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mmu_circFam20a_815
Basic information of circular RNA
PanCircBase ID:
mmu_circFam20a_815
mm39_Chr. Position ID:
chr11|109566668|109576353|-
Gene name:
Fam20a
Transcript:
ENSMUST00000155559.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
8,7,6,5,4,3,2
Exon/intron offsets:
0,1311,1928,2513,6994,8795,9500
Genomic length:
9685
Exon/intron sizes in nt:
1,10,18,11,16,93,79,51,000
Flanking exon/introns:
chr11:109566013-109566668|chr11:109576353-109612137
Splice length:
815
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ACGGCACAAGATATACAAAGAACAATTCAACCTTACCTCCTTGGATCCCCCGCTCCAGTTTCGACCAGAGGCCAGCTGGGTCCAGTTCCACTTGGGGATCAACAGCCACGGGCTGTACTCCAGGTCCAGCCTTGCCATCAGCAAGCTCCTCCATGACATGAGACACTTCCCCACCATCAGTGCTGATTACAGCCAGGATGAAAAAGCCTTGCTAGGGGCCTGTGACTGCTCACAGATTGTGAAACCCAGTGGGGTCCACCTGAAATTGGTTCTGAGGTTCTCGGACTTCGGGAAAGCCATGTTCAAACCCATGAGACAGCAGCGAGAGGAGGAGACGCCTGAGGACTTCTTCTATTTCATAGACTTTCAGAGACACAATGCTGAGATCGCAGCTTTCCACCTGGACAGGATTCTGGACTTCCGACGGGTACCGCCAACAGTAGGGAGGCTAGTGAATGTCACCAAGGAAATCCTAGAGGTCACCAAGAACGAGATCCTACAGAGTGTGTTCTTTGTGTCTCCAGCTAACAACGTGTGCTTCTTCGCCAAGTGTCCGTACATGTGCAAGACCGAGTACGCTGTCTGTGGCAACCCACACCTGCTGGAAGGCTCCCTCTCCGCCTTCCTGCCATCCCTCAACCTAGCCCCCAGACTGTCTGTGCCCAACCCCTGGATCCGTTCCTACTCGCTGTCAGGAAAAGAGGAGTGGGAGCTCAACCCCCTTTACTGTGACACAGTCAAGCAGATCTACCCGTACAACAGCAGCAACAGACTCCTCGGCATCATTGACATGGCCGTCTTTGACTTCCTGATTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTACCCGTACAACAGCAGCA
60.04
GCCTCTGGTCGAAACTGGAG
60.39
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTACCCGTACAACAGCAGC
59.75
CCTCTGGTCGAAACTGGAGC
60.39
140
PCR template sequence:
AACCCCCTTTACTGTGACACAGTCAAGCAGATCTACCCGTACAACAGCAGCAACAGACTCCTCGGCATCATTGACATGGCCGTCTTTGACTTCCTGATTGACGGCACAAGATATACAAAGAACAATTCAACCTTACCTCCTTGGATCCCCCGCTCCAGTTTCGACCAGAGGCCAGCTGGGTCCAGTTCCACTTGGGGATC
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-181b-5p(1), mmu-miR-370-3p(1), mmu-miR-335-3p(1), mmu-miR-3470b(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GACTTCCTGATTGACGGCACAAGATA
siRNA sets
TATCTTGTGCCGTCAATCA, TCTTGTGCCGTCAATCAGG, ATCTTGTGCCGTCAATCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFAM20A_815_ORF_1
1.0487
0.322106017
0.980084093
819
ORF sequence:
ATGAGACACTTCCCCACCATCAGTGCTGATTACAGCCAGGATGAAAAAGCCTTGCTAGGGGCCTGTGACTGCTCACAGATTGTGAAACCCAGTGGGGTCCACCTGAAATTGGTTCTGAGGTTCTCGGACTTCGGGAAAGCCATGTTCAAACCCATGAGACAGCAGCGAGAGGAGGAGACGCCTGAGGACTTCTTCTATTTCATAGACTTTCAGAGACACAATGCTGAGATCGCAGCTTTCCACCTGGACAGGATTCTGGACTTCCGACGGGTACCGCCAACAGTAGGGAGGCTAGTGAATGTCACCAAGGAAATCCTAGAGGTCACCAAGAACGAGATCCTACAGAGTGTGTTCTTTGTGTCTCCAGCTAACAACGTGTGCTTCTTCGCCAAGTGTCCGTACATGTGCAAGACCGAGTACGCTGTCTGTGGCAACCCACACCTGCTGGAAGGCTCCCTCTCCGCCTTCCTGCCATCCCTCAACCTAGCCCCCAGACTGTCTGTGCCCAACCCCTGGATCCGTTCCTACTCGCTGTCAGGAAAAGAGGAGTGGGAGCTCAACCCCCTTTACTGTGACACAGTCAAGCAGATCTACCCGTACAACAGCAGCAACAGACTCCTCGGCATCATTGACATGGCCGTCTTTGACTTCCTGATTGACGGCACAAGATATACAAAGAACAATTCAACCTTACCTCCTTGGATCCCCCGCTCCAGTTTCGACCAGAGGCCAGCTGGGTCCAGTTCCACTTGGGGATCAACAGCCACGGGCTGTACTCCAGGTCCAGCCTTGCCATCAGCAAGCTCCTCCATGACATGA
Peptide sequence:
MRHFPTISADYSQDEKALLGACDCSQIVKPSGVHLKLVLRFSDFGKAMFKPMRQQREEETPEDFFYFIDFQRHNAEIAAFHLDRILDFRRVPPTVGRLVNVTKEILEVTKNEILQSVFFVSPANNVCFFAKCPYMCKTEYAVCGNPHLLEGSLSAFLPSLNLAPRLSVPNPWIRSYSLSGKEEWELNPLYCDTVKQIYPYNSSNRLLGIIDMAVFDFLIDGTRYTKNNSTLPPWIPRSSFDQRPAGSSSTWGSTATGCTPGPALPSASSSMT
IRESfinder result
IRESfinder score
0.596596478
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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