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mmu_circVps13a_1794
Basic information of circular RNA
PanCircBase ID:
mmu_circVps13a_1794
mm39_Chr. Position ID:
chr19|16712078|16743904|-
Gene name:
Vps13a
Transcript:
ENSMUST00000068156.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
18
Exon/intron indexes:
19,18,17,16,15,14,13,12,11,10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,200,6048,6462,7724,8281,10071,10946,11236,14811,15132,15407,17404,19537,24872,25226,27434,31782
Genomic length:
31826
Exon/intron sizes in nt:
115,187,143,95,130,63,172,107,128,58,81,60,60,110,102,96,43,44
Flanking exon/introns:
chr19:16703057-16712078|chr19:16743904-16758033
Splice length:
1794
Other database IDs:
CIRCpedia: MMU_CIRCpedia_11687, circAtlas: mmu-Vps13a_0010
circBase: hsa_circ_0138998, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_149150
Human Ortholog IDs:
Mature spliced Sequence:
GAGCTGTGGCCCTCAAGAACCTTGTAATTAAAGAAAATGCATTGCATGAATTGGATGTACCATTCAAAGTTAAAGTTGGTCATATAGGTAGTCTTAAACTTAAAATTCCATGGAAAAACCTTTATACTCAACCAGTTGAAGCTGTTTTGGAAGAAATTTTTTTACTCATAGTGCCTTCTTCTAGAATACAGTATGATCCTATCAAAGAAGAAAAGCAACTCATGGAAACAAAGCAACAGGAACTAAAAAGAATAGAAAAAGCAAAACAGAAAGTATTTGATAAAGAAAAGCCTCGGGAGGAGAAACAGGACACGTTTACAGAAAAGTTAGTTACTCAGATCATACAGAACCTTCAAGTGCAAATCTCCAGCATCCATATTCGTTATGAAGACGATATCACAAATGGAGACAAACCACTCTCTTTTGGTATTTCCCTTCAAAATATCAGCCTTCAGACAACTGATCAATACTGGATCCCATGTTTACATGATAATACTGAAAAGCTAGTCCGGAAGCTAATCCGATTAGATAATCTCTTTGCTTACTGGAATGTGAACTCTGAGATGTTTTATCTGAATGATTACGATGAATCGCTGAAAGCCTTGAAAAATGGTATTGTGAATGAAAATATTGTTCCAGAAGGTTATGATTTTGTTTTTCGACCTATATCTGCTAGTGCCAAACTTCAGATGAATCGACGATCAGATTTTGACTTTTCTGACCCCAAAATAAACCTGGCTGTTGATTTACATACCATAGCAATTGAGTTTAATAAACCACAGTATTTCAGCCTCATGGAGCTTCTCGAGTCAATTGACATGATGACACAAAACCAGCCGTACAGAAAGTTCAAGCCCAGTGTGCCTCTCCACCTCCACGCCAAAGAGTGGTGGGCTTATGCTATACATAGTATTCTTGAAGTAAATGTTTGTCCCAGTTTACGGATGTGGTCGTGGGAGCATATTAGAAACCATAGATACAAAATGAAACGATACAGAGAATTTTATAAGAAAAAATTAACAAGTAAGAAGCCATCTCCTGAAATTCTCATGTCTTTGGAGGAGTTGGAGAAAACTTTGGATGTTTTTAATATAACCATAGCTAGACAACAGGCAGAAGTTGAGGCAAAGAAAGCTGGATATAAAATTTACAAAGAAGGAGTCAAAGATCCAGAAGATAATGCAGGATGGTTTGGCTGGTTGTGGACTTGGTCAGAATCAAATGCTAATCAACAACAAGATGTGAAGCCTGGAATTCTGGAAGAAATGTTGACACCTGAAGAAAAGTCGTTACTTTATGAAGCAATTGGTTATAGTGAAACAGCAGTTGACCCAACCTTGCCAAAAACATTTGAAGCCTTGAAGTTTTTTGTTCACTTGAAAAGCATGTCTATTGTTCTAAGAGAAAATCACCAAAAGCCGGAGCTGTTAAACGTTGTAGTGGAAGGACTTAGTACTTCTGTTGTGCAAAGACCAGGAGCACAAGCCATAAAATTTGAAACCAAAATTGATTCATTTCATATTACTGGCTTACCAGATGATTTCAAAAAACCCCACCTACTGTCTTCATTGGATGATACGTCACTCCTCCAGATTACATTTGAGATAAATCCTTTAAATGAAACTGTTGCTCAGAGGTGCACCATAGAGGCTGAGCCTCTAGAGATAATATATGATGCAAGGACAGTCAATAGTATAGTGGAGTTCTTCAGACCTCCGAAAGATGTCCATCTAGCCCAACTTACTTCAGTAACTTTGACAAAACTTGAAGAATTTCGAGCAAAAACAGCAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGAGTTCTTCAGACCTCCGA
58.45
ACATCCAATTCATGCAATGCA
57.1
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGACCTCCGAAAGATGTCCA
59.45
ACATCCAATTCATGCAATGCA
57.1
144
PCR template sequence:
ATAGTGGAGTTCTTCAGACCTCCGAAAGATGTCCATCTAGCCCAACTTACTTCAGTAACTTTGACAAAACTTGAAGAATTTCGAGCAAAAACAGCAACAGGAGCTGTGGCCCTCAAGAACCTTGTAATTAAAGAAAATGCATTGCATGAATTGGATGTACCATTCAAAGTTAAAGTTGGTCATATAGGTAGTCTTAAACT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(2), mmu-miR-23b-3p(1), mmu-miR-140-5p(1), mmu-miR-200c-3p(1), mmu-miR-23a-3p(1), mmu-miR-136-5p(1), mmu-miR-382-3p(1), mmu-miR-96-5p(1), mmu-miR-511-3p(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAAACAGCAACAGGAGCTGTGGCCCT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVPS13A_1794_ORF_1
0.9188
0.027154454
0.999999999
3366
ORF sequence:
ATGGAAACAAAGCAACAGGAACTAAAAAGAATAGAAAAAGCAAAACAGAAAGTATTTGATAAAGAAAAGCCTCGGGAGGAGAAACAGGACACGTTTACAGAAAAGTTAGTTACTCAGATCATACAGAACCTTCAAGTGCAAATCTCCAGCATCCATATTCGTTATGAAGACGATATCACAAATGGAGACAAACCACTCTCTTTTGGTATTTCCCTTCAAAATATCAGCCTTCAGACAACTGATCAATACTGGATCCCATGTTTACATGATAATACTGAAAAGCTAGTCCGGAAGCTAATCCGATTAGATAATCTCTTTGCTTACTGGAATGTGAACTCTGAGATGTTTTATCTGAATGATTACGATGAATCGCTGAAAGCCTTGAAAAATGGTATTGTGAATGAAAATATTGTTCCAGAAGGTTATGATTTTGTTTTTCGACCTATATCTGCTAGTGCCAAACTTCAGATGAATCGACGATCAGATTTTGACTTTTCTGACCCCAAAATAAACCTGGCTGTTGATTTACATACCATAGCAATTGAGTTTAATAAACCACAGTATTTCAGCCTCATGGAGCTTCTCGAGTCAATTGACATGATGACACAAAACCAGCCGTACAGAAAGTTCAAGCCCAGTGTGCCTCTCCACCTCCACGCCAAAGAGTGGTGGGCTTATGCTATACATAGTATTCTTGAAGTAAATGTTTGTCCCAGTTTACGGATGTGGTCGTGGGAGCATATTAGAAACCATAGATACAAAATGAAACGATACAGAGAATTTTATAAGAAAAAATTAACAAGTAAGAAGCCATCTCCTGAAATTCTCATGTCTTTGGAGGAGTTGGAGAAAACTTTGGATGTTTTTAATATAACCATAGCTAGACAACAGGCAGAAGTTGAGGCAAAGAAAGCTGGATATAAAATTTACAAAGAAGGAGTCAAAGATCCAGAAGATAATGCAGGATGGTTTGGCTGGTTGTGGACTTGGTCAGAATCAAATGCTAATCAACAACAAGATGTGAAGCCTGGAATTCTGGAAGAAATGTTGACACCTGAAGAAAAGTCGTTACTTTATGAAGCAATTGGTTATAGTGAAACAGCAGTTGACCCAACCTTGCCAAAAACATTTGAAGCCTTGAAGTTTTTTGTTCACTTGAAAAGCATGTCTATTGTTCTAAGAGAAAATCACCAAAAGCCGGAGCTGTTAAACGTTGTAGTGGAAGGACTTAGTACTTCTGTTGTGCAAAGACCAGGAGCACAAGCCATAAAATTTGAAACCAAAATTGATTCATTTCATATTACTGGCTTACCAGATGATTTCAAAAAACCCCACCTACTGTCTTCATTGGATGATACGTCACTCCTCCAGATTACATTTGAGATAAATCCTTTAAATGAAACTGTTGCTCAGAGGTGCACCATAGAGGCTGAGCCTCTAGAGATAATATATGATGCAAGGACAGTCAATAGTATAGTGGAGTTCTTCAGACCTCCGAAAGATGTCCATCTAGCCCAACTTACTTCAGTAACTTTGACAAAACTTGAAGAATTTCGAGCAAAAACAGCAACAGGAGCTGTGGCCCTCAAGAACCTTGTAATTAAAGAAAATGCATTGCATGAATTGGATGTACCATTCAAAGTTAAAGTTGGTCATATAGGTAGTCTTAAACTTAAAATTCCATGGAAAAACCTTTATACTCAACCAGTTGAAGCTGTTTTGGAAGAAATTTTTTTACTCATAGTGCCTTCTTCTAGAATACAGTATGATCCTATCAAAGAAGAAAAGCAACTCATGGAAACAAAGCAACAGGAACTAAAAAGAATAGAAAAAGCAAAACAGAAAGTATTTGATAAAGAAAAGCCTCGGGAGGAGAAACAGGACACGTTTACAGAAAAGTTAGTTACTCAGATCATACAGAACCTTCAAGTGCAAATCTCCAGCATCCATATTCGTTATGAAGACGATATCACAAATGGAGACAAACCACTCTCTTTTGGTATTTCCCTTCAAAATATCAGCCTTCAGACAACTGATCAATACTGGATCCCATGTTTACATGATAATACTGAAAAGCTAGTCCGGAAGCTAATCCGATTAGATAATCTCTTTGCTTACTGGAATGTGAACTCTGAGATGTTTTATCTGAATGATTACGATGAATCGCTGAAAGCCTTGAAAAATGGTATTGTGAATGAAAATATTGTTCCAGAAGGTTATGATTTTGTTTTTCGACCTATATCTGCTAGTGCCAAACTTCAGATGAATCGACGATCAGATTTTGACTTTTCTGACCCCAAAATAAACCTGGCTGTTGATTTACATACCATAGCAATTGAGTTTAATAAACCACAGTATTTCAGCCTCATGGAGCTTCTCGAGTCAATTGACATGATGACACAAAACCAGCCGTACAGAAAGTTCAAGCCCAGTGTGCCTCTCCACCTCCACGCCAAAGAGTGGTGGGCTTATGCTATACATAGTATTCTTGAAGTAAATGTTTGTCCCAGTTTACGGATGTGGTCGTGGGAGCATATTAGAAACCATAGATACAAAATGAAACGATACAGAGAATTTTATAAGAAAAAATTAACAAGTAAGAAGCCATCTCCTGAAATTCTCATGTCTTTGGAGGAGTTGGAGAAAACTTTGGATGTTTTTAATATAACCATAGCTAGACAACAGGCAGAAGTTGAGGCAAAGAAAGCTGGATATAAAATTTACAAAGAAGGAGTCAAAGATCCAGAAGATAATGCAGGATGGTTTGGCTGGTTGTGGACTTGGTCAGAATCAAATGCTAATCAACAACAAGATGTGAAGCCTGGAATTCTGGAAGAAATGTTGACACCTGAAGAAAAGTCGTTACTTTATGAAGCAATTGGTTATAGTGAAACAGCAGTTGACCCAACCTTGCCAAAAACATTTGAAGCCTTGAAGTTTTTTGTTCACTTGAAAAGCATGTCTATTGTTCTAAGAGAAAATCACCAAAAGCCGGAGCTGTTAAACGTTGTAGTGGAAGGACTTAGTACTTCTGTTGTGCAAAGACCAGGAGCACAAGCCATAAAATTTGAAACCAAAATTGATTCATTTCATATTACTGGCTTACCAGATGATTTCAAAAAACCCCACCTACTGTCTTCATTGGATGATACGTCACTCCTCCAGATTACATTTGAGATAAATCCTTTAAATGAAACTGTTGCTCAGAGGTGCACCATAGAGGCTGAGCCTCTAGAGATAATATATGATGCAAGGACAGTCAATAGTATAGTGGAGTTCTTCAGACCTCCGAAAGATGTCCATCTAGCCCAACTTACTTCAGTAACTTTGACAAAACTTGAAGAATTTCGAGCAAAAACAGCAACA
Peptide sequence:
METKQQELKRIEKAKQKVFDKEKPREEKQDTFTEKLVTQIIQNLQVQISSIHIRYEDDITNGDKPLSFGISLQNISLQTTDQYWIPCLHDNTEKLVRKLIRLDNLFAYWNVNSEMFYLNDYDESLKALKNGIVNENIVPEGYDFVFRPISASAKLQMNRRSDFDFSDPKINLAVDLHTIAIEFNKPQYFSLMELLESIDMMTQNQPYRKFKPSVPLHLHAKEWWAYAIHSILEVNVCPSLRMWSWEHIRNHRYKMKRYREFYKKKLTSKKPSPEILMSLEELEKTLDVFNITIARQQAEVEAKKAGYKIYKEGVKDPEDNAGWFGWLWTWSESNANQQQDVKPGILEEMLTPEEKSLLYEAIGYSETAVDPTLPKTFEALKFFVHLKSMSIVLRENHQKPELLNVVVEGLSTSVVQRPGAQAIKFETKIDSFHITGLPDDFKKPHLLSSLDDTSLLQITFEINPLNETVAQRCTIEAEPLEIIYDARTVNSIVEFFRPPKDVHLAQLTSVTLTKLEEFRAKTATGAVALKNLVIKENALHELDVPFKVKVGHIGSLKLKIPWKNLYTQPVEAVLEEIFLLIVPSSRIQYDPIKEEKQLMETKQQELKRIEKAKQKVFDKEKPREEKQDTFTEKLVTQIIQNLQVQISSIHIRYEDDITNGDKPLSFGISLQNISLQTTDQYWIPCLHDNTEKLVRKLIRLDNLFAYWNVNSEMFYLNDYDESLKALKNGIVNENIVPEGYDFVFRPISASAKLQMNRRSDFDFSDPKINLAVDLHTIAIEFNKPQYFSLMELLESIDMMTQNQPYRKFKPSVPLHLHAKEWWAYAIHSILEVNVCPSLRMWSWEHIRNHRYKMKRYREFYKKKLTSKKPSPEILMSLEELEKTLDVFNITIARQQAEVEAKKAGYKIYKEGVKDPEDNAGWFGWLWTWSESNANQQQDVKPGILEEMLTPEEKSLLYEAIGYSETAVDPTLPKTFEALKFFVHLKSMSIVLRENHQKPELLNVVVEGLSTSVVQRPGAQAIKFETKIDSFHITGLPDDFKKPHLLSSLDDTSLLQITFEINPLNETVAQRCTIEAEPLEIIYDARTVNSIVEFFRPPKDVHLAQLTSVTLTKLEEFRAKTAT
IRESfinder result
IRESfinder score
0.738857072
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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