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mmu_circVps35l_1198
Basic information of circular RNA
PanCircBase ID:
mmu_circVps35l_1198
mm39_Chr. Position ID:
chr7|118378910|118412867|+
Gene name:
Vps35l
Transcript:
ENSMUST00000059390.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
14
Exon/intron indexes:
13,14,15,16,17,18,19,20,21,22,23,24,25,26
Exon/intron offsets:
0,489,10322,11680,12874,14854,17278,20750,21573,24416,27303,30190,32117,33842
Genomic length:
33957
Exon/intron sizes in nt:
78,123,47,112,117,54,81,63,86,81,64,99,78,115
Flanking exon/introns:
chr7:118374608-118378910|chr7:118412867-118425406
Splice length:
1198
Other database IDs:
circBase: hsa_circ_0005699, circAtlas: hsa-C16orf62_0032, CIRCpedia: HSA_CIRCpedia_16826
Human Ortholog IDs:
Mature spliced Sequence:
GTGGGGATCGAAGTGGCCCCGCACCTCAAGGAGAGCCTCAATAAGAACTTCTTTGACTTCCTGCTGACATTTAAACAGATTCATGGGGACACTGTCCAGAACCAGCTGGTGGCCCAGGGTGTGGAGCTGCTGTCCTATCTCCCTCTGTACTCGCCTGCCATGGGCTGGATCTTCCAGTGTGTCTCCTACCACGCTCCAGAGGCTTTGCTGACGGAGATGATGGAAAGATGTAAGAAACTAGGGAACAATGCTTTGCTGTTGAACTCCGTGATGTCAGCTTTCAGGGCTGAGTTCGTTGCCACCAGGTCTATGGACTTCATCGGCATGATCAAAGAGTGTGACGAGTCCGGCTTCCCCAAGCATCTCCTTTTTCGTTCATTGGGGTTAAACTTGGCTTTGGCTGATCCTCCTGAGAACGATCGACTTCAGATTCTCAATGAAGCTTGGAAAGTCATCACTAAACTGAAGAGTCCTCAGGACTACATTAATTGTGCCGAGGTTTGGGTAGAGTACACCTGCAGGCATTTCACGAAACGAGAAGTTAACACTGTTCTGGCTGACGTCATCAAGCACATGACTCCGGATCGAGCATTTGAGGACTCTTACCCCCAGCTCCAGTCAATCATTCAGAAAGTCATCGCCCACTTCCACGATTTCTCAGTTCTTTTCTCAGTGGAAAAGTTTCTACCATTTCTGGACATGTTCCAGAAAGAGAGTGTGCGGGTGGAGGTTTGCAAGTGCATCATGGAAGCCTTTATCAAGCACCAGCAGGAGCCAACCAAGGACCCTGTCATCCTCAATGCCCTTTTGCACATTTGCAAGACAATGCACGACTCCGTGAACGCTCTCACTCTTGAGGATGAGAAAAGGACGCTGGCCCACTTGATCAATGGATTTATAAAAATGGTGTCCTTTGGCCGTGATTTTGAACAGCAGCTCAGCTTTTACGTCGAGTCCAGGTCTATGTTTTGCAACCTGGAACCTGTTCTTGTGCAGTTGATCCATAGTGTGAACCGGTTGGCAATGGAAACAAGGAAAGTCATGAAGGGAAACCACTCCAGAAAGACAGCTGCGTTTGTCCGGGCCTGTGTTGCCTACTGCTTCATCACCATCCCGTCCCTGGTAGGGATCTTCACCCGCCTCAACCTCTACCTGCATTCCGGTCAGGTTGCCTTGGCCAACCAGTGCCTCTCCCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTTCATCACCATCCCGTC
60.11
TTGAGGCTCTCCTTGAGGTG
59.02
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTTCATCACCATCCCGTC
60.11
TGAGGCTCTCCTTGAGGTGC
61.55
140
PCR template sequence:
TGCTTCATCACCATCCCGTCCCTGGTAGGGATCTTCACCCGCCTCAACCTCTACCTGCATTCCGGTCAGGTTGCCTTGGCCAACCAGTGCCTCTCCCAAGGTGGGGATCGAAGTGGCCCCGCACCTCAAGGAGAGCCTCAATAAGAACTTCTTTGACTTCCTGCTGACATTTAAACAGATTCATGGGGACACTGTCCAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-140-5p(1), mmu-miR-15b-5p(1), mmu-miR-33-5p(1), mmu-miR-203-3p(1), mmu-miR-320-3p(1), mmu-miR-138-5p(1), mmu-miR-214-3p(1), mmu-miR-218-5p(1), mmu-miR-370-3p(1), mmu-miR-325-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-3061-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGCCTCTCCCAAGGTGGGGATCGAAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVPS35L_1198_ORF_1
1.2081
0.277842276
0.997264774
1083
ORF sequence:
ATGGGCTGGATCTTCCAGTGTGTCTCCTACCACGCTCCAGAGGCTTTGCTGACGGAGATGATGGAAAGATGTAAGAAACTAGGGAACAATGCTTTGCTGTTGAACTCCGTGATGTCAGCTTTCAGGGCTGAGTTCGTTGCCACCAGGTCTATGGACTTCATCGGCATGATCAAAGAGTGTGACGAGTCCGGCTTCCCCAAGCATCTCCTTTTTCGTTCATTGGGGTTAAACTTGGCTTTGGCTGATCCTCCTGAGAACGATCGACTTCAGATTCTCAATGAAGCTTGGAAAGTCATCACTAAACTGAAGAGTCCTCAGGACTACATTAATTGTGCCGAGGTTTGGGTAGAGTACACCTGCAGGCATTTCACGAAACGAGAAGTTAACACTGTTCTGGCTGACGTCATCAAGCACATGACTCCGGATCGAGCATTTGAGGACTCTTACCCCCAGCTCCAGTCAATCATTCAGAAAGTCATCGCCCACTTCCACGATTTCTCAGTTCTTTTCTCAGTGGAAAAGTTTCTACCATTTCTGGACATGTTCCAGAAAGAGAGTGTGCGGGTGGAGGTTTGCAAGTGCATCATGGAAGCCTTTATCAAGCACCAGCAGGAGCCAACCAAGGACCCTGTCATCCTCAATGCCCTTTTGCACATTTGCAAGACAATGCACGACTCCGTGAACGCTCTCACTCTTGAGGATGAGAAAAGGACGCTGGCCCACTTGATCAATGGATTTATAAAAATGGTGTCCTTTGGCCGTGATTTTGAACAGCAGCTCAGCTTTTACGTCGAGTCCAGGTCTATGTTTTGCAACCTGGAACCTGTTCTTGTGCAGTTGATCCATAGTGTGAACCGGTTGGCAATGGAAACAAGGAAAGTCATGAAGGGAAACCACTCCAGAAAGACAGCTGCGTTTGTCCGGGCCTGTGTTGCCTACTGCTTCATCACCATCCCGTCCCTGGTAGGGATCTTCACCCGCCTCAACCTCTACCTGCATTCCGGTCAGGTTGCCTTGGCCAACCAGTGCCTCTCCCAAGGTGGGGATCGAAGTGGCCCCGCACCTCAAGGAGAGCCTCAATAA
Peptide sequence:
MGWIFQCVSYHAPEALLTEMMERCKKLGNNALLLNSVMSAFRAEFVATRSMDFIGMIKECDESGFPKHLLFRSLGLNLALADPPENDRLQILNEAWKVITKLKSPQDYINCAEVWVEYTCRHFTKREVNTVLADVIKHMTPDRAFEDSYPQLQSIIQKVIAHFHDFSVLFSVEKFLPFLDMFQKESVRVEVCKCIMEAFIKHQQEPTKDPVILNALLHICKTMHDSVNALTLEDEKRTLAHLINGFIKMVSFGRDFEQQLSFYVESRSMFCNLEPVLVQLIHSVNRLAMETRKVMKGNHSRKTAAFVRACVAYCFITIPSLVGIFTRLNLYLHSGQVALANQCLSQGGDRSGPAPQGEPQ
IRESfinder result
IRESfinder score
0.6217135
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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