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mmu_circVps13a_906
Basic information of circular RNA
PanCircBase ID:
mmu_circVps13a_906
mm39_Chr. Position ID:
chr19|16680867|16692491|-
Gene name:
Vps13a
Transcript:
ENSMUST00000068156.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
31,30,29,28,27,26,25,24
Exon/intron offsets:
0,184,1028,2371,3823,6767,7283,11545
Genomic length:
11624
Exon/intron sizes in nt:
104,117,154,60,80,157,155,79
Flanking exon/introns:
chr19:16678652-16680867|chr19:16692491-16697692
Splice length:
906
Other database IDs:
CIRCpedia: MMU_CIRCpedia_11670, circAtlas: mmu-Vps13a_0013
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_347399
Human Ortholog IDs:
Mature spliced Sequence:
ATTCAAGCATCTGCTTTGCCAGTATCACACATTTCTCAGAAGTTAATCCCTTTATTGGAACAGCCTGTTACTGAAGATGACTCAGAGGAAGAATTTTTTGATGCACCATGTAGTCCCTTGGAGGAGTGTCCTCAAGTGTCATGTAGAGATAAATGTACTCGACAGAAAAAATTACAAAAGAAAGATTGTGTGATGAATCTTATTCAACTTAGGATGAGATTTGAAGTAGCAGAGGTGTCCATTCAGTTTTATCACCTGGTGGGAGACTGTGAACTACCTGTGCTGGAAATGGGTGCTTTAGGATTGGGAACAGAAGCTGAGTTTAGAACATTTGACTTGAAAGGAAGTGCCTTTTTGAAAGAATTATGGCTAAAATGTCCAGAATATTTAGATGAAAACAAGAAACCAGTTTATTTGATCACGACCCTGGATAACACAATGGAAGATTTATTAACATTGGAATTCATGAAGGTTGAAAAAAATGCACCAAATTTGAATAGTACCTATAACAATGTTTTACAACTTATTAAGGTGAATTTTTCCTCTTTGGATATTCATTTACACACTGAAGCACTTCTGAATACAATGAATTATCTTAATAATATTCTTCCGGAATTAAGGGAAAAATCTGCCTCGGTGTCTGCTGCAGAGCCGGAAGACAAAGGGGACATCATTAAAAAACTTGCTTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAAGGGCTTGATTCTGAGATGATTATGAAACCTCTAGTCACTGAAATAAATGCAAAGCTAAGGAATATAATTGTGTTAGATTCTGATAAAATGGCTATCTACAAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTCACTGAAATAAATGCAAAGCT
57.66
ACAGGCTGTTCCAATAAAGGGA
59.62
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTCACTGAAATAAATGCAAAGCT
57.66
TCTTCAGTAACAGGCTGTTCCA
59.3
150
PCR template sequence:
TGATTCTGAGATGATTATGAAACCTCTAGTCACTGAAATAAATGCAAAGCTAAGGAATATAATTGTGTTAGATTCTGATAAAATGGCTATCTACAAAAAGATTCAAGCATCTGCTTTGCCAGTATCACACATTTCTCAGAAGTTAATCCCTTTATTGGAACAGCCTGTTACTGAAGATGACTCAGAGGAAGAATTTTTTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-196a-5p(1), mmu-miR-214-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-425-5p(1), mmu-miR-466a-5p(1), mmu-miR-466p-5p(1), mmu-miR-539-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TATCTACAAAAAGATTCAAGCATCTG
siRNA sets
GATGCTTGAATCTTTTTGT, ATGCTTGAATCTTTTTGTA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVPS13A_906_ORF_1
0.8931
-0.022615635
0.999655605
1620
ORF sequence:
ATGAATCTTATTCAACTTAGGATGAGATTTGAAGTAGCAGAGGTGTCCATTCAGTTTTATCACCTGGTGGGAGACTGTGAACTACCTGTGCTGGAAATGGGTGCTTTAGGATTGGGAACAGAAGCTGAGTTTAGAACATTTGACTTGAAAGGAAGTGCCTTTTTGAAAGAATTATGGCTAAAATGTCCAGAATATTTAGATGAAAACAAGAAACCAGTTTATTTGATCACGACCCTGGATAACACAATGGAAGATTTATTAACATTGGAATTCATGAAGGTTGAAAAAAATGCACCAAATTTGAATAGTACCTATAACAATGTTTTACAACTTATTAAGGTGAATTTTTCCTCTTTGGATATTCATTTACACACTGAAGCACTTCTGAATACAATGAATTATCTTAATAATATTCTTCCGGAATTAAGGGAAAAATCTGCCTCGGTGTCTGCTGCAGAGCCGGAAGACAAAGGGGACATCATTAAAAAACTTGCTTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAAGGGCTTGATTCTGAGATGATTATGAAACCTCTAGTCACTGAAATAAATGCAAAGCTAAGGAATATAATTGTGTTAGATTCTGATAAAATGGCTATCTACAAAAAGATTCAAGCATCTGCTTTGCCAGTATCACACATTTCTCAGAAGTTAATCCCTTTATTGGAACAGCCTGTTACTGAAGATGACTCAGAGGAAGAATTTTTTGATGCACCATGTAGTCCCTTGGAGGAGTGTCCTCAAGTGTCATGTAGAGATAAATGTACTCGACAGAAAAAATTACAAAAGAAAGATTGTGTGATGAATCTTATTCAACTTAGGATGAGATTTGAAGTAGCAGAGGTGTCCATTCAGTTTTATCACCTGGTGGGAGACTGTGAACTACCTGTGCTGGAAATGGGTGCTTTAGGATTGGGAACAGAAGCTGAGTTTAGAACATTTGACTTGAAAGGAAGTGCCTTTTTGAAAGAATTATGGCTAAAATGTCCAGAATATTTAGATGAAAACAAGAAACCAGTTTATTTGATCACGACCCTGGATAACACAATGGAAGATTTATTAACATTGGAATTCATGAAGGTTGAAAAAAATGCACCAAATTTGAATAGTACCTATAACAATGTTTTACAACTTATTAAGGTGAATTTTTCCTCTTTGGATATTCATTTACACACTGAAGCACTTCTGAATACAATGAATTATCTTAATAATATTCTTCCGGAATTAAGGGAAAAATCTGCCTCGGTGTCTGCTGCAGAGCCGGAAGACAAAGGGGACATCATTAAAAAACTTGCTTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAAGGGCTTGATTCTGAGATGATTATGAAACCTCTAGTCACTGAAATAAATGCAAAGCTAAGGAATATAATTGTGTTAGATTCTGATAAAATGGCTATCTACAAAAAG
Peptide sequence:
MNLIQLRMRFEVAEVSIQFYHLVGDCELPVLEMGALGLGTEAEFRTFDLKGSAFLKELWLKCPEYLDENKKPVYLITTLDNTMEDLLTLEFMKVEKNAPNLNSTYNNVLQLIKVNFSSLDIHLHTEALLNTMNYLNNILPELREKSASVSAAEPEDKGDIIKKLALKLPTNEDIITLQLLAELSCLQIFIQDQKQNISEIKIEGLDSEMIMKPLVTEINAKLRNIIVLDSDKMAIYKKIQASALPVSHISQKLIPLLEQPVTEDDSEEEFFDAPCSPLEECPQVSCRDKCTRQKKLQKKDCVMNLIQLRMRFEVAEVSIQFYHLVGDCELPVLEMGALGLGTEAEFRTFDLKGSAFLKELWLKCPEYLDENKKPVYLITTLDNTMEDLLTLEFMKVEKNAPNLNSTYNNVLQLIKVNFSSLDIHLHTEALLNTMNYLNNILPELREKSASVSAAEPEDKGDIIKKLALKLPTNEDIITLQLLAELSCLQIFIQDQKQNISEIKIEGLDSEMIMKPLVTEINAKLRNIIVLDSDKMAIYKK
IRESfinder result
IRESfinder score
0.791912325
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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