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mmu_circBard1_589
Basic information of circular RNA
PanCircBase ID:
mmu_circBard1_589
mm39_Chr. Position ID:
chr1|71085836|71106347|-
Gene name:
Bard1
Transcript:
ENSMUST00000027393.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
9,8,7,6,5
Exon/intron offsets:
0,962,6935,18801,20430
Genomic length:
20511
Exon/intron sizes in nt:
93,133,109,173,81
Flanking exon/introns:
chr1:71070615-71085836|chr1:71106347-71113701
Splice length:
589
Other database IDs:
CIRCpedia: MMU_CIRCpedia_37786, circAtlas: mmu-Bard1_0005
circBase: hsa_circ_0007935, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_39553
Human Ortholog IDs:
Mature spliced Sequence:
GGTGATATACCTTCTGTTGAATACCTCTTGCAAAATGGAAACGACCCAAATGTTAAAGACCATGCTGGATGGACACCGTTGCATGAAGCCTGCAGTCATGGGCACCTGAAGGTAGTGGAGTTGCTGCTCCAGCATAATGCCCTGGTGAACACCCCTGGCTATCAGAATGACTCGCCACTCCACGATGCCGTCAAGAGTGGCCACATCGATATAGTCAAGGTGTTACTGTCCCACGGTGCTTCCAGGAATGCTGTTAACATATTTGGTGTGCGGCCTGTGGACTATACAGACAATGAGAATATAAGATCATTATTGCTGCTGCCAGAGGAGAATGAATCATTCTCAACTAGCCAGTGCTCTATCGTGAACACCGGGCAGCGAAAGAATGGGCCGCTGGTATTTATAGGCAGTGGGCTTTCTTCACAGCAGCAGAAAATGCTCAGCAAACTTGAGACAGTTCTTAAGGCTAAAAAGTGTATGGAATTTGACAGTACAGTAACTCATGTCATTGTTCCTGATGAGGAAGCGCAGAGTACTCTGAAGTGTATGCTTGGGATTCTCAGTGGATGCTGGATCCTGAAGTTTGATT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGATGAGGAAGCGCAGAGT
59.82
CATGACTGCAGGCTTCATGC
59.9
175
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTGATGAGGAAGCGCAGAG
60.53
CATGACTGCAGGCTTCATGC
59.9
176
PCR template sequence:
AGTACAGTAACTCATGTCATTGTTCCTGATGAGGAAGCGCAGAGTACTCTGAAGTGTATGCTTGGGATTCTCAGTGGATGCTGGATCCTGAAGTTTGATTGGTGATATACCTTCTGTTGAATACCTCTTGCAAAATGGAAACGACCCAAATGTTAAAGACCATGCTGGATGGACACCGTTGCATGAAGCCTGCAGTCATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-322-5p(2), mmu-miR-15b-5p(2), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-1904(1), mmu-miR-202-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGAAGTTTGATTGGTGATATACCTT
siRNA sets
GTATATCACCAATCAAACT, TATCACCAATCAAACTTCA, TATATCACCAATCAAACTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCBARD1_589_ORF_1
0.9314
0.036827542
0.096162654
159
ORF sequence:
ATGCTCAGCAAACTTGAGACAGTTCTTAAGGCTAAAAAGTGTATGGAATTTGACAGTACAGTAACTCATGTCATTGTTCCTGATGAGGAAGCGCAGAGTACTCTGAAGTGTATGCTTGGGATTCTCAGTGGATGCTGGATCCTGAAGTTTGATTGGTGA
Peptide sequence:
MLSKLETVLKAKKCMEFDSTVTHVIVPDEEAQSTLKCMLGILSGCWILKFDW
IRESfinder result
IRESfinder score
0.457936411
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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