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mmu_circGapvd1_2311
Basic information of circular RNA
PanCircBase ID:
mmu_circGapvd1_2311
mm39_Chr. Position ID:
chr2|34581117|34617314|-
Gene name:
Gapvd1
Transcript:
ENSMUST00000102800.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
17
Exon/intron indexes:
21,20,19,18,17,16,15,14,13,12,11,10,9,8,7,6,5
Exon/intron offsets:
0,2267,4380,8720,9657,13060,13530,14914,15592,18006,21059,24099,26210,29462,33937,34273,36110
Genomic length:
36197
Exon/intron sizes in nt:
110,130,123,81,88,365,78,120,135,141,174,126,67,161,190,135,87
Flanking exon/introns:
chr2:34580633-34581117|chr2:34617314-34618342
Splice length:
2311
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTGGCCGCCTTTTGCAGCAGCTAGCAATGACTGGCACTGAAGAAGGAGATCCCCGGACCAAAAATAGCCTTGGAAAATTTGACAAAGGCTGTGTCGCTGCTTTCCTTGATGTTGTAATTGGGGGCCGTGCAGTGGAGACTCCGCCAATGTCCTCTGTTAATCTTCTGGAAGGCTTGAGCAGAACTGTGGTGTATATAAGTTACAGTCAGCTTATTACTCTGGTAAATTTTATGAAGAGTGTGATGTCTGGAGATCAACTGAAAGAAGATAGAATGGCTCTTGACAATTTGTTGGCAAACCTGCCCCAGGCTAAGCCAGGGAAGAGCAGCAGTCTGGACATGACTCCCTATAGCACTCCTCAGATGTCTCCAGCAACCACTCCAGCCAACAAGAAGAATCGATTACCTATAGCAACTCGGAGCAGAAGCCGAAGTAATATGTTAATGGACCTACATATGGATCATGAAGGATCATCTCAAGAAACCATCCAGGAGGTACAGCCAGAAGAGGTGCTGGTCATTTCCTTAGGGACAGGCCCTCAGCTCACTCCAGGGATGATGTCAGAAAATGAGGTTCTAAACATGCAGCTTTCGGATGGAGGACAAGGAGATGTCCCTGTTGATGAAAACAAACTCCACGGTCCTTCCAATCGCTCCAATTCGGTGTCTTCTCTCGACCTGGAGGGAGAGTCTGTATCTGAACTTGGGGCAGGACCTTCTGGGAGTAACGGAGTTGAAGCACTGCAGCTGTTAGAGCACGAGCAAGCTACAACACAAGATAATCTTGATGATAAACTGAGGAAGTTTGAGATTCGTGACATGATGGGACTAACAGATGACAGGGACATATCCGAGACTGTGAGTGAGACCTGGAGCACTGATGTCCTGGGAAGTGACTTCGACCCGAACGTTGATGAAGATCGTTTGCAAGAGATTGCAGGTGCAGCAGCAGAGAACGTGTTAGGTAGTTTGCTGTGCCTTCCAGGTTCAGGGTCAGTTCTCCTTGACCCTTGCACTGGCTCTACCATATCAGAGACCACAAGTGAAGCTTGGAGTGTAGAGGTATTGCCAAGTGACTCAGAGGCTCCAGACTTAAAGCAGGAAGAGCGCCTCCAAGAGCTGGAGAGCTGTTCTGGACTGGGCAGCACATCTGATGATACGGATGTCAGGGAGGTCAGTTCCCGCCCCAGCACACCAGGCCTCAGTGTTGTGTCCGGTATAAGTGCTACATCGGAGGATATTCCCAATAAGATCGAAGACCTGAGATCTGAGTGCAGCTCTGATTTTGGGGGCAAAGATTCTGTAACTAGTCCAGATATGGATGACATAGCCCATGGCGCTCATCAGCTGACCTCTCCTCCCTCTCAGTCAGAGTCTCTGCTTGCCATGTTTGATCCACTGTCCTCACATGAAGGGGCCTCTGCTGTGGTAAGGCCAAAGGTTCACTATGCCCGACCCTCGCATCCACCTCCGGATCCTCCAATCCTGGAAGGTGCAGTGGGAGGAAATGAGGCCAGGTTGCCAAACTTTGGCTCTCACGTTTTAACTGCAGCTGAAATGGAGGCGTTCAAGCAGAGACACTCATACCCTGAGAGATTGGTTCGCAGCAGAAGCTCTGATATAGTGTCTTCTGTGCGGCGGCCCATGAGTGACCCCAGCTGGAACCGACGTCCAGGGAATGAAGAACTTCCTCCAGCTGCAGCCACTGGTGCTACTTCTTTGGTGGCTGCACCTCACTCGTCATCTTCGTCCCCGAGTAAGGACTCTTCTAGAGGAGAGACTGAGGAACGCAAGGACAGTGACGATGAGAGGTCAGACAGGAGCAGGCCTTGGTGGAGGAAGCGCTTTGTTTCAGCTATGCCTAAAGCTCCTATACCATTTAGAAAGAAAGAAAAACAAGAAAAAGACAAAGATGATCTGGGTCCTGACAGATTCTCAACACTCACAGATGAGCCCAGCCCTAGGCTCAGTGCTCAAGCTCAGGTTGCTGAAGATATTCTGGACAAGTACCGGAATGCCATTAAACGGACCAGCCCCAGTGAAGGAGCAATGGCAAATGATGAGAGTGCAGAGGTCATGGGTGATGGTGAAAGTGCCCACGACTCTCCTCGTGAGGAAGCACTGCAGAACATCTCAGCCGACGACCTCCCGGACTCCGCCAGCCAGGCAGCCCACCCTCAGGACTCTGCTTTCTCTTACAGAGATGTAAAAAAGAAGCTGAGGCTCGCACTTTGCTCTGCAGACTCTGTGGCCTTCCCAGTGCTAACTCATTCAACAAGGAATGGATTGCCAGACCACACAGACCCAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGCTCTGCAGACTCTGTGG
59.97
AGGCTATTTTTGGTCCGGGG
60.03
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGCTCTGCAGACTCTGTGG
59.97
GGCTATTTTTGGTCCGGGGA
60.03
150
PCR template sequence:
AAGAAGCTGAGGCTCGCACTTTGCTCTGCAGACTCTGTGGCCTTCCCAGTGCTAACTCATTCAACAAGGAATGGATTGCCAGACCACACAGACCCAGAAGGTTGGCCGCCTTTTGCAGCAGCTAGCAATGACTGGCACTGAAGAAGGAGATCCCCGGACCAAAAATAGCCTTGGAAAATTTGACAAAGGCTGTGTCGCTG
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
ACAGACCCAGAAGGTTGGCCGCCTTT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGAPVD1_2311_ORF_1
1.0788
0.218931646
0.999999463
2340
ORF sequence:
ATGGATTGCCAGACCACACAGACCCAGAAGGTTGGCCGCCTTTTGCAGCAGCTAGCAATGACTGGCACTGAAGAAGGAGATCCCCGGACCAAAAATAGCCTTGGAAAATTTGACAAAGGCTGTGTCGCTGCTTTCCTTGATGTTGTAATTGGGGGCCGTGCAGTGGAGACTCCGCCAATGTCCTCTGTTAATCTTCTGGAAGGCTTGAGCAGAACTGTGGTGTATATAAGTTACAGTCAGCTTATTACTCTGGTAAATTTTATGAAGAGTGTGATGTCTGGAGATCAACTGAAAGAAGATAGAATGGCTCTTGACAATTTGTTGGCAAACCTGCCCCAGGCTAAGCCAGGGAAGAGCAGCAGTCTGGACATGACTCCCTATAGCACTCCTCAGATGTCTCCAGCAACCACTCCAGCCAACAAGAAGAATCGATTACCTATAGCAACTCGGAGCAGAAGCCGAAGTAATATGTTAATGGACCTACATATGGATCATGAAGGATCATCTCAAGAAACCATCCAGGAGGTACAGCCAGAAGAGGTGCTGGTCATTTCCTTAGGGACAGGCCCTCAGCTCACTCCAGGGATGATGTCAGAAAATGAGGTTCTAAACATGCAGCTTTCGGATGGAGGACAAGGAGATGTCCCTGTTGATGAAAACAAACTCCACGGTCCTTCCAATCGCTCCAATTCGGTGTCTTCTCTCGACCTGGAGGGAGAGTCTGTATCTGAACTTGGGGCAGGACCTTCTGGGAGTAACGGAGTTGAAGCACTGCAGCTGTTAGAGCACGAGCAAGCTACAACACAAGATAATCTTGATGATAAACTGAGGAAGTTTGAGATTCGTGACATGATGGGACTAACAGATGACAGGGACATATCCGAGACTGTGAGTGAGACCTGGAGCACTGATGTCCTGGGAAGTGACTTCGACCCGAACGTTGATGAAGATCGTTTGCAAGAGATTGCAGGTGCAGCAGCAGAGAACGTGTTAGGTAGTTTGCTGTGCCTTCCAGGTTCAGGGTCAGTTCTCCTTGACCCTTGCACTGGCTCTACCATATCAGAGACCACAAGTGAAGCTTGGAGTGTAGAGGTATTGCCAAGTGACTCAGAGGCTCCAGACTTAAAGCAGGAAGAGCGCCTCCAAGAGCTGGAGAGCTGTTCTGGACTGGGCAGCACATCTGATGATACGGATGTCAGGGAGGTCAGTTCCCGCCCCAGCACACCAGGCCTCAGTGTTGTGTCCGGTATAAGTGCTACATCGGAGGATATTCCCAATAAGATCGAAGACCTGAGATCTGAGTGCAGCTCTGATTTTGGGGGCAAAGATTCTGTAACTAGTCCAGATATGGATGACATAGCCCATGGCGCTCATCAGCTGACCTCTCCTCCCTCTCAGTCAGAGTCTCTGCTTGCCATGTTTGATCCACTGTCCTCACATGAAGGGGCCTCTGCTGTGGTAAGGCCAAAGGTTCACTATGCCCGACCCTCGCATCCACCTCCGGATCCTCCAATCCTGGAAGGTGCAGTGGGAGGAAATGAGGCCAGGTTGCCAAACTTTGGCTCTCACGTTTTAACTGCAGCTGAAATGGAGGCGTTCAAGCAGAGACACTCATACCCTGAGAGATTGGTTCGCAGCAGAAGCTCTGATATAGTGTCTTCTGTGCGGCGGCCCATGAGTGACCCCAGCTGGAACCGACGTCCAGGGAATGAAGAACTTCCTCCAGCTGCAGCCACTGGTGCTACTTCTTTGGTGGCTGCACCTCACTCGTCATCTTCGTCCCCGAGTAAGGACTCTTCTAGAGGAGAGACTGAGGAACGCAAGGACAGTGACGATGAGAGGTCAGACAGGAGCAGGCCTTGGTGGAGGAAGCGCTTTGTTTCAGCTATGCCTAAAGCTCCTATACCATTTAGAAAGAAAGAAAAACAAGAAAAAGACAAAGATGATCTGGGTCCTGACAGATTCTCAACACTCACAGATGAGCCCAGCCCTAGGCTCAGTGCTCAAGCTCAGGTTGCTGAAGATATTCTGGACAAGTACCGGAATGCCATTAAACGGACCAGCCCCAGTGAAGGAGCAATGGCAAATGATGAGAGTGCAGAGGTCATGGGTGATGGTGAAAGTGCCCACGACTCTCCTCGTGAGGAAGCACTGCAGAACATCTCAGCCGACGACCTCCCGGACTCCGCCAGCCAGGCAGCCCACCCTCAGGACTCTGCTTTCTCTTACAGAGATGTAAAAAAGAAGCTGAGGCTCGCACTTTGCTCTGCAGACTCTGTGGCCTTCCCAGTGCTAACTCATTCAACAAGGAATGGATTGCCAGACCACACAGACCCAGAA
Peptide sequence:
MDCQTTQTQKVGRLLQQLAMTGTEEGDPRTKNSLGKFDKGCVAAFLDVVIGGRAVETPPMSSVNLLEGLSRTVVYISYSQLITLVNFMKSVMSGDQLKEDRMALDNLLANLPQAKPGKSSSLDMTPYSTPQMSPATTPANKKNRLPIATRSRSRSNMLMDLHMDHEGSSQETIQEVQPEEVLVISLGTGPQLTPGMMSENEVLNMQLSDGGQGDVPVDENKLHGPSNRSNSVSSLDLEGESVSELGAGPSGSNGVEALQLLEHEQATTQDNLDDKLRKFEIRDMMGLTDDRDISETVSETWSTDVLGSDFDPNVDEDRLQEIAGAAAENVLGSLLCLPGSGSVLLDPCTGSTISETTSEAWSVEVLPSDSEAPDLKQEERLQELESCSGLGSTSDDTDVREVSSRPSTPGLSVVSGISATSEDIPNKIEDLRSECSSDFGGKDSVTSPDMDDIAHGAHQLTSPPSQSESLLAMFDPLSSHEGASAVVRPKVHYARPSHPPPDPPILEGAVGGNEARLPNFGSHVLTAAEMEAFKQRHSYPERLVRSRSSDIVSSVRRPMSDPSWNRRPGNEELPPAAATGATSLVAAPHSSSSSPSKDSSRGETEERKDSDDERSDRSRPWWRKRFVSAMPKAPIPFRKKEKQEKDKDDLGPDRFSTLTDEPSPRLSAQAQVAEDILDKYRNAIKRTSPSEGAMANDESAEVMGDGESAHDSPREEALQNISADDLPDSASQAAHPQDSAFSYRDVKKKLRLALCSADSVAFPVLTHSTRNGLPDHTDPE
IRESfinder result
IRESfinder score
0.378707815
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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