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mmu_circVps13a_1344
Basic information of circular RNA
PanCircBase ID:
mmu_circVps13a_1344
mm39_Chr. Position ID:
chr19|16659233|16669261|-
Gene name:
Vps13a
Transcript:
ENSMUST00000068156.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
41,40,39,38,37,36,35
Exon/intron offsets:
0,914,3408,4559,5214,6077,9877
Genomic length:
10028
Exon/intron sizes in nt:
3,57,93,23,32,15,17,01,00,000
Flanking exon/introns:
chr19:16657475-16659233|chr19:16669261-16672822
Splice length:
1344
Other database IDs:
circAtlas: mmu-Vps13a_0174
Human Ortholog IDs:
Mature spliced Sequence:
TTCATTCTTAGTCAGGAAGACTTAACAACCGTCTTTCAAACATTGCATGGCAATATATGGTATGGACAAGATCTGAGTGCTCCATCTTCTGCAAATAAGGACCCAGAGACCATGACCAGTGGGGTCACCAGTCCTCCTGACCATTCGCCAGCTACTGTGGTGACCGCTGCTGTGGTGGAGGTGCACCCACAGGCTTCTCAAGCGCACACGATGCTGAACGTGAGCTTCCAGACCGATTACCTCACCATGGCACTCTACAGTCCGGGGCCGGATGAGGCCTCCTTTACAGATGTTCGCGATCCTTCTCTGGAACTTGCTGAATTTAAGTTGGAGAATATTATAAGTAGTTTAAAAATATATACAGATGATTCTACAGTCTTTTCTTTCTCAGTAAAAAACTGTATTTTAGATGATAAAAGGTCACATGTCATGAAAGCCACTCCTAGAATGATAGGATTGACTGTTGGCTTTGACAAGAAGGACATGGTGGATATAAAGTATAGAAAAATCAAAACTTTTGTTGTGACTGATGCAGTTGTCCAAGAAATGTACGTTTGTGCGAGTGTGGAGTTTCTGATGACTGTTGCCCATATCTTTTTTGATGCCTACATGACTAGTACGGCTTTAGAAACCAGCGTTCAAACAAGGACTACTAGAGAAGCACCTGCACAGGAATTAGGGAAGTGGGAAATGAATATTCTTATTAAAAATCCAGAGATTGTGTTTGTGGCTGACATGACAAGAAACGATGCTCCTGCCTTAGTCATTACGACACAGTGTGAAATTTGCTGCAAAGGTGAACCTACAAGCAATACAGTGACTGCTGCCATTAAAGATCTCCAAGTCAGAGCGTGCCCATTTCTTCCAGTCAAGAGAAAGGGCAAAGTCACCACTGTTTTGCAGCCTTGTGACTTGTTTTATCAGGCTACTCAATTAGGTAGAGATCCACAAATGATTGATATATCAGTAAAATCTCTTACGCTAAAGGTTTCACCAGTTATCATAAATACCATAATAACTATTACTTCAGCACTTTACACAACTAAGGAAACTGTCCCAGAAGAAAACACTTCTAATATAGCACATTTATGGGACAAGAAGGATACAAAGAATCTAAAAATGTGGTTTCTTGAAGAATCAAATGAAAGTGAAAAAGTAGTTCCCACGAATGAAGTGATGCCGGGAGGAGAGACACTGAACTTGCGTATTGATTCTATTTTTATTGTTCTGGAGGCTGGAATCGGTCATAGAACAGTGCCGATGCTGTTGGCAAAGGCGTGCTTCTCGGGGGAAAGCAAAAACTGGCTCTCTCTAATCAATCTTCACTGTCACCTGGAACTGGAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGGGGGAAAGCAAAAACTGG
59.97
TGCAGAAGATGGAGCACTCA
59.02
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGGGGGAAAGCAAAAACTGG
59.97
TGCAGAAGATGGAGCACTCAG
60.07
152
PCR template sequence:
TCATAGAACAGTGCCGATGCTGTTGGCAAAGGCGTGCTTCTCGGGGGAAAGCAAAAACTGGCTCTCTCTAATCAATCTTCACTGTCACCTGGAACTGGAATTCATTCTTAGTCAGGAAGACTTAACAACCGTCTTTCAAACATTGCATGGCAATATATGGTATGGACAAGATCTGAGTGCTCCATCTTCTGCAAATAAGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
18
Interacting miRNAs (#binding sites)
mmu-miR-212-3p(2), mmu-miR-20b-5p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-106b-5p(1), mmu-miR-217-5p(1), mmu-miR-326-3p(1), mmu-miR-503-5p(1), mmu-miR-351-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-207(1), mmu-miR-3065-5p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCTGGAACTGGAATTCATTCTTAGTC
siRNA sets
AATGAATTCCAGTTCCAGG, ACTAAGAATGAATTCCAGT, GACTAAGAATGAATTCCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVPS13A_1344_ORF_1
1.0806
0.037327582
0.999999805
2577
ORF sequence:
ATGACCAGTGGGGTCACCAGTCCTCCTGACCATTCGCCAGCTACTGTGGTGACCGCTGCTGTGGTGGAGGTGCACCCACAGGCTTCTCAAGCGCACACGATGCTGAACGTGAGCTTCCAGACCGATTACCTCACCATGGCACTCTACAGTCCGGGGCCGGATGAGGCCTCCTTTACAGATGTTCGCGATCCTTCTCTGGAACTTGCTGAATTTAAGTTGGAGAATATTATAAGTAGTTTAAAAATATATACAGATGATTCTACAGTCTTTTCTTTCTCAGTAAAAAACTGTATTTTAGATGATAAAAGGTCACATGTCATGAAAGCCACTCCTAGAATGATAGGATTGACTGTTGGCTTTGACAAGAAGGACATGGTGGATATAAAGTATAGAAAAATCAAAACTTTTGTTGTGACTGATGCAGTTGTCCAAGAAATGTACGTTTGTGCGAGTGTGGAGTTTCTGATGACTGTTGCCCATATCTTTTTTGATGCCTACATGACTAGTACGGCTTTAGAAACCAGCGTTCAAACAAGGACTACTAGAGAAGCACCTGCACAGGAATTAGGGAAGTGGGAAATGAATATTCTTATTAAAAATCCAGAGATTGTGTTTGTGGCTGACATGACAAGAAACGATGCTCCTGCCTTAGTCATTACGACACAGTGTGAAATTTGCTGCAAAGGTGAACCTACAAGCAATACAGTGACTGCTGCCATTAAAGATCTCCAAGTCAGAGCGTGCCCATTTCTTCCAGTCAAGAGAAAGGGCAAAGTCACCACTGTTTTGCAGCCTTGTGACTTGTTTTATCAGGCTACTCAATTAGGTAGAGATCCACAAATGATTGATATATCAGTAAAATCTCTTACGCTAAAGGTTTCACCAGTTATCATAAATACCATAATAACTATTACTTCAGCACTTTACACAACTAAGGAAACTGTCCCAGAAGAAAACACTTCTAATATAGCACATTTATGGGACAAGAAGGATACAAAGAATCTAAAAATGTGGTTTCTTGAAGAATCAAATGAAAGTGAAAAAGTAGTTCCCACGAATGAAGTGATGCCGGGAGGAGAGACACTGAACTTGCGTATTGATTCTATTTTTATTGTTCTGGAGGCTGGAATCGGTCATAGAACAGTGCCGATGCTGTTGGCAAAGGCGTGCTTCTCGGGGGAAAGCAAAAACTGGCTCTCTCTAATCAATCTTCACTGTCACCTGGAACTGGAATTCATTCTTAGTCAGGAAGACTTAACAACCGTCTTTCAAACATTGCATGGCAATATATGGTATGGACAAGATCTGAGTGCTCCATCTTCTGCAAATAAGGACCCAGAGACCATGACCAGTGGGGTCACCAGTCCTCCTGACCATTCGCCAGCTACTGTGGTGACCGCTGCTGTGGTGGAGGTGCACCCACAGGCTTCTCAAGCGCACACGATGCTGAACGTGAGCTTCCAGACCGATTACCTCACCATGGCACTCTACAGTCCGGGGCCGGATGAGGCCTCCTTTACAGATGTTCGCGATCCTTCTCTGGAACTTGCTGAATTTAAGTTGGAGAATATTATAAGTAGTTTAAAAATATATACAGATGATTCTACAGTCTTTTCTTTCTCAGTAAAAAACTGTATTTTAGATGATAAAAGGTCACATGTCATGAAAGCCACTCCTAGAATGATAGGATTGACTGTTGGCTTTGACAAGAAGGACATGGTGGATATAAAGTATAGAAAAATCAAAACTTTTGTTGTGACTGATGCAGTTGTCCAAGAAATGTACGTTTGTGCGAGTGTGGAGTTTCTGATGACTGTTGCCCATATCTTTTTTGATGCCTACATGACTAGTACGGCTTTAGAAACCAGCGTTCAAACAAGGACTACTAGAGAAGCACCTGCACAGGAATTAGGGAAGTGGGAAATGAATATTCTTATTAAAAATCCAGAGATTGTGTTTGTGGCTGACATGACAAGAAACGATGCTCCTGCCTTAGTCATTACGACACAGTGTGAAATTTGCTGCAAAGGTGAACCTACAAGCAATACAGTGACTGCTGCCATTAAAGATCTCCAAGTCAGAGCGTGCCCATTTCTTCCAGTCAAGAGAAAGGGCAAAGTCACCACTGTTTTGCAGCCTTGTGACTTGTTTTATCAGGCTACTCAATTAGGTAGAGATCCACAAATGATTGATATATCAGTAAAATCTCTTACGCTAAAGGTTTCACCAGTTATCATAAATACCATAATAACTATTACTTCAGCACTTTACACAACTAAGGAAACTGTCCCAGAAGAAAACACTTCTAATATAGCACATTTATGGGACAAGAAGGATACAAAGAATCTAAAAATGTGGTTTCTTGAAGAATCAAATGAAAGTGAAAAAGTAGTTCCCACGAATGAAGTGATGCCGGGAGGAGAGACACTGAACTTGCGTATTGATTCTATTTTTATTGTTCTGGAGGCTGGAATCGGTCATAGAACAGTGCCGATGCTGTTGGCAAAGGCGTGCTTCTCGGGGGAAAGCAAAAACTGGCTCTCTCTAATCAATCTTCACTGTCACCTGGAACTGGAA
Peptide sequence:
MTSGVTSPPDHSPATVVTAAVVEVHPQASQAHTMLNVSFQTDYLTMALYSPGPDEASFTDVRDPSLELAEFKLENIISSLKIYTDDSTVFSFSVKNCILDDKRSHVMKATPRMIGLTVGFDKKDMVDIKYRKIKTFVVTDAVVQEMYVCASVEFLMTVAHIFFDAYMTSTALETSVQTRTTREAPAQELGKWEMNILIKNPEIVFVADMTRNDAPALVITTQCEICCKGEPTSNTVTAAIKDLQVRACPFLPVKRKGKVTTVLQPCDLFYQATQLGRDPQMIDISVKSLTLKVSPVIINTIITITSALYTTKETVPEENTSNIAHLWDKKDTKNLKMWFLEESNESEKVVPTNEVMPGGETLNLRIDSIFIVLEAGIGHRTVPMLLAKACFSGESKNWLSLINLHCHLELEFILSQEDLTTVFQTLHGNIWYGQDLSAPSSANKDPETMTSGVTSPPDHSPATVVTAAVVEVHPQASQAHTMLNVSFQTDYLTMALYSPGPDEASFTDVRDPSLELAEFKLENIISSLKIYTDDSTVFSFSVKNCILDDKRSHVMKATPRMIGLTVGFDKKDMVDIKYRKIKTFVVTDAVVQEMYVCASVEFLMTVAHIFFDAYMTSTALETSVQTRTTREAPAQELGKWEMNILIKNPEIVFVADMTRNDAPALVITTQCEICCKGEPTSNTVTAAIKDLQVRACPFLPVKRKGKVTTVLQPCDLFYQATQLGRDPQMIDISVKSLTLKVSPVIINTIITITSALYTTKETVPEENTSNIAHLWDKKDTKNLKMWFLEESNESEKVVPTNEVMPGGETLNLRIDSIFIVLEAGIGHRTVPMLLAKACFSGESKNWLSLINLHCHLELE
IRESfinder result
IRESfinder score
0.621832054
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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