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mmu_circGapvd1_2384
Basic information of circular RNA
PanCircBase ID:
mmu_circGapvd1_2384
mm39_Chr. Position ID:
chr2|34580473|34615525|-
Gene name:
Gapvd1
Transcript:
ENSMUST00000102800.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
17
Exon/intron indexes:
22,21,20,19,18,17,16,15,14,13,12,11,10,9,8,7,6
Exon/intron offsets:
0,644,2911,5024,9364,10301,13704,14174,15558,16236,18650,21703,24743,26854,30106,34581,34917
Genomic length:
35052
Exon/intron sizes in nt:
16,01,10,13,01,23,81,80,00,00,00,00,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr2:34579057-34580473|chr2:34615525-34617227
Splice length:
2384
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GGCTGTGTCGCTGCTTTCCTTGATGTTGTAATTGGGGGCCGTGCAGTGGAGACTCCGCCAATGTCCTCTGTTAATCTTCTGGAAGGCTTGAGCAGAACTGTGGTGTATATAAGTTACAGTCAGCTTATTACTCTGGTAAATTTTATGAAGAGTGTGATGTCTGGAGATCAACTGAAAGAAGATAGAATGGCTCTTGACAATTTGTTGGCAAACCTGCCCCAGGCTAAGCCAGGGAAGAGCAGCAGTCTGGACATGACTCCCTATAGCACTCCTCAGATGTCTCCAGCAACCACTCCAGCCAACAAGAAGAATCGATTACCTATAGCAACTCGGAGCAGAAGCCGAAGTAATATGTTAATGGACCTACATATGGATCATGAAGGATCATCTCAAGAAACCATCCAGGAGGTACAGCCAGAAGAGGTGCTGGTCATTTCCTTAGGGACAGGCCCTCAGCTCACTCCAGGGATGATGTCAGAAAATGAGGTTCTAAACATGCAGCTTTCGGATGGAGGACAAGGAGATGTCCCTGTTGATGAAAACAAACTCCACGGTCCTTCCAATCGCTCCAATTCGGTGTCTTCTCTCGACCTGGAGGGAGAGTCTGTATCTGAACTTGGGGCAGGACCTTCTGGGAGTAACGGAGTTGAAGCACTGCAGCTGTTAGAGCACGAGCAAGCTACAACACAAGATAATCTTGATGATAAACTGAGGAAGTTTGAGATTCGTGACATGATGGGACTAACAGATGACAGGGACATATCCGAGACTGTGAGTGAGACCTGGAGCACTGATGTCCTGGGAAGTGACTTCGACCCGAACGTTGATGAAGATCGTTTGCAAGAGATTGCAGGTGCAGCAGCAGAGAACGTGTTAGGTAGTTTGCTGTGCCTTCCAGGTTCAGGGTCAGTTCTCCTTGACCCTTGCACTGGCTCTACCATATCAGAGACCACAAGTGAAGCTTGGAGTGTAGAGGTATTGCCAAGTGACTCAGAGGCTCCAGACTTAAAGCAGGAAGAGCGCCTCCAAGAGCTGGAGAGCTGTTCTGGACTGGGCAGCACATCTGATGATACGGATGTCAGGGAGGTCAGTTCCCGCCCCAGCACACCAGGCCTCAGTGTTGTGTCCGGTATAAGTGCTACATCGGAGGATATTCCCAATAAGATCGAAGACCTGAGATCTGAGTGCAGCTCTGATTTTGGGGGCAAAGATTCTGTAACTAGTCCAGATATGGATGACATAGCCCATGGCGCTCATCAGCTGACCTCTCCTCCCTCTCAGTCAGAGTCTCTGCTTGCCATGTTTGATCCACTGTCCTCACATGAAGGGGCCTCTGCTGTGGTAAGGCCAAAGGTTCACTATGCCCGACCCTCGCATCCACCTCCGGATCCTCCAATCCTGGAAGGTGCAGTGGGAGGAAATGAGGCCAGGTTGCCAAACTTTGGCTCTCACGTTTTAACTGCAGCTGAAATGGAGGCGTTCAAGCAGAGACACTCATACCCTGAGAGATTGGTTCGCAGCAGAAGCTCTGATATAGTGTCTTCTGTGCGGCGGCCCATGAGTGACCCCAGCTGGAACCGACGTCCAGGGAATGAAGAACTTCCTCCAGCTGCAGCCACTGGTGCTACTTCTTTGGTGGCTGCACCTCACTCGTCATCTTCGTCCCCGAGTAAGGACTCTTCTAGAGGAGAGACTGAGGAACGCAAGGACAGTGACGATGAGAGGTCAGACAGGAGCAGGCCTTGGTGGAGGAAGCGCTTTGTTTCAGCTATGCCTAAAGCTCCTATACCATTTAGAAAGAAAGAAAAACAAGAAAAAGACAAAGATGATCTGGGTCCTGACAGATTCTCAACACTCACAGATGAGCCCAGCCCTAGGCTCAGTGCTCAAGCTCAGGTTGCTGAAGATATTCTGGACAAGTACCGGAATGCCATTAAACGGACCAGCCCCAGTGAAGGAGCAATGGCAAATGATGAGAGTGCAGAGGTCATGGGTGATGGTGAAAGTGCCCACGACTCTCCTCGTGAGGAAGCACTGCAGAACATCTCAGCCGACGACCTCCCGGACTCCGCCAGCCAGGCAGCCCACCCTCAGGACTCTGCTTTCTCTTACAGAGATGTAAAAAAGAAGCTGAGGCTCGCACTTTGCTCTGCAGACTCTGTGGCCTTCCCAGTGCTAACTCATTCAACAAGGAATGGATTGCCAGACCACACAGACCCAGAAGACAATGAAATTGTATGCTTCTTAAAAGTTCAAATAGCTGAAGCAATTAATTTACAAGATAAGAGCTTAATGGCTCAACTTCAAGAAACAATGCGTTGTGTGTGCCGCTTTGACAATAGGACTTGTAGGAAGTTGCTGGCATCCATTGCTGAAGACTACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGTGTGCCGCTTTGACAAT
59.97
AGTTCTGCTCAAGCCTTCCA
59.23
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTGTGTGCCGCTTTGACAAT
59.97
CTGCTCAAGCCTTCCAGAAGA
60
159
PCR template sequence:
AGAGCTTAATGGCTCAACTTCAAGAAACAATGCGTTGTGTGTGCCGCTTTGACAATAGGACTTGTAGGAAGTTGCTGGCATCCATTGCTGAAGACTACAGGGCTGTGTCGCTGCTTTCCTTGATGTTGTAATTGGGGGCCGTGCAGTGGAGACTCCGCCAATGTCCTCTGTTAATCTTCTGGAAGGCTTGAGCAGAACTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
19
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-146a-5p(1), mmu-miR-130a-3p(1), mmu-miR-196a-5p(1), mmu-miR-320-3p(1), mmu-miR-339-5p(1), mmu-miR-503-5p(1), mmu-miR-182-5p(1), mmu-miR-130b-3p(1), mmu-miR-301b-3p(1), mmu-miR-190b-5p(1), mmu-miR-669d-5p(1), mmu-miR-452-3p(1), mmu-miR-490-3p(1), mmu-miR-1904(1), mmu-miR-146b-5p(1), mmu-miR-339-3p(1), mmu-miR-542-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGAAGACTACAGGGCTGTGTCGCTG
siRNA sets
ACAGCCCTGTAGTCTTCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGAPVD1_2384_ORF_1
1.1054
0.196097561
0.999999494
2355
ORF sequence:
ATGTCCTCTGTTAATCTTCTGGAAGGCTTGAGCAGAACTGTGGTGTATATAAGTTACAGTCAGCTTATTACTCTGGTAAATTTTATGAAGAGTGTGATGTCTGGAGATCAACTGAAAGAAGATAGAATGGCTCTTGACAATTTGTTGGCAAACCTGCCCCAGGCTAAGCCAGGGAAGAGCAGCAGTCTGGACATGACTCCCTATAGCACTCCTCAGATGTCTCCAGCAACCACTCCAGCCAACAAGAAGAATCGATTACCTATAGCAACTCGGAGCAGAAGCCGAAGTAATATGTTAATGGACCTACATATGGATCATGAAGGATCATCTCAAGAAACCATCCAGGAGGTACAGCCAGAAGAGGTGCTGGTCATTTCCTTAGGGACAGGCCCTCAGCTCACTCCAGGGATGATGTCAGAAAATGAGGTTCTAAACATGCAGCTTTCGGATGGAGGACAAGGAGATGTCCCTGTTGATGAAAACAAACTCCACGGTCCTTCCAATCGCTCCAATTCGGTGTCTTCTCTCGACCTGGAGGGAGAGTCTGTATCTGAACTTGGGGCAGGACCTTCTGGGAGTAACGGAGTTGAAGCACTGCAGCTGTTAGAGCACGAGCAAGCTACAACACAAGATAATCTTGATGATAAACTGAGGAAGTTTGAGATTCGTGACATGATGGGACTAACAGATGACAGGGACATATCCGAGACTGTGAGTGAGACCTGGAGCACTGATGTCCTGGGAAGTGACTTCGACCCGAACGTTGATGAAGATCGTTTGCAAGAGATTGCAGGTGCAGCAGCAGAGAACGTGTTAGGTAGTTTGCTGTGCCTTCCAGGTTCAGGGTCAGTTCTCCTTGACCCTTGCACTGGCTCTACCATATCAGAGACCACAAGTGAAGCTTGGAGTGTAGAGGTATTGCCAAGTGACTCAGAGGCTCCAGACTTAAAGCAGGAAGAGCGCCTCCAAGAGCTGGAGAGCTGTTCTGGACTGGGCAGCACATCTGATGATACGGATGTCAGGGAGGTCAGTTCCCGCCCCAGCACACCAGGCCTCAGTGTTGTGTCCGGTATAAGTGCTACATCGGAGGATATTCCCAATAAGATCGAAGACCTGAGATCTGAGTGCAGCTCTGATTTTGGGGGCAAAGATTCTGTAACTAGTCCAGATATGGATGACATAGCCCATGGCGCTCATCAGCTGACCTCTCCTCCCTCTCAGTCAGAGTCTCTGCTTGCCATGTTTGATCCACTGTCCTCACATGAAGGGGCCTCTGCTGTGGTAAGGCCAAAGGTTCACTATGCCCGACCCTCGCATCCACCTCCGGATCCTCCAATCCTGGAAGGTGCAGTGGGAGGAAATGAGGCCAGGTTGCCAAACTTTGGCTCTCACGTTTTAACTGCAGCTGAAATGGAGGCGTTCAAGCAGAGACACTCATACCCTGAGAGATTGGTTCGCAGCAGAAGCTCTGATATAGTGTCTTCTGTGCGGCGGCCCATGAGTGACCCCAGCTGGAACCGACGTCCAGGGAATGAAGAACTTCCTCCAGCTGCAGCCACTGGTGCTACTTCTTTGGTGGCTGCACCTCACTCGTCATCTTCGTCCCCGAGTAAGGACTCTTCTAGAGGAGAGACTGAGGAACGCAAGGACAGTGACGATGAGAGGTCAGACAGGAGCAGGCCTTGGTGGAGGAAGCGCTTTGTTTCAGCTATGCCTAAAGCTCCTATACCATTTAGAAAGAAAGAAAAACAAGAAAAAGACAAAGATGATCTGGGTCCTGACAGATTCTCAACACTCACAGATGAGCCCAGCCCTAGGCTCAGTGCTCAAGCTCAGGTTGCTGAAGATATTCTGGACAAGTACCGGAATGCCATTAAACGGACCAGCCCCAGTGAAGGAGCAATGGCAAATGATGAGAGTGCAGAGGTCATGGGTGATGGTGAAAGTGCCCACGACTCTCCTCGTGAGGAAGCACTGCAGAACATCTCAGCCGACGACCTCCCGGACTCCGCCAGCCAGGCAGCCCACCCTCAGGACTCTGCTTTCTCTTACAGAGATGTAAAAAAGAAGCTGAGGCTCGCACTTTGCTCTGCAGACTCTGTGGCCTTCCCAGTGCTAACTCATTCAACAAGGAATGGATTGCCAGACCACACAGACCCAGAAGACAATGAAATTGTATGCTTCTTAAAAGTTCAAATAGCTGAAGCAATTAATTTACAAGATAAGAGCTTAATGGCTCAACTTCAAGAAACAATGCGTTGTGTGTGCCGCTTTGACAATAGGACTTGTAGGAAGTTGCTGGCATCCATTGCTGAAGACTACAGGGCTGTGTCGCTGCTTTCCTTGATGTTGTAA
Peptide sequence:
MSSVNLLEGLSRTVVYISYSQLITLVNFMKSVMSGDQLKEDRMALDNLLANLPQAKPGKSSSLDMTPYSTPQMSPATTPANKKNRLPIATRSRSRSNMLMDLHMDHEGSSQETIQEVQPEEVLVISLGTGPQLTPGMMSENEVLNMQLSDGGQGDVPVDENKLHGPSNRSNSVSSLDLEGESVSELGAGPSGSNGVEALQLLEHEQATTQDNLDDKLRKFEIRDMMGLTDDRDISETVSETWSTDVLGSDFDPNVDEDRLQEIAGAAAENVLGSLLCLPGSGSVLLDPCTGSTISETTSEAWSVEVLPSDSEAPDLKQEERLQELESCSGLGSTSDDTDVREVSSRPSTPGLSVVSGISATSEDIPNKIEDLRSECSSDFGGKDSVTSPDMDDIAHGAHQLTSPPSQSESLLAMFDPLSSHEGASAVVRPKVHYARPSHPPPDPPILEGAVGGNEARLPNFGSHVLTAAEMEAFKQRHSYPERLVRSRSSDIVSSVRRPMSDPSWNRRPGNEELPPAAATGATSLVAAPHSSSSSPSKDSSRGETEERKDSDDERSDRSRPWWRKRFVSAMPKAPIPFRKKEKQEKDKDDLGPDRFSTLTDEPSPRLSAQAQVAEDILDKYRNAIKRTSPSEGAMANDESAEVMGDGESAHDSPREEALQNISADDLPDSASQAAHPQDSAFSYRDVKKKLRLALCSADSVAFPVLTHSTRNGLPDHTDPEDNEIVCFLKVQIAEAINLQDKSLMAQLQETMRCVCRFDNRTCRKLLASIAEDYRAVSLLSLML
IRESfinder result
IRESfinder score
0.397265945
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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