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mmu_circGtf2h3_476
Basic information of circular RNA
PanCircBase ID:
mmu_circGtf2h3_476
mm39_Chr. Position ID:
chr5|124720510|124728441|+
Gene name:
Gtf2h3
Transcript:
ENSMUST00000031333.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
2,3,4,5,6,7
Exon/intron offsets:
0,1486,1688,6177,6923,7902
Genomic length:
7931
Exon/intron sizes in nt:
80,107,167,63,30,29
Flanking exon/introns:
chr5:124717264-124720510|chr5:124728441-124728931
Splice length:
476
Other database IDs:
circAtlas: mmu-Gtf2h3_0003
Human Ortholog IDs:
Mature spliced Sequence:
AAGATGAGTTGAACCTTCTGGTGATCATAGTTGACACCAACCCGATTTGGTGGGGAAAGCAAGCATTAAAGGAATCTCAGTTTACTTTATCCAAATGCATGGATGCAGTGATGGTGCTGGCGAATTCTCACCTGTTCATGAACCGCTCCAACCAGCTGGCTGTCATCGCCAGTCACATTCAGGAAAGCCGGCTCTTATACCCGGGGAAGAACGGTGGACTTGGAGACTTCTTCGGAGACCCTGGCAATGCGCTCCCCGACTGTAACCCCTCTGGGAGTAAAGATGGGAAATACGAGCTGTTGACAGTTGCAAACGAGGTGATCGCTGAGGAGATCAAGGATCTGATGACCAAGAGTGACATCAAGGGCCAGCATACGGAGACACTACTGGCAGGATCCCTGGCCAAAGCTCTGTGCTACATTCACAGAGTGAACAAGGCAGTTAAAGATAATCAGGAGATGAAATCAAGGATTTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACACTACTGGCAGGATCCCT
59.96
TTTCCCCACCAAATCGGGTT
59.81
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACACTACTGGCAGGATCCCT
59.96
CTTTCCCCACCAAATCGGGT
60.25
155
PCR template sequence:
GGAGACACTACTGGCAGGATCCCTGGCCAAAGCTCTGTGCTACATTCACAGAGTGAACAAGGCAGTTAAAGATAATCAGGAGATGAAATCAAGGATTTTGAAGATGAGTTGAACCTTCTGGTGATCATAGTTGACACCAACCCGATTTGGTGGGGAAAGCAAGCATTAAAGGAATCTCAGTTTACTTTATCCAAATGCAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-134-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-328-3p(1), mmu-miR-541-5p(1), mmu-miR-362-5p(1), mmu-miR-3470b(1), mmu-miR-542-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATCAAGGATTTTGAAGATGAGTTGAA
siRNA sets
AACTCATCTTCAAAATCCT, CAACTCATCTTCAAAATCC, TCATCTTCAAAATCCTTGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGTF2H3_476_ORF_1
1.267
0.391349854
0.818354539
390
ORF sequence:
ATGGATGCAGTGATGGTGCTGGCGAATTCTCACCTGTTCATGAACCGCTCCAACCAGCTGGCTGTCATCGCCAGTCACATTCAGGAAAGCCGGCTCTTATACCCGGGGAAGAACGGTGGACTTGGAGACTTCTTCGGAGACCCTGGCAATGCGCTCCCCGACTGTAACCCCTCTGGGAGTAAAGATGGGAAATACGAGCTGTTGACAGTTGCAAACGAGGTGATCGCTGAGGAGATCAAGGATCTGATGACCAAGAGTGACATCAAGGGCCAGCATACGGAGACACTACTGGCAGGATCCCTGGCCAAAGCTCTGTGCTACATTCACAGAGTGAACAAGGCAGTTAAAGATAATCAGGAGATGAAATCAAGGATTTTGAAGATGAGTTGA
Peptide sequence:
MDAVMVLANSHLFMNRSNQLAVIASHIQESRLLYPGKNGGLGDFFGDPGNALPDCNPSGSKDGKYELLTVANEVIAEEIKDLMTKSDIKGQHTETLLAGSLAKALCYIHRVNKAVKDNQEMKSRILKMS
IRESfinder result
IRESfinder score
0.300912995
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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