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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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Institute of Life sciences, Bhubaneswar, India

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