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mmu_circVps13a_1058_2

Basic information of circular RNA
PanCircBase ID:

mmu_circVps13a_1058_2

mm39_Chr. Position ID:

chr19|16699758|16719932|-

Gene name:

Vps13a

Transcript:

ENSMUST00000068156.8

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

8

Exon/intron indexes:

22,21,20,19,18,17,16,15

Exon/intron offsets:

0,1245,3162,12320,12520,18368,18782,20044

Genomic length:

20174

Exon/intron sizes in nt:

11,81,33,13,71,15,18,70,00,00,000

Flanking exon/introns:

chr19:16697831-16699758|chr19:16719932-16720359

Splice length:

1058

Other database IDs:

Human Ortholog IDs:
Mature spliced Sequence:

GCAAAGAAAGCTGGATATAAAATTTACAAAGAAGGAGTCAAAGATCCAGAAGATAATGCAGGATGGTTTGGCTGGTTGTGGACTTGGTCAGAATCAAATGCTAATCAACAACAAGATGTGAAGCCTGGAATTCTGGAAGAAATGTTGACACCTGAAGAAAAGTCGTTACTTTATGAAGCAATTGGTTATAGTGAAACAGCAGTTGACCCAACCTTGCCAAAAACATTTGAAGCCTTGAAGTTTTTTGTTCACTTGAAAAGCATGTCTATTGTTCTAAGAGAAAATCACCAAAAGCCGGAGCTGTTAAACGTTGTAGTGGAAGGACTTAGTACTTCTGTTGTGCAAAGACCAGGAGCACAAGCCATAAAATTTGAAACCAAAATTGATTCATTTCATATTACTGGCTTACCAGATGATTTCAAAAAACCCCACCTACTGTCTTCATTGGATGATACGTCACTCCTCCAGATTACATTTGAGATAAATCCTTTAAATGAAACTGTTGCTCAGAGGTGCACCATAGAGGCTGAGCCTCTAGAGATAATATATGATGCAAGGACAGTCAATAGTATAGTGGAGTTCTTCAGACCTCCGAAAGATGTCCATCTAGCCCAACTTACTTCAGTAACTTTGACAAAACTTGAAGAATTTCGAGCAAAAACAGCAACAGGTTTGCTGTATGTTATTGAAACACAGAAAGTTCTTGATCTCAGAATTAATGTAAAGGCTTCATATGTTATTGTCCCACAATATGGAAATTTTAGCCCTACGTCAAATCTACTTCTCCTGGATCTTGGTCATTTAAAGGTGTCAAGTAAGCGTCGATCACTGCTGCCAGATGTGAGACCCAGTGAGGCCAGCCTTGAAGATATAATGCACAGAGCGTATGACTCCTTTGATATTCAGCTTACGAGCATACAGTTGCTCTACAGTAGAGTGGGTGATAATTGGAAAGAGGCACGAAAGCTCAATGTATCTACACAGCATATTTTGATACCTATGCATGTCAATGTGGAGCTCTCTAAAGCCATGGTTTTCATGGATATCAAGATGCCCAA

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

TGCATGTCAATGTGGAGCTCT

60

TCCACAACCAGCCAAACCAT

60.11

140

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TGCATGTCAATGTGGAGCTCT

60

TGACCAAGTCCACAACCAGC

60.47

148

PCR template sequence:

CACGAAAGCTCAATGTATCTACACAGCATATTTTGATACCTATGCATGTCAATGTGGAGCTCTCTAAAGCCATGGTTTTCATGGATATCAAGATGCCCAAGCAAAGAAAGCTGGATATAAAATTTACAAAGAAGGAGTCAAAGATCCAGAAGATAATGCAGGATGGTTTGGCTGGTTGTGGACTTGGTCAGAATCAAATG

Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs

3

Interacting miRNAs (#binding sites)

mmu-miR-135a-5p(1), mmu-miR-153-3p(1), mmu-miR-29b-2-5p(1)

siRNAs for circular RNA silencing
Junction sequence

TCAAGATGCCCAAGCAAAGAAAGCTG

siRNA sets

CAGCTTTCTTTGCTTGGGC, TTTCTTTGCTTGGGCATCT, CTTTCTTTGCTTGGGCATC

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCVPS13A_1058_2_ORF_1

1.0263

0.004987908

0.984123983

1038

ORF sequence:

ATGTTGACACCTGAAGAAAAGTCGTTACTTTATGAAGCAATTGGTTATAGTGAAACAGCAGTTGACCCAACCTTGCCAAAAACATTTGAAGCCTTGAAGTTTTTTGTTCACTTGAAAAGCATGTCTATTGTTCTAAGAGAAAATCACCAAAAGCCGGAGCTGTTAAACGTTGTAGTGGAAGGACTTAGTACTTCTGTTGTGCAAAGACCAGGAGCACAAGCCATAAAATTTGAAACCAAAATTGATTCATTTCATATTACTGGCTTACCAGATGATTTCAAAAAACCCCACCTACTGTCTTCATTGGATGATACGTCACTCCTCCAGATTACATTTGAGATAAATCCTTTAAATGAAACTGTTGCTCAGAGGTGCACCATAGAGGCTGAGCCTCTAGAGATAATATATGATGCAAGGACAGTCAATAGTATAGTGGAGTTCTTCAGACCTCCGAAAGATGTCCATCTAGCCCAACTTACTTCAGTAACTTTGACAAAACTTGAAGAATTTCGAGCAAAAACAGCAACAGGTTTGCTGTATGTTATTGAAACACAGAAAGTTCTTGATCTCAGAATTAATGTAAAGGCTTCATATGTTATTGTCCCACAATATGGAAATTTTAGCCCTACGTCAAATCTACTTCTCCTGGATCTTGGTCATTTAAAGGTGTCAAGTAAGCGTCGATCACTGCTGCCAGATGTGAGACCCAGTGAGGCCAGCCTTGAAGATATAATGCACAGAGCGTATGACTCCTTTGATATTCAGCTTACGAGCATACAGTTGCTCTACAGTAGAGTGGGTGATAATTGGAAAGAGGCACGAAAGCTCAATGTATCTACACAGCATATTTTGATACCTATGCATGTCAATGTGGAGCTCTCTAAAGCCATGGTTTTCATGGATATCAAGATGCCCAAGCAAAGAAAGCTGGATATAAAATTTACAAAGAAGGAGTCAAAGATCCAGAAGATAATGCAGGATGGTTTGGCTGGTTGTGGACTTGGTCAGAATCAAATGCTAATCAACAACAAGATGTGA

Peptide sequence:

MLTPEEKSLLYEAIGYSETAVDPTLPKTFEALKFFVHLKSMSIVLRENHQKPELLNVVVEGLSTSVVQRPGAQAIKFETKIDSFHITGLPDDFKKPHLLSSLDDTSLLQITFEINPLNETVAQRCTIEAEPLEIIYDARTVNSIVEFFRPPKDVHLAQLTSVTLTKLEEFRAKTATGLLYVIETQKVLDLRINVKASYVIVPQYGNFSPTSNLLLLDLGHLKVSSKRRSLLPDVRPSEASLEDIMHRAYDSFDIQLTSIQLLYSRVGDNWKEARKLNVSTQHILIPMHVNVELSKAMVFMDIKMPKQRKLDIKFTKKESKIQKIMQDGLAGCGLGQNQMLINNKM

IRESfinder result

IRESfinder score

0.694464817

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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