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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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