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mmu_circGramd3_420
Basic information of circular RNA
PanCircBase ID:
mmu_circGramd3_420
mm39_Chr. Position ID:
chr18|56609674|56618528|+
Gene name:
Gramd3
Transcript:
ENSMUST00000237355.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
5,6,7,8,9
Exon/intron offsets:
0,2246,6018,8609,8773
Genomic length:
8854
Exon/intron sizes in nt:
67,104,96,72,81
Flanking exon/introns:
chr18:56607202-56609674|chr18:56618528-56621822
Splice length:
420
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_101547
Human Ortholog IDs:
Mature spliced Sequence:
TACAAGGCGAACATGCACTTTCACAAGTTATTCCTGGATGTCCCAACTGAGGAGCCACTGAGGCAAAGCTTTACCTGTGCTCTTCAGAAAGAAATTCTGTACCAAGGAAAGCTCTTTGTGTCGGAAAACTGGATTTGTTTTCATTCCAAGGTCTTTGGAAAAGACACTAAGATCTCCATTCCAGCTTTCTCGGTAACCTTGATCAAGAAAACCAAAACTGCCCTTCTGGTGCCAAACGCCCTGATCATCGCGACGGTCACAGACAGGTACATATTCGTTTCCTTGCTGTCCAGAGACTCAACCTACAAACTGATAAAATCTGTGTGCGGACACTTAGAGAACACAAGTGTTGGTAACAGTCCCAACCCATCTTCTGCTGAAAACAGTTTCCGGGCAGATCGCCCTTCGTCTCTGCCTCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCAACCCATCTTCTGCTGA
59.67
AGCACAGGTAAAGCTTTGCC
59.04
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCCAACCCATCTTCTGCTG
59.67
AGCACAGGTAAAGCTTTGCC
59.04
142
PCR template sequence:
TGTGTGCGGACACTTAGAGAACACAAGTGTTGGTAACAGTCCCAACCCATCTTCTGCTGAAAACAGTTTCCGGGCAGATCGCCCTTCGTCTCTGCCTCTGTACAAGGCGAACATGCACTTTCACAAGTTATTCCTGGATGTCCCAACTGAGGAGCCACTGAGGCAAAGCTTTACCTGTGCTCTTCAGAAAGAAATTCTGT
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-93-5p(1), mmu-miR-709(1), mmu-miR-320-3p(1), mmu-miR-96-5p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTCTCTGCCTCTGTACAAGGCGAACA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGRAMD3_420_ORF_1
0.9642
0.143467614
0.956562059
828
ORF sequence:
ATGCACTTTCACAAGTTATTCCTGGATGTCCCAACTGAGGAGCCACTGAGGCAAAGCTTTACCTGTGCTCTTCAGAAAGAAATTCTGTACCAAGGAAAGCTCTTTGTGTCGGAAAACTGGATTTGTTTTCATTCCAAGGTCTTTGGAAAAGACACTAAGATCTCCATTCCAGCTTTCTCGGTAACCTTGATCAAGAAAACCAAAACTGCCCTTCTGGTGCCAAACGCCCTGATCATCGCGACGGTCACAGACAGGTACATATTCGTTTCCTTGCTGTCCAGAGACTCAACCTACAAACTGATAAAATCTGTGTGCGGACACTTAGAGAACACAAGTGTTGGTAACAGTCCCAACCCATCTTCTGCTGAAAACAGTTTCCGGGCAGATCGCCCTTCGTCTCTGCCTCTGTACAAGGCGAACATGCACTTTCACAAGTTATTCCTGGATGTCCCAACTGAGGAGCCACTGAGGCAAAGCTTTACCTGTGCTCTTCAGAAAGAAATTCTGTACCAAGGAAAGCTCTTTGTGTCGGAAAACTGGATTTGTTTTCATTCCAAGGTCTTTGGAAAAGACACTAAGATCTCCATTCCAGCTTTCTCGGTAACCTTGATCAAGAAAACCAAAACTGCCCTTCTGGTGCCAAACGCCCTGATCATCGCGACGGTCACAGACAGGTACATATTCGTTTCCTTGCTGTCCAGAGACTCAACCTACAAACTGATAAAATCTGTGTGCGGACACTTAGAGAACACAAGTGTTGGTAACAGTCCCAACCCATCTTCTGCTGAAAACAGTTTCCGGGCAGATCGCCCTTCGTCTCTGCCTCTG
Peptide sequence:
MHFHKLFLDVPTEEPLRQSFTCALQKEILYQGKLFVSENWICFHSKVFGKDTKISIPAFSVTLIKKTKTALLVPNALIIATVTDRYIFVSLLSRDSTYKLIKSVCGHLENTSVGNSPNPSSAENSFRADRPSSLPLYKANMHFHKLFLDVPTEEPLRQSFTCALQKEILYQGKLFVSENWICFHSKVFGKDTKISIPAFSVTLIKKTKTALLVPNALIIATVTDRYIFVSLLSRDSTYKLIKSVCGHLENTSVGNSPNPSSAENSFRADRPSSLPL
IRESfinder result
IRESfinder score
0.616602746
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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