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mmu_circRab3gap2_631
Basic information of circular RNA
PanCircBase ID:
mmu_circRab3gap2_631
mm39_Chr. Position ID:
chr1|184965157|184972957|+
Gene name:
Rab3gap2
Transcript:
ENSMUST00000194740.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
3,4,5,6,7,8,9
Exon/intron offsets:
0,1160,2343,2470,2999,5818,7701
Genomic length:
7800
Exon/intron sizes in nt:
124,82,48,76,102,100,99
Flanking exon/introns:
chr1:184954106-184965157|chr1:184972957-184978832
Splice length:
631
Other database IDs:
CIRCpedia: MMU_CIRCpedia_40097, circAtlas: mmu-Rab3gap2_0002
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_110569
Human Ortholog IDs:
Mature spliced Sequence:
GAAGAAGAAGGAAATACTTCTAAAACACAAAAAAATTCCTGGCTTCAAGAATGTGTTTTATCCTTATCTCCAACCAGTGACCTTATGGTTATAGCTCGGGAGCAGAAGGCCGCATTCCTAGTGCCAAAATGGAAACATGGTGATAAAGGGAAGGAAGAAATGCAGTTTGCTGTTGGTTGGAGCGGCTCCGTAAGTGCAGAGGAAGGGGAGTATGTAACCAGTGCCCTGTGCATCCCACTGGCGAGTCAGAAGAGGAGTTCCACTGGGCGCCCTGACTGGACCTGCATTGTGGTGGGCTTCACATCGGGCTATGTGCGCTTCTACACTGAGAGTGGAGTGCTTTTGCTTGCACAACTTTTGAATGAGGACAAAGTGCTTCAGCTTAAATGCAGGACCTATGAAATCCCAAGACACCCTGGAGTGACTGAGCAGAATGAAGAACTGAGCATCTTATATCCAGCCGCCATTGTGACGATTGATGGATTTAGTCTCTTTCAGTCTCTTCGAGCCTGTCGAAACCAAGTAGCAAAAGCTGCAGCATCAGGCAATGAGAACATTCAGCCACCACCATTAGCTTATAAGAAATGGGGTCTTCAAGATATTGACACCATCATCGATCATGCTAGTATTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGAACATTCAGCCACCACCA
59.52
CCATAAGGTCACTGGTTGGAGA
59.43
169
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCAGCCACCACCATTAGCTT
59.3
CCATAAGGTCACTGGTTGGAGA
59.43
162
PCR template sequence:
GCTGCAGCATCAGGCAATGAGAACATTCAGCCACCACCATTAGCTTATAAGAAATGGGGTCTTCAAGATATTGACACCATCATCGATCATGCTAGTATTGGAAGAAGAAGGAAATACTTCTAAAACACAAAAAAATTCCTGGCTTCAAGAATGTGTTTTATCCTTATCTCCAACCAGTGACCTTATGGTTATAGCTCGGG
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-1904(2), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-96-5p(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CATGCTAGTATTGGAAGAAGAAGGAA
siRNA sets
TTCTTCTTCCAATACTAGC, TTCCTTCTTCTTCCAATAC, TCTTCTTCCAATACTAGCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAB3GAP2_631_ORF_1
0.8419
0.142279649
0.818707123
642
ORF sequence:
ATGCTAGTATTGGAAGAAGAAGGAAATACTTCTAAAACACAAAAAAATTCCTGGCTTCAAGAATGTGTTTTATCCTTATCTCCAACCAGTGACCTTATGGTTATAGCTCGGGAGCAGAAGGCCGCATTCCTAGTGCCAAAATGGAAACATGGTGATAAAGGGAAGGAAGAAATGCAGTTTGCTGTTGGTTGGAGCGGCTCCGTAAGTGCAGAGGAAGGGGAGTATGTAACCAGTGCCCTGTGCATCCCACTGGCGAGTCAGAAGAGGAGTTCCACTGGGCGCCCTGACTGGACCTGCATTGTGGTGGGCTTCACATCGGGCTATGTGCGCTTCTACACTGAGAGTGGAGTGCTTTTGCTTGCACAACTTTTGAATGAGGACAAAGTGCTTCAGCTTAAATGCAGGACCTATGAAATCCCAAGACACCCTGGAGTGACTGAGCAGAATGAAGAACTGAGCATCTTATATCCAGCCGCCATTGTGACGATTGATGGATTTAGTCTCTTTCAGTCTCTTCGAGCCTGTCGAAACCAAGTAGCAAAAGCTGCAGCATCAGGCAATGAGAACATTCAGCCACCACCATTAGCTTATAAGAAATGGGGTCTTCAAGATATTGACACCATCATCGATCATGCTAGTATT
Peptide sequence:
MLVLEEEGNTSKTQKNSWLQECVLSLSPTSDLMVIAREQKAAFLVPKWKHGDKGKEEMQFAVGWSGSVSAEEGEYVTSALCIPLASQKRSSTGRPDWTCIVVGFTSGYVRFYTESGVLLLAQLLNEDKVLQLKCRTYEIPRHPGVTEQNEELSILYPAAIVTIDGFSLFQSLRACRNQVAKAAASGNENIQPPPLAYKKWGLQDIDTIIDHASI
IRESfinder result
IRESfinder score
0.707392194
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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