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mmu_circFam20c_467
Basic information of circular RNA
PanCircBase ID:
mmu_circFam20c_467
mm39_Chr. Position ID:
chr5|138743555|138780864|+
Gene name:
Fam20c
Transcript:
ENSMUST00000026972.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
2,3,4,5
Exon/intron offsets:
0,8828,35386,37193
Genomic length:
37309
Exon/intron sizes in nt:
1,79,79,93,116
Flanking exon/introns:
chr5:138741980-138743555|chr5:138780864-138791961
Splice length:
467
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GCCGCATGAAGGTGCTGAAGGCGCAGAATTCTTGCCCACTGGTGAGGCAGCTGTGAACCTCTATCCCAACTGGCTCAAATTCCACATTGGCATCAACCGGTATGAGCTGTACTCCAGACACAACCCAGCCATCGATGCCTTACTGCGGGACCTCGGCTCTCAGAAGATCACCAGCGTCGCCATGAAGTCAGGGGGCACGCAGCTGAAGCTCATCATGACCTTCCAGAATTACGGGCAGGCGCTATTCAAACCCATGAAGCAGACGAGAGAGCAGGAGACGCCGCCTGACTTTTTTTATTTCTCTGACTATGAGAGGCACAATGCGGAGATCGCTGCCTTCCACCTGGACAGGATCCTGGATTTCCGCAGAGTCCCTCCAGTGGCTGGTAGGATGATCAACATGACCAAGGAGATCCGGGATGTGACGCGGGATAAGAAGCTATGGAGAACTTTCTTTGTGTCTCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGACCAAGGAGATCCGGGAT
60.03
CGGTTGATGCCAATGTGGAA
59.11
165
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATGACCAAGGAGATCCGGGA
60.03
CGGTTGATGCCAATGTGGAA
59.11
166
PCR template sequence:
AGAGTCCCTCCAGTGGCTGGTAGGATGATCAACATGACCAAGGAGATCCGGGATGTGACGCGGGATAAGAAGCTATGGAGAACTTTCTTTGTGTCTCCAGGCCGCATGAAGGTGCTGAAGGCGCAGAATTCTTGCCCACTGGTGAGGCAGCTGTGAACCTCTATCCCAACTGGCTCAAATTCCACATTGGCATCAACCGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(1), mmu-miR-31-5p(1), mmu-miR-433-3p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTGTGTCTCCAGGCCGCATGAAGGT
siRNA sets
TTCATGCGGCCTGGAGACA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFAM20C_467_ORF_1
1.1657
0.429570769
0.901108358
492
ORF sequence:
ATGGAGAACTTTCTTTGTGTCTCCAGGCCGCATGAAGGTGCTGAAGGCGCAGAATTCTTGCCCACTGGTGAGGCAGCTGTGAACCTCTATCCCAACTGGCTCAAATTCCACATTGGCATCAACCGGTATGAGCTGTACTCCAGACACAACCCAGCCATCGATGCCTTACTGCGGGACCTCGGCTCTCAGAAGATCACCAGCGTCGCCATGAAGTCAGGGGGCACGCAGCTGAAGCTCATCATGACCTTCCAGAATTACGGGCAGGCGCTATTCAAACCCATGAAGCAGACGAGAGAGCAGGAGACGCCGCCTGACTTTTTTTATTTCTCTGACTATGAGAGGCACAATGCGGAGATCGCTGCCTTCCACCTGGACAGGATCCTGGATTTCCGCAGAGTCCCTCCAGTGGCTGGTAGGATGATCAACATGACCAAGGAGATCCGGGATGTGACGCGGGATAAGAAGCTATGGAGAACTTTCTTTGTGTCTCCA
Peptide sequence:
MENFLCVSRPHEGAEGAEFLPTGEAAVNLYPNWLKFHIGINRYELYSRHNPAIDALLRDLGSQKITSVAMKSGGTQLKLIMTFQNYGQALFKPMKQTREQETPPDFFYFSDYERHNAEIAAFHLDRILDFRRVPPVAGRMINMTKEIRDVTRDKKLWRTFFVSP
IRESfinder result
IRESfinder score
0.356871472
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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