGGGAATGGTGGTATTTTGCCCTGAACGCTAACTTGTATGAGATCAGAGAGCAGAGGAAGTGTTGGACCTGGGATTTCTTGTTGCATCGTGCCCGAGATGCTGTGTTTTACACTGACAGATATTTCAACAAGTTAAAAGGAGGCGTGCTGTCTGCAGATGACAAGGAGGAGATGTGTCGCATTGAGGAGGAGCAGAGCTTTGAGGAATTGAAGATTCTGCGCGAACTCGTTCATGATAGATTTTATAAGCAGGAGGAGCTAGCAGAGAGTCTTCGAGAACCGCAGTTTGATTCTCCGGGAACCTCACCTGGTGATCCAGATGGCAGCGGAGGCAGCGGGATGCTGCAGTACCTGCAGTCCTGGTTTCCAGGGTGGGGCGGCTGGTATGGACAGCAGAGCCCTGAAGGGAAAGTGGTAGAAGGACTGACAGCGGAGTCACATGAGCACTGGACACCGGAAGAGATCTTGGGTACGGAGGAGTTCTTTGACCCCACTGCAGATGCTTCATGTATGAATACCTATACAAAGCGAGATCACGTCTTTGCCAAGCTGAATGTGCAGCTACAGCGGGGTACTGTGACTCTCCTGCACAAGGAGCAGGGCACTGCTCATGCCAACGAGAGTGCATTCATGCAGCTCGAGTTCTCAGATGTAAAACTTCTAGCAGAGTCTCTTCCCCGAAGAAACTCCTCCTTGCTTTTGGTCCGGTTGGGTGGACTGTTCCTCCGAGACCTGGCTACAGAAGGAACCATGTTTCCTCTCCTGGTCTTCCCTAATCCGCAGAAAGAAGTAGGCAGAGTCTCACAGTCTTTTGGTCTTCAAACTGCATCAGAAGACAGAAGTGATCAATACTCTGCTGCGGACCCAGACAACCCAGTCTTTGAGATGCTCTATGAGAGAAACCCAGTGCACAGCCACTTTGAGAGGCGGTTGCATGTCAGCACAAGGCCCTTGAACATCATCTACAACCCACAGGCTATTAAAAAAGTGGCAGACTTTTTCTACAAGGGAAAGGTTCATACCTCAGGCTTTGGCTATCAGTCTGAGCTGGAGTTAAGGGTAGCTGAAGCAGCCCGAAGACAATATGACAAGCTGAAGGTGCAGACCAAGGCTGAGATCCGACAGACCCTTGACCGTTTGCTTGTGGGAGATTTTATTGAGGAAAGTAAGCGGTGGACTGTTCGCCTGGACATCTCTGCCCCTCAAGTGATATTTCCAGATGATTTCACCTTCAAGAATCCCGTGTTGGTTGTTGTGGACCTTGGAAGAATGCTTTTGACCAACACCCAAGGTACAGAAACTAATGCGAAAGAAGCGATTAGACGTGGCTGA
Peptide sequence:
MRKKRLDVAEFSIYWDVNCTLLGDLPQAELQEAMARSMESRSHHYILEPVCASALLKRNCSKEPLRSRHSPRIECDIQLETIPLKLSQLQYRQIMAFLKELERKERQLKFRKWKPKVAVSKNCREWWYFALNANLYEIREQRKCWTWDFLLHRARDAVFYTDRYFNKLKGGVLSADDKEEMCRIEEEQSFEELKILRELVHDRFYKQEELAESLREPQFDSPGTSPGDPDGSGGSGMLQYLQSWFPGWGGWYGQQSPEGKVVEGLTAESHEHWTPEEILGTEEFFDPTADASCMNTYTKRDHVFAKLNVQLQRGTVTLLHKEQGTAHANESAFMQLEFSDVKLLAESLPRRNSSLLLVRLGGLFLRDLATEGTMFPLLVFPNPQKEVGRVSQSFGLQTASEDRSDQYSAADPDNPVFEMLYERNPVHSHFERRLHVSTRPLNIIYNPQAIKKVADFFYKGKVHTSGFGYQSELELRVAEAARRQYDKLKVQTKAEIRQTLDRLLVGDFIEESKRWTVRLDISAPQVIFPDDFTFKNPVLVVVDLGRMLLTNTQGTETNAKEAIRRG
IRESfinder result
IRESfinder score
0.532698147
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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