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mmu_circGtf3a_631
Basic information of circular RNA
PanCircBase ID:
mmu_circGtf3a_631
mm39_Chr. Position ID:
chr5|146887996|146891993|+
Gene name:
Gtf3a
Transcript:
ENSMUST00000146511.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
3,4,5,6,7,8
Exon/intron offsets:
0,687,1540,2040,2661,3937
Genomic length:
3997
Exon/intron sizes in nt:
97,89,74,81,230,60
Flanking exon/introns:
chr5:146887443-146887996|chr5:146891993-146892177
Splice length:
631
Other database IDs:
CIRCpedia: MMU_CIRCpedia_37351, circAtlas: mmu-Gtf3a_0001
circBase: hsa_circ_0029819, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_115129
Human Ortholog IDs:
Mature spliced Sequence:
TTGTGCAGATGATGGCTGTAATCAGAAATTCAACACAAAATCAAACTTGAAGAAACACATTGAACGCAAACATGGAAACCCACAAAAACAGTATGTGTGCAGTTATGAGGGTTGCAAGAAGGCCTTTAAGAAGCACCAGCAGCTGAGAACCCATCAGTGCCAGCACACCAGCGAGCCGCTCTTCAGGTGTACCCACGAGGGATGCGGGAAGCACTTTGCCTCGCCCAGCAGGCTGAAACGGCATGGGAAAGTTCACGAGGGCTACCTGTGTCAAAAGGGATGTTCTTTCATGGGAAAAACGTGGACAGAGCTCCTGAAACACATGAGAGAAGCCCATAAAGAGGACATAACCTGCAATGTATGTCAGAGGATGTTCAAGCGCAGAGATTACCTTAAGCAGCACATGAAGACTCACGCCCCGGAAAGGGATGTGTACCGCTGTCCGCGGCAAGGCTGCGGAAGAACCTACACAACCGTGTTCAACCTGCAGAGCCACATTCTCTCCTTCCACGAGGAAAAGCGCCCATTTGTGTGTGAGCACGCTGGCTGTGGCAAGACATTCGCAATGAAACAGAGTCTCATGAGGCACAGTGTCGTGCACGATCCCGACAAGAAGAGGATGAAGCTCAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGCTGTGGCAAGACATTC
59.48
TGTGGGTTTCCATGTTTGCG
59.61
173
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGCTGTGGCAAGACATTC
59.48
GTGGGTTTCCATGTTTGCGT
59.61
172
PCR template sequence:
GTGTGAGCACGCTGGCTGTGGCAAGACATTCGCAATGAAACAGAGTCTCATGAGGCACAGTGTCGTGCACGATCCCGACAAGAAGAGGATGAAGCTCAAATTGTGCAGATGATGGCTGTAATCAGAAATTCAACACAAAATCAAACTTGAAGAAACACATTGAACGCAAACATGGAAACCCACAAAAACAGTATGTGTGC
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-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-138-5p(1), mmu-miR-431-5p(1), mmu-miR-370-3p(1), mmu-miR-342-3p(1), mmu-miR-377-3p(1), mmu-miR-1198-5p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GATGAAGCTCAAATTGTGCAGATGAT
siRNA sets
ATCATCTGCACAATTTGAG, TCATCTGCACAATTTGAGC, CATCTGCACAATTTGAGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGTF3A_631_ORF_1
0.9462
0.235146605
0.500741742
354
ORF sequence:
ATGGGAAAAACGTGGACAGAGCTCCTGAAACACATGAGAGAAGCCCATAAAGAGGACATAACCTGCAATGTATGTCAGAGGATGTTCAAGCGCAGAGATTACCTTAAGCAGCACATGAAGACTCACGCCCCGGAAAGGGATGTGTACCGCTGTCCGCGGCAAGGCTGCGGAAGAACCTACACAACCGTGTTCAACCTGCAGAGCCACATTCTCTCCTTCCACGAGGAAAAGCGCCCATTTGTGTGTGAGCACGCTGGCTGTGGCAAGACATTCGCAATGAAACAGAGTCTCATGAGGCACAGTGTCGTGCACGATCCCGACAAGAAGAGGATGAAGCTCAAATTGTGCAGATGA
Peptide sequence:
MGKTWTELLKHMREAHKEDITCNVCQRMFKRRDYLKQHMKTHAPERDVYRCPRQGCGRTYTTVFNLQSHILSFHEEKRPFVCEHAGCGKTFAMKQSLMRHSVVHDPDKKRMKLKLCR
IRESfinder result
IRESfinder score
0.293236874
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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