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mmu_circGigyf2_552
Basic information of circular RNA
PanCircBase ID:
mmu_circGigyf2_552
mm39_Chr. Position ID:
chr1|87334723|87335445|+
Gene name:
Gigyf2
Transcript:
ENSMUST00000172794.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
10,11,12
Exon/intron offsets:
0,291,533
Genomic length:
722
Exon/intron sizes in nt:
20,01,63,189
Flanking exon/introns:
chr1:87331568-87334723|chr1:87335445-87338383
Splice length:
552
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GCTGGCGGGAACACATGGAACGCCGTCGGAGGTTTGAGTTTGATTTTCGAGACCGAGATGATGAGCGTGGTTACCGAAGGGTGCGCTCTGGCAGTGGGAGCATAGATGACGACAGGGATAGCTTGCCGGAGTGGTGCTTAGAGGATGCTGAGGAAGAAATGGGCACGTTTGACTCTTCTGGGGCATTCCTCTCTCTAAAAAAAGTGCAGAAAGAACCTATTCCTGAAGAGCAGGAAATGGACTTTAGGCCTGTGGAGGAGGGAGAGGAGCGCTCTGACTCTGACAGCAGCCATAACGAAGAGGCCAAAGAACCGGATAAGACAAACCGAAGAGAGGGGGAGAAAACAGACAGAGCAGGGGCTGAAGCTAGTGAGGAAGTACCTCAGACGTCATTGTCATCTGCTAGACCAGGTACCCCTTCAGATCATCAGCCTCAAGAAGCCACACAGTTTGAGAGGAAAGATGAACCCAAAGCTGAACAAGTGGAAAAGGCTGAAGAAGAGAATCGGTCAGAAAATAGTCTCTCAGCCAAGGTCCCCAGCAGAGGGGATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCCAAAGCTGAACAAGTGGA
60.06
CCTTCGGTAACCACGCTCAT
60.11
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCCAAAGCTGAACAAGTGGA
60.06
AACCACGCTCATCATCTCGG
60.18
158
PCR template sequence:
GAGAGGAAAGATGAACCCAAAGCTGAACAAGTGGAAAAGGCTGAAGAAGAGAATCGGTCAGAAAATAGTCTCTCAGCCAAGGTCCCCAGCAGAGGGGATGGCTGGCGGGAACACATGGAACGCCGTCGGAGGTTTGAGTTTGATTTTCGAGACCGAGATGATGAGCGTGGTTACCGAAGGGTGCGCTCTGGCAGTGGGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-339-5p(1), mmu-miR-1198-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGCAGAGGGGATGGCTGGCGGGAACA
siRNA sets
TGTTCCCGCCAGCCATCCC, GTTCCCGCCAGCCATCCCC, TTCCCGCCAGCCATCCCCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGIGYF2_552_ORF_1
1.1441
0.368278779
0.998020669
1089
ORF sequence:
ATGGAACGCCGTCGGAGGTTTGAGTTTGATTTTCGAGACCGAGATGATGAGCGTGGTTACCGAAGGGTGCGCTCTGGCAGTGGGAGCATAGATGACGACAGGGATAGCTTGCCGGAGTGGTGCTTAGAGGATGCTGAGGAAGAAATGGGCACGTTTGACTCTTCTGGGGCATTCCTCTCTCTAAAAAAAGTGCAGAAAGAACCTATTCCTGAAGAGCAGGAAATGGACTTTAGGCCTGTGGAGGAGGGAGAGGAGCGCTCTGACTCTGACAGCAGCCATAACGAAGAGGCCAAAGAACCGGATAAGACAAACCGAAGAGAGGGGGAGAAAACAGACAGAGCAGGGGCTGAAGCTAGTGAGGAAGTACCTCAGACGTCATTGTCATCTGCTAGACCAGGTACCCCTTCAGATCATCAGCCTCAAGAAGCCACACAGTTTGAGAGGAAAGATGAACCCAAAGCTGAACAAGTGGAAAAGGCTGAAGAAGAGAATCGGTCAGAAAATAGTCTCTCAGCCAAGGTCCCCAGCAGAGGGGATGGCTGGCGGGAACACATGGAACGCCGTCGGAGGTTTGAGTTTGATTTTCGAGACCGAGATGATGAGCGTGGTTACCGAAGGGTGCGCTCTGGCAGTGGGAGCATAGATGACGACAGGGATAGCTTGCCGGAGTGGTGCTTAGAGGATGCTGAGGAAGAAATGGGCACGTTTGACTCTTCTGGGGCATTCCTCTCTCTAAAAAAAGTGCAGAAAGAACCTATTCCTGAAGAGCAGGAAATGGACTTTAGGCCTGTGGAGGAGGGAGAGGAGCGCTCTGACTCTGACAGCAGCCATAACGAAGAGGCCAAAGAACCGGATAAGACAAACCGAAGAGAGGGGGAGAAAACAGACAGAGCAGGGGCTGAAGCTAGTGAGGAAGTACCTCAGACGTCATTGTCATCTGCTAGACCAGGTACCCCTTCAGATCATCAGCCTCAAGAAGCCACACAGTTTGAGAGGAAAGATGAACCCAAAGCTGAACAAGTGGAAAAGGCTGAAGAAGAGAATCGGTCAGAAAATAGTCTCTCAGCCAAGGTCCCCAGCAGAGGGGAT
Peptide sequence:
MERRRRFEFDFRDRDDERGYRRVRSGSGSIDDDRDSLPEWCLEDAEEEMGTFDSSGAFLSLKKVQKEPIPEEQEMDFRPVEEGEERSDSDSSHNEEAKEPDKTNRREGEKTDRAGAEASEEVPQTSLSSARPGTPSDHQPQEATQFERKDEPKAEQVEKAEEENRSENSLSAKVPSRGDGWREHMERRRRFEFDFRDRDDERGYRRVRSGSGSIDDDRDSLPEWCLEDAEEEMGTFDSSGAFLSLKKVQKEPIPEEQEMDFRPVEEGEERSDSDSSHNEEAKEPDKTNRREGEKTDRAGAEASEEVPQTSLSSARPGTPSDHQPQEATQFERKDEPKAEQVEKAEEENRSENSLSAKVPSRGD
IRESfinder result
IRESfinder score
0.36364636
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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