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mmu_circFam13b_770
Basic information of circular RNA
PanCircBase ID:
mmu_circFam13b_770
mm39_Chr. Position ID:
chr18|34590716|34620192|-
Gene name:
Fam13b
Transcript:
ENSMUST00000040506.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
12,11,10,9,8,7
Exon/intron offsets:
0,4397,5297,7492,15886,29315
Genomic length:
29476
Exon/intron sizes in nt:
2,11,14,84,96,51,36,160
Flanking exon/introns:
chr18:34587836-34590716|chr18:34620192-34627209
Splice length:
770
Other database IDs:
circAtlas: mmu-Fam13b_0087
Human Ortholog IDs:
Mature spliced Sequence:
GTTAATGAACTTTCTGAGGAAGAAGAGGAAGATGAAAAGCTGGAGCATATAGAAGAACTTCCAGAAGAAGGTGTAGAAAAGTCAGCTGGCATGCCAGAGGTGCTGCAGTTAAGGATGACTGAAAACCTTCTGGACTCAGACAGTGTTACAGCATCAACAAGGATTGATGCTGCTGCTGCTACTACTACTAATGCCAGTGATGGTAACATTAAGTGTTCAAAACCTGTGGCTGGTACTACTGCAGATAATGAAGTCATGCAGCAAGATTTTGTATTTGAGGATCAGAAAAATAATGAGTCTGTAGGTATACTGTTAGAGCCTTGTAGTGACCACGGGGATAGTGAAGATGGCTGTCCTGAGAGGAAGGAATATTTATTATGTGACAGTGATAAATTGCCGCACTTGATTCTGGATTCTAGTAGCAAGATACGTGATTTGAATGCCAACACTGAATTGGAAGTAACGGAAGGTCAGAGTGTTGGTGTTCAAGGAGAAGCAGCGTGTATACAGATTGCGCAGTTAGATCTGAAGAACGTTTCTGATGGTGATAAATGGGAAGAGCCGTTTCCTGCATTTAAGTCTTGGCAGGAAGACTGTGAGTCTGGAGAAGCTCAGCTGTCTCCACAGGCTGCCAGGATGACTCACCACCCCCTGGGAGAGGACTGCCCTCCAGTATTATCTCATCGTAGTTTAGATTTTGGGCAAAGCCAACGTTTCCTACATGATCCAGAAGCGTTGGATTTCTCGTCAAAGGCACTTTCCTTCACTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAAAGCCAACGTTTCCTACA
59.66
GGCATGCCAGCTGACTTTTC
60.11
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACATGATCCAGAAGCGTTGG
58.26
GGCATGCCAGCTGACTTTTC
60.11
146
PCR template sequence:
CAGTATTATCTCATCGTAGTTTAGATTTTGGGCAAAGCCAACGTTTCCTACATGATCCAGAAGCGTTGGATTTCTCGTCAAAGGCACTTTCCTTCACTAGGTTAATGAACTTTCTGAGGAAGAAGAGGAAGATGAAAAGCTGGAGCATATAGAAGAACTTCCAGAAGAAGGTGTAGAAAAGTCAGCTGGCATGCCAGAGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-miR-207(2), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-429-3p(1), mmu-miR-200c-3p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-503-5p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-335-3p(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
TTTCCTTCACTAGGTTAATGAACTTT
siRNA sets
AAAGTTCATTAACCTAGTG, ATTAACCTAGTGAAGGAAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFAM13B_770_ORF_1
1.156
0.0693855
0.919583448
732
ORF sequence:
ATGCCAGAGGTGCTGCAGTTAAGGATGACTGAAAACCTTCTGGACTCAGACAGTGTTACAGCATCAACAAGGATTGATGCTGCTGCTGCTACTACTACTAATGCCAGTGATGGTAACATTAAGTGTTCAAAACCTGTGGCTGGTACTACTGCAGATAATGAAGTCATGCAGCAAGATTTTGTATTTGAGGATCAGAAAAATAATGAGTCTGTAGGTATACTGTTAGAGCCTTGTAGTGACCACGGGGATAGTGAAGATGGCTGTCCTGAGAGGAAGGAATATTTATTATGTGACAGTGATAAATTGCCGCACTTGATTCTGGATTCTAGTAGCAAGATACGTGATTTGAATGCCAACACTGAATTGGAAGTAACGGAAGGTCAGAGTGTTGGTGTTCAAGGAGAAGCAGCGTGTATACAGATTGCGCAGTTAGATCTGAAGAACGTTTCTGATGGTGATAAATGGGAAGAGCCGTTTCCTGCATTTAAGTCTTGGCAGGAAGACTGTGAGTCTGGAGAAGCTCAGCTGTCTCCACAGGCTGCCAGGATGACTCACCACCCCCTGGGAGAGGACTGCCCTCCAGTATTATCTCATCGTAGTTTAGATTTTGGGCAAAGCCAACGTTTCCTACATGATCCAGAAGCGTTGGATTTCTCGTCAAAGGCACTTTCCTTCACTAGGTTAATGAACTTTCTGAGGAAGAAGAGGAAGATGAAAAGCTGGAGCATATAG
Peptide sequence:
MPEVLQLRMTENLLDSDSVTASTRIDAAAATTTNASDGNIKCSKPVAGTTADNEVMQQDFVFEDQKNNESVGILLEPCSDHGDSEDGCPERKEYLLCDSDKLPHLILDSSSKIRDLNANTELEVTEGQSVGVQGEAACIQIAQLDLKNVSDGDKWEEPFPAFKSWQEDCESGEAQLSPQAARMTHHPLGEDCPPVLSHRSLDFGQSQRFLHDPEALDFSSKALSFTRLMNFLRKKRKMKSWSI
IRESfinder result
IRESfinder score
0.45116648
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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