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mmu_circVps13d_699
Basic information of circular RNA
PanCircBase ID:
mmu_circVps13d_699
mm39_Chr. Position ID:
chr4|144771530|144784132|-
Gene name:
Vps13d
Transcript:
ENSMUST00000036579.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
65,64,63,62,61
Exon/intron offsets:
0,1310,9156,11509,12452
Genomic length:
12602
Exon/intron sizes in nt:
1,68,13,51,49,97,150
Flanking exon/introns:
chr4:144746839-144771530|chr4:144784132-144789074
Splice length:
699
Other database IDs:
circBase: mmu_circ_0011394, CIRCpedia: MMU_CIRCpedia_9548, circAtlas: mmu-Vps13d_0008
circBase: hsa_circ_0004222, circAtlas: hsa-VPS13D_0005, CIRCpedia: HSA_CIRCpedia_27636
Human Ortholog IDs:
Mature spliced Sequence:
GTGGACAATCAGCTCATTGGCACTACTCAGCCCTTCATGCTCTATGTGACCCCCCTGAGCAATGAGAACGAGGTCATTGAGACAGGTCCTGCTGTGCAAGTCAATGCAGTGAAGTTCCCCAGTAAGAGCGCACTGACCAACATCTACAAGCACCTGATGGTCACGGCTCAGAGGTTCACAGTACAAATTGAGGAGAAACTGCTGCTCAAGCTACTAAGTTTCTTTGGCTACGATCAGGCAGAATCAGAGGTGGAAAAGTATGATGAAAACATCCATGAGAAAACAGCAGAGCAGGGAGGAACTCCAACTCGATACTACTTTGAGAACCTCAAGATCAGCATCCCCCAGATCAAGCTCAGTGTGTTCACCTCCAACAAGCTGCCACTGGACCTTAAGGCTCTGAAAAGCACCCTAGGATTCCCACTGATTCGGTTTGAAGATGCTGTGATCAATCTGGATCCCTTCACTCGGGTGCATCCCTATGAGACCAAGGAGTTCATCATCAATGACATCCTCAAGCACTTCCAGGAGGAACTCCTTAGCCAGGCAGCTCGGATCCTAGGATCGGTAGACTTCCTTGGCAATCCCATGGGCCTTTTGAATGATGTATCCGAAGGGGTCACTGGACTGATAAAGTATGGAAATGTCGGGGGTCTCATAAGAAATGTTACCCATGGAGTGTCAAATTCTGCCGCCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGAAATGTCGGGGGTCTCAT
59.45
CACAGCAGGACCTGTCTCAA
59.61
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATGGAAATGTCGGGGGTCTC
59.45
CACAGCAGGACCTGTCTCAA
59.61
158
PCR template sequence:
GAATGATGTATCCGAAGGGGTCACTGGACTGATAAAGTATGGAAATGTCGGGGGTCTCATAAGAAATGTTACCCATGGAGTGTCAAATTCTGCCGCCAAGGTGGACAATCAGCTCATTGGCACTACTCAGCCCTTCATGCTCTATGTGACCCCCCTGAGCAATGAGAACGAGGTCATTGAGACAGGTCCTGCTGTGCAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-322-5p(1), mmu-miR-33-5p(1), mmu-miR-433-3p(1), mmu-miR-22-3p(1), mmu-miR-501-3p(1), mmu-miR-541-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTCTGCCGCCAAGGTGGACAATCAGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVPS13D_699_ORF_1
1.2409
0.420341209
0.999812038
1362
ORF sequence:
ATGCTCTATGTGACCCCCCTGAGCAATGAGAACGAGGTCATTGAGACAGGTCCTGCTGTGCAAGTCAATGCAGTGAAGTTCCCCAGTAAGAGCGCACTGACCAACATCTACAAGCACCTGATGGTCACGGCTCAGAGGTTCACAGTACAAATTGAGGAGAAACTGCTGCTCAAGCTACTAAGTTTCTTTGGCTACGATCAGGCAGAATCAGAGGTGGAAAAGTATGATGAAAACATCCATGAGAAAACAGCAGAGCAGGGAGGAACTCCAACTCGATACTACTTTGAGAACCTCAAGATCAGCATCCCCCAGATCAAGCTCAGTGTGTTCACCTCCAACAAGCTGCCACTGGACCTTAAGGCTCTGAAAAGCACCCTAGGATTCCCACTGATTCGGTTTGAAGATGCTGTGATCAATCTGGATCCCTTCACTCGGGTGCATCCCTATGAGACCAAGGAGTTCATCATCAATGACATCCTCAAGCACTTCCAGGAGGAACTCCTTAGCCAGGCAGCTCGGATCCTAGGATCGGTAGACTTCCTTGGCAATCCCATGGGCCTTTTGAATGATGTATCCGAAGGGGTCACTGGACTGATAAAGTATGGAAATGTCGGGGGTCTCATAAGAAATGTTACCCATGGAGTGTCAAATTCTGCCGCCAAGGTGGACAATCAGCTCATTGGCACTACTCAGCCCTTCATGCTCTATGTGACCCCCCTGAGCAATGAGAACGAGGTCATTGAGACAGGTCCTGCTGTGCAAGTCAATGCAGTGAAGTTCCCCAGTAAGAGCGCACTGACCAACATCTACAAGCACCTGATGGTCACGGCTCAGAGGTTCACAGTACAAATTGAGGAGAAACTGCTGCTCAAGCTACTAAGTTTCTTTGGCTACGATCAGGCAGAATCAGAGGTGGAAAAGTATGATGAAAACATCCATGAGAAAACAGCAGAGCAGGGAGGAACTCCAACTCGATACTACTTTGAGAACCTCAAGATCAGCATCCCCCAGATCAAGCTCAGTGTGTTCACCTCCAACAAGCTGCCACTGGACCTTAAGGCTCTGAAAAGCACCCTAGGATTCCCACTGATTCGGTTTGAAGATGCTGTGATCAATCTGGATCCCTTCACTCGGGTGCATCCCTATGAGACCAAGGAGTTCATCATCAATGACATCCTCAAGCACTTCCAGGAGGAACTCCTTAGCCAGGCAGCTCGGATCCTAGGATCGGTAGACTTCCTTGGCAATCCCATGGGCCTTTTGAATGATGTATCCGAAGGGGTCACTGGACTGATAAAGTATGGAAATGTCGGGGGTCTCATAAGAAATGTTACCCATGGAGTGTCAAATTCTGCCGCCAAG
Peptide sequence:
MLYVTPLSNENEVIETGPAVQVNAVKFPSKSALTNIYKHLMVTAQRFTVQIEEKLLLKLLSFFGYDQAESEVEKYDENIHEKTAEQGGTPTRYYFENLKISIPQIKLSVFTSNKLPLDLKALKSTLGFPLIRFEDAVINLDPFTRVHPYETKEFIINDILKHFQEELLSQAARILGSVDFLGNPMGLLNDVSEGVTGLIKYGNVGGLIRNVTHGVSNSAAKVDNQLIGTTQPFMLYVTPLSNENEVIETGPAVQVNAVKFPSKSALTNIYKHLMVTAQRFTVQIEEKLLLKLLSFFGYDQAESEVEKYDENIHEKTAEQGGTPTRYYFENLKISIPQIKLSVFTSNKLPLDLKALKSTLGFPLIRFEDAVINLDPFTRVHPYETKEFIINDILKHFQEELLSQAARILGSVDFLGNPMGLLNDVSEGVTGLIKYGNVGGLIRNVTHGVSNSAAK
IRESfinder result
IRESfinder score
0.553853939
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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