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mmu_circVps13a_1433
Basic information of circular RNA
PanCircBase ID:
mmu_circVps13a_1433
mm39_Chr. Position ID:
chr19|16680867|16703057|-
Gene name:
Vps13a
Transcript:
ENSMUST00000068156.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
31,30,29,28,27,26,25,24,23,22,21,20
Exon/intron offsets:
0,184,1028,2371,3823,6767,7283,11545,16825,18891,20136,22053
Genomic length:
22190
Exon/intron sizes in nt:
10,41,17,15,46,08,01,50,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr19:16678652-16680867|chr19:16703057-16712078
Splice length:
1433
Other database IDs:
circAtlas: mmu-Vps13a_0033
circBase: hsa_circ_0139008, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_125565
Human Ortholog IDs:
Mature spliced Sequence:
GTTTGCTGTATGTTATTGAAACACAGAAAGTTCTTGATCTCAGAATTAATGTAAAGGCTTCATATGTTATTGTCCCACAATATGGAAATTTTAGCCCTACGTCAAATCTACTTCTCCTGGATCTTGGTCATTTAAAGGTGTCAAGTAAGCGTCGATCACTGCTGCCAGATGTGAGACCCAGTGAGGCCAGCCTTGAAGATATAATGCACAGAGCGTATGACTCCTTTGATATTCAGCTTACGAGCATACAGTTGCTCTACAGTAGAGTGGGTGATAATTGGAAAGAGGCACGAAAGCTCAATGTATCTACACAGCATATTTTGATACCTATGCATGTCAATGTGGAGCTCTCTAAAGCCATGGTTTTCATGGATATCAAGATGCCCAAATTCAAGATTTCTGGAAAGTTACCTCTTGTTTCATTACGAATTTCGGATAAAAAACTGCAAGGCATTATGGAGTTGTTGGGAAGCATTCCAAAGCCTGAACCTGTAACTGATGTATCTGCCCCTGCCAGATCATTCCAGATTCAAGCATCTGCTTTGCCAGTATCACACATTTCTCAGAAGTTAATCCCTTTATTGGAACAGCCTGTTACTGAAGATGACTCAGAGGAAGAATTTTTTGATGCACCATGTAGTCCCTTGGAGGAGTGTCCTCAAGTGTCATGTAGAGATAAATGTACTCGACAGAAAAAATTACAAAAGAAAGATTGTGTGATGAATCTTATTCAACTTAGGATGAGATTTGAAGTAGCAGAGGTGTCCATTCAGTTTTATCACCTGGTGGGAGACTGTGAACTACCTGTGCTGGAAATGGGTGCTTTAGGATTGGGAACAGAAGCTGAGTTTAGAACATTTGACTTGAAAGGAAGTGCCTTTTTGAAAGAATTATGGCTAAAATGTCCAGAATATTTAGATGAAAACAAGAAACCAGTTTATTTGATCACGACCCTGGATAACACAATGGAAGATTTATTAACATTGGAATTCATGAAGGTTGAAAAAAATGCACCAAATTTGAATAGTACCTATAACAATGTTTTACAACTTATTAAGGTGAATTTTTCCTCTTTGGATATTCATTTACACACTGAAGCACTTCTGAATACAATGAATTATCTTAATAATATTCTTCCGGAATTAAGGGAAAAATCTGCCTCGGTGTCTGCTGCAGAGCCGGAAGACAAAGGGGACATCATTAAAAAACTTGCTTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAAGGGCTTGATTCTGAGATGATTATGAAACCTCTAGTCACTGAAATAAATGCAAAGCTAAGGAATATAATTGTGTTAGATTCTGATAAAATGGCTATCTACAAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTCACTGAAATAAATGCAAAGCT
57.66
TGTGGGACAATAACATATGAAGCC
59.11
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTCACTGAAATAAATGCAAAGCT
57.66
GTGGGACAATAACATATGAAGCCT
58.87
151
PCR template sequence:
TGATTCTGAGATGATTATGAAACCTCTAGTCACTGAAATAAATGCAAAGCTAAGGAATATAATTGTGTTAGATTCTGATAAAATGGCTATCTACAAAAAGGTTTGCTGTATGTTATTGAAACACAGAAAGTTCTTGATCTCAGAATTAATGTAAAGGCTTCATATGTTATTGTCCCACAATATGGAAATTTTAGCCCTAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
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-153-3p(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), mmu-miR-532-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TATCTACAAAAAGGTTTGCTGTATGT
siRNA sets
TACAGCAAACCTTTTTGTA, CATACAGCAAACCTTTTTG, ACAGCAAACCTTTTTGTAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVPS13A_1433_ORF_1
0.8712
-0.023197613
0.995851927
1284
ORF sequence:
ATGCACAGAGCGTATGACTCCTTTGATATTCAGCTTACGAGCATACAGTTGCTCTACAGTAGAGTGGGTGATAATTGGAAAGAGGCACGAAAGCTCAATGTATCTACACAGCATATTTTGATACCTATGCATGTCAATGTGGAGCTCTCTAAAGCCATGGTTTTCATGGATATCAAGATGCCCAAATTCAAGATTTCTGGAAAGTTACCTCTTGTTTCATTACGAATTTCGGATAAAAAACTGCAAGGCATTATGGAGTTGTTGGGAAGCATTCCAAAGCCTGAACCTGTAACTGATGTATCTGCCCCTGCCAGATCATTCCAGATTCAAGCATCTGCTTTGCCAGTATCACACATTTCTCAGAAGTTAATCCCTTTATTGGAACAGCCTGTTACTGAAGATGACTCAGAGGAAGAATTTTTTGATGCACCATGTAGTCCCTTGGAGGAGTGTCCTCAAGTGTCATGTAGAGATAAATGTACTCGACAGAAAAAATTACAAAAGAAAGATTGTGTGATGAATCTTATTCAACTTAGGATGAGATTTGAAGTAGCAGAGGTGTCCATTCAGTTTTATCACCTGGTGGGAGACTGTGAACTACCTGTGCTGGAAATGGGTGCTTTAGGATTGGGAACAGAAGCTGAGTTTAGAACATTTGACTTGAAAGGAAGTGCCTTTTTGAAAGAATTATGGCTAAAATGTCCAGAATATTTAGATGAAAACAAGAAACCAGTTTATTTGATCACGACCCTGGATAACACAATGGAAGATTTATTAACATTGGAATTCATGAAGGTTGAAAAAAATGCACCAAATTTGAATAGTACCTATAACAATGTTTTACAACTTATTAAGGTGAATTTTTCCTCTTTGGATATTCATTTACACACTGAAGCACTTCTGAATACAATGAATTATCTTAATAATATTCTTCCGGAATTAAGGGAAAAATCTGCCTCGGTGTCTGCTGCAGAGCCGGAAGACAAAGGGGACATCATTAAAAAACTTGCTTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAAGGGCTTGATTCTGAGATGATTATGAAACCTCTAGTCACTGAAATAAATGCAAAGCTAAGGAATATAATTGTGTTAGATTCTGATAAAATGGCTATCTACAAAAAGGTTTGCTGTATGTTATTGAAACACAGAAAGTTCTTGATCTCAGAATTAATGTAA
Peptide sequence:
MHRAYDSFDIQLTSIQLLYSRVGDNWKEARKLNVSTQHILIPMHVNVELSKAMVFMDIKMPKFKISGKLPLVSLRISDKKLQGIMELLGSIPKPEPVTDVSAPARSFQIQASALPVSHISQKLIPLLEQPVTEDDSEEEFFDAPCSPLEECPQVSCRDKCTRQKKLQKKDCVMNLIQLRMRFEVAEVSIQFYHLVGDCELPVLEMGALGLGTEAEFRTFDLKGSAFLKELWLKCPEYLDENKKPVYLITTLDNTMEDLLTLEFMKVEKNAPNLNSTYNNVLQLIKVNFSSLDIHLHTEALLNTMNYLNNILPELREKSASVSAAEPEDKGDIIKKLALKLPTNEDIITLQLLAELSCLQIFIQDQKQNISEIKIEGLDSEMIMKPLVTEINAKLRNIIVLDSDKMAIYKKVCCMLLKHRKFLISELM
IRESfinder result
IRESfinder score
0.754192379
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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