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mmu_circVps13a_2257
Basic information of circular RNA
PanCircBase ID:
mmu_circVps13a_2257
mm39_Chr. Position ID:
chr19|16687634|16727545|-
Gene name:
Vps13a
Transcript:
ENSMUST00000068156.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
19
Exon/intron indexes:
26,25,24,23,22,21,20,19,18,17,16,15,14,13,12,11,10,9,8
Exon/intron offsets:
0,516,4778,10058,12124,13369,15286,24444,24644,30492,30906,32168,32725,34515,35390,35680,39255,39576,39851
Genomic length:
39911
Exon/intron sizes in nt:
157,155,79,139,118,133,137,115,187,143,95,130,63,172,107,128,58,81,60
Flanking exon/introns:
chr19:16684770-16687634|chr19:16727545-16729482
Splice length:
2257
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
ACAACTGATCAATACTGGATCCCATGTTTACATGATAATACTGAAAAGCTAGTCCGGAAGCTAATCCGATTAGATAATCTCTTTGCTTACTGGAATGTGAACTCTGAGATGTTTTATCTGAATGATTACGATGAATCGCTGAAAGCCTTGAAAAATGGTATTGTGAATGAAAATATTGTTCCAGAAGGTTATGATTTTGTTTTTCGACCTATATCTGCTAGTGCCAAACTTCAGATGAATCGACGATCAGATTTTGACTTTTCTGACCCCAAAATAAACCTGGCTGTTGATTTACATACCATAGCAATTGAGTTTAATAAACCACAGTATTTCAGCCTCATGGAGCTTCTCGAGTCAATTGACATGATGACACAAAACCAGCCGTACAGAAAGTTCAAGCCCAGTGTGCCTCTCCACCTCCACGCCAAAGAGTGGTGGGCTTATGCTATACATAGTATTCTTGAAGTAAATGTTTGTCCCAGTTTACGGATGTGGTCGTGGGAGCATATTAGAAACCATAGATACAAAATGAAACGATACAGAGAATTTTATAAGAAAAAATTAACAAGTAAGAAGCCATCTCCTGAAATTCTCATGTCTTTGGAGGAGTTGGAGAAAACTTTGGATGTTTTTAATATAACCATAGCTAGACAACAGGCAGAAGTTGAGGCAAAGAAAGCTGGATATAAAATTTACAAAGAAGGAGTCAAAGATCCAGAAGATAATGCAGGATGGTTTGGCTGGTTGTGGACTTGGTCAGAATCAAATGCTAATCAACAACAAGATGTGAAGCCTGGAATTCTGGAAGAAATGTTGACACCTGAAGAAAAGTCGTTACTTTATGAAGCAATTGGTTATAGTGAAACAGCAGTTGACCCAACCTTGCCAAAAACATTTGAAGCCTTGAAGTTTTTTGTTCACTTGAAAAGCATGTCTATTGTTCTAAGAGAAAATCACCAAAAGCCGGAGCTGTTAAACGTTGTAGTGGAAGGACTTAGTACTTCTGTTGTGCAAAGACCAGGAGCACAAGCCATAAAATTTGAAACCAAAATTGATTCATTTCATATTACTGGCTTACCAGATGATTTCAAAAAACCCCACCTACTGTCTTCATTGGATGATACGTCACTCCTCCAGATTACATTTGAGATAAATCCTTTAAATGAAACTGTTGCTCAGAGGTGCACCATAGAGGCTGAGCCTCTAGAGATAATATATGATGCAAGGACAGTCAATAGTATAGTGGAGTTCTTCAGACCTCCGAAAGATGTCCATCTAGCCCAACTTACTTCAGTAACTTTGACAAAACTTGAAGAATTTCGAGCAAAAACAGCAACAGGTTTGCTGTATGTTATTGAAACACAGAAAGTTCTTGATCTCAGAATTAATGTAAAGGCTTCATATGTTATTGTCCCACAATATGGAAATTTTAGCCCTACGTCAAATCTACTTCTCCTGGATCTTGGTCATTTAAAGGTGTCAAGTAAGCGTCGATCACTGCTGCCAGATGTGAGACCCAGTGAGGCCAGCCTTGAAGATATAATGCACAGAGCGTATGACTCCTTTGATATTCAGCTTACGAGCATACAGTTGCTCTACAGTAGAGTGGGTGATAATTGGAAAGAGGCACGAAAGCTCAATGTATCTACACAGCATATTTTGATACCTATGCATGTCAATGTGGAGCTCTCTAAAGCCATGGTTTTCATGGATATCAAGATGCCCAAATTCAAGATTTCTGGAAAGTTACCTCTTGTTTCATTACGAATTTCGGATAAAAAACTGCAAGGCATTATGGAGTTGTTGGGAAGCATTCCAAAGCCTGAACCTGTAACTGATGTATCTGCCCCTGCCAGATCATTCCAGATTCAAGCATCTGCTTTGCCAGTATCACACATTTCTCAGAAGTTAATCCCTTTATTGGAACAGCCTGTTACTGAAGATGACTCAGAGGAAGAATTTTTTGATGCACCATGTAGTCCCTTGGAGGAGTGTCCTCAAGTGTCATGTAGAGATAAATGTACTCGACAGAAAAAATTACAAAAGAAAGATTGTGTGATGAATCTTATTCAACTTAGGATGAGATTTGAAGTAGCAGAGGTGTCCATTCAGTTTTATCACCTGGTGGGAGACTGTGAACTACCTGTGCTGGAAATGGGTGCTTTAGGATTGGGAACAGAAGCTGAGTTTAGAACATTTGACTTGAAAGGAAGTGCCTTTTTGAAAGAATTATGGCTAAAATGTCCAGAATATTTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGATTGGGAACAGAAGCTGA
59.01
AGCTTCCGGACTAGCTTTTCA
59.38
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGATTGGGAACAGAAGCTGAG
60.03
AGCTTCCGGACTAGCTTTTCA
59.38
154
PCR template sequence:
GGTGCTTTAGGATTGGGAACAGAAGCTGAGTTTAGAACATTTGACTTGAAAGGAAGTGCCTTTTTGAAAGAATTATGGCTAAAATGTCCAGAATATTTAGACAACTGATCAATACTGGATCCCATGTTTACATGATAATACTGAAAAGCTAGTCCGGAAGCTAATCCGATTAGATAATCTCTTTGCTTACTGGAATGTGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(2), mmu-miR-23b-3p(1), mmu-miR-200c-3p(1), mmu-miR-196a-5p(1), mmu-miR-23a-3p(1), mmu-miR-153-3p(1), mmu-miR-382-3p(1), mmu-miR-96-5p(1), mmu-miR-511-3p(1), mmu-miR-425-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-466a-5p(1), mmu-miR-466p-5p(1), mmu-miR-532-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCAGAATATTTAGACAACTGATCAAT
siRNA sets
ATTGATCAGTTGTCTAAAT, AGTTGTCTAAATATTCTGG, ATCAGTTGTCTAAATATTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVPS13A_2257_ORF_1
0.9254
0.000265209
0.99999347
2157
ORF sequence:
ATGTTTTATCTGAATGATTACGATGAATCGCTGAAAGCCTTGAAAAATGGTATTGTGAATGAAAATATTGTTCCAGAAGGTTATGATTTTGTTTTTCGACCTATATCTGCTAGTGCCAAACTTCAGATGAATCGACGATCAGATTTTGACTTTTCTGACCCCAAAATAAACCTGGCTGTTGATTTACATACCATAGCAATTGAGTTTAATAAACCACAGTATTTCAGCCTCATGGAGCTTCTCGAGTCAATTGACATGATGACACAAAACCAGCCGTACAGAAAGTTCAAGCCCAGTGTGCCTCTCCACCTCCACGCCAAAGAGTGGTGGGCTTATGCTATACATAGTATTCTTGAAGTAAATGTTTGTCCCAGTTTACGGATGTGGTCGTGGGAGCATATTAGAAACCATAGATACAAAATGAAACGATACAGAGAATTTTATAAGAAAAAATTAACAAGTAAGAAGCCATCTCCTGAAATTCTCATGTCTTTGGAGGAGTTGGAGAAAACTTTGGATGTTTTTAATATAACCATAGCTAGACAACAGGCAGAAGTTGAGGCAAAGAAAGCTGGATATAAAATTTACAAAGAAGGAGTCAAAGATCCAGAAGATAATGCAGGATGGTTTGGCTGGTTGTGGACTTGGTCAGAATCAAATGCTAATCAACAACAAGATGTGAAGCCTGGAATTCTGGAAGAAATGTTGACACCTGAAGAAAAGTCGTTACTTTATGAAGCAATTGGTTATAGTGAAACAGCAGTTGACCCAACCTTGCCAAAAACATTTGAAGCCTTGAAGTTTTTTGTTCACTTGAAAAGCATGTCTATTGTTCTAAGAGAAAATCACCAAAAGCCGGAGCTGTTAAACGTTGTAGTGGAAGGACTTAGTACTTCTGTTGTGCAAAGACCAGGAGCACAAGCCATAAAATTTGAAACCAAAATTGATTCATTTCATATTACTGGCTTACCAGATGATTTCAAAAAACCCCACCTACTGTCTTCATTGGATGATACGTCACTCCTCCAGATTACATTTGAGATAAATCCTTTAAATGAAACTGTTGCTCAGAGGTGCACCATAGAGGCTGAGCCTCTAGAGATAATATATGATGCAAGGACAGTCAATAGTATAGTGGAGTTCTTCAGACCTCCGAAAGATGTCCATCTAGCCCAACTTACTTCAGTAACTTTGACAAAACTTGAAGAATTTCGAGCAAAAACAGCAACAGGTTTGCTGTATGTTATTGAAACACAGAAAGTTCTTGATCTCAGAATTAATGTAAAGGCTTCATATGTTATTGTCCCACAATATGGAAATTTTAGCCCTACGTCAAATCTACTTCTCCTGGATCTTGGTCATTTAAAGGTGTCAAGTAAGCGTCGATCACTGCTGCCAGATGTGAGACCCAGTGAGGCCAGCCTTGAAGATATAATGCACAGAGCGTATGACTCCTTTGATATTCAGCTTACGAGCATACAGTTGCTCTACAGTAGAGTGGGTGATAATTGGAAAGAGGCACGAAAGCTCAATGTATCTACACAGCATATTTTGATACCTATGCATGTCAATGTGGAGCTCTCTAAAGCCATGGTTTTCATGGATATCAAGATGCCCAAATTCAAGATTTCTGGAAAGTTACCTCTTGTTTCATTACGAATTTCGGATAAAAAACTGCAAGGCATTATGGAGTTGTTGGGAAGCATTCCAAAGCCTGAACCTGTAACTGATGTATCTGCCCCTGCCAGATCATTCCAGATTCAAGCATCTGCTTTGCCAGTATCACACATTTCTCAGAAGTTAATCCCTTTATTGGAACAGCCTGTTACTGAAGATGACTCAGAGGAAGAATTTTTTGATGCACCATGTAGTCCCTTGGAGGAGTGTCCTCAAGTGTCATGTAGAGATAAATGTACTCGACAGAAAAAATTACAAAAGAAAGATTGTGTGATGAATCTTATTCAACTTAGGATGAGATTTGAAGTAGCAGAGGTGTCCATTCAGTTTTATCACCTGGTGGGAGACTGTGAACTACCTGTGCTGGAAATGGGTGCTTTAGGATTGGGAACAGAAGCTGAGTTTAGAACATTTGACTTGAAAGGAAGTGCCTTTTTGAAAGAATTATGGCTAAAATGTCCAGAATATTTAGACAACTGA
Peptide sequence:
MFYLNDYDESLKALKNGIVNENIVPEGYDFVFRPISASAKLQMNRRSDFDFSDPKINLAVDLHTIAIEFNKPQYFSLMELLESIDMMTQNQPYRKFKPSVPLHLHAKEWWAYAIHSILEVNVCPSLRMWSWEHIRNHRYKMKRYREFYKKKLTSKKPSPEILMSLEELEKTLDVFNITIARQQAEVEAKKAGYKIYKEGVKDPEDNAGWFGWLWTWSESNANQQQDVKPGILEEMLTPEEKSLLYEAIGYSETAVDPTLPKTFEALKFFVHLKSMSIVLRENHQKPELLNVVVEGLSTSVVQRPGAQAIKFETKIDSFHITGLPDDFKKPHLLSSLDDTSLLQITFEINPLNETVAQRCTIEAEPLEIIYDARTVNSIVEFFRPPKDVHLAQLTSVTLTKLEEFRAKTATGLLYVIETQKVLDLRINVKASYVIVPQYGNFSPTSNLLLLDLGHLKVSSKRRSLLPDVRPSEASLEDIMHRAYDSFDIQLTSIQLLYSRVGDNWKEARKLNVSTQHILIPMHVNVELSKAMVFMDIKMPKFKISGKLPLVSLRISDKKLQGIMELLGSIPKPEPVTDVSAPARSFQIQASALPVSHISQKLIPLLEQPVTEDDSEEEFFDAPCSPLEECPQVSCRDKCTRQKKLQKKDCVMNLIQLRMRFEVAEVSIQFYHLVGDCELPVLEMGALGLGTEAEFRTFDLKGSAFLKELWLKCPEYLDN
IRESfinder result
IRESfinder score
0.706622681
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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