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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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Institute of Life sciences, Bhubaneswar, India

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