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mmu_circFam13b_731
Basic information of circular RNA
PanCircBase ID:
mmu_circFam13b_731
mm39_Chr. Position ID:
chr18|34596013|34627829|-
Gene name:
Fam13b
Transcript:
ENSMUST00000040506.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
10,9,8,7,6,5
Exon/intron offsets:
0,2195,10589,24018,31196,31638
Genomic length:
31816
Exon/intron sizes in nt:
4,96,51,36,16,11,42,170
Flanking exon/introns:
chr18:34595261-34596013|chr18:34627829-34630386
Splice length:
731
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATTATAATAATGAAGATGAATTTGGAAGAAAGTTGAGGTTCCTCTTGCAACAGCTTCCACCTGTTAATTACAGTTTGTTAAAGTTTCTGTGTAGGTTTTTAGCCAATGTAGCATCACATCATGAAGAAATTTGGTCTGCAAATTCTTTGGCTGCTGTTTTTGGTCCAGATGTCTTCCACATTTACACGGATGTGGAAGATATGAAAGAGCAGGAAATTGTGAGCAGGATAATGGCGGGACTTCTAGAAAATTATTACGAGTTTTTTGAGAATGAAGAGGAAGATTTTTCATCAAATGATTTGAGTTCAATTACTGAGCAGGTTAATGAACTTTCTGAGGAAGAAGAGGAAGATGAAAAGCTGGAGCATATAGAAGAACTTCCAGAAGAAGGTGTAGAAAAGTCAGCTGGCATGCCAGAGGTGCTGCAGTTAAGGATGACTGAAAACCTTCTGGACTCAGACAGTGTTACAGCATCAACAAGGATTGATGCTGCTGCTGCTACTACTACTAATGCCAGTGATGGTAACATTAAGTGTTCAAAACCTGTGGCTGGTACTACTGCAGATAATGAAGTCATGCAGCAAGATTTTGTATTTGAGGATCAGAAAAATAATGAGTCTGTAGGTATACTGTTAGAGCCTTGTAGTGACCACGGGGATAGTGAAGATGGCTGTCCTGAGAGGAAGGAATATTTATTATGTGACAGTGATAAATTGCCGCACTTGATTCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTGACCACGGGGATAGTGA
59.96
TGGAAGCTGTTGCAAGAGGA
59.53
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTGACCACGGGGATAGTGA
59.96
AGCTGTTGCAAGAGGAACCT
59.52
142
PCR template sequence:
GTTAGAGCCTTGTAGTGACCACGGGGATAGTGAAGATGGCTGTCCTGAGAGGAAGGAATATTTATTATGTGACAGTGATAAATTGCCGCACTTGATTCTGATTATAATAATGAAGATGAATTTGGAAGAAAGTTGAGGTTCCTCTTGCAACAGCTTCCACCTGTTAATTACAGTTTGTTAAAGTTTCTGTGTAGGTTTTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-221-3p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-222-3p(1), mmu-miR-503-5p(1), mmu-miR-433-3p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCACTTGATTCTGATTATAATAATGA
siRNA sets
ATTATTATAATCAGAATCA, ATTATAATCAGAATCAAGT, TATTATAATCAGAATCAAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFAM13B_731_ORF_1
1.1705
0.134812367
0.823797836
567
ORF sequence:
ATGAAAGAGCAGGAAATTGTGAGCAGGATAATGGCGGGACTTCTAGAAAATTATTACGAGTTTTTTGAGAATGAAGAGGAAGATTTTTCATCAAATGATTTGAGTTCAATTACTGAGCAGGTTAATGAACTTTCTGAGGAAGAAGAGGAAGATGAAAAGCTGGAGCATATAGAAGAACTTCCAGAAGAAGGTGTAGAAAAGTCAGCTGGCATGCCAGAGGTGCTGCAGTTAAGGATGACTGAAAACCTTCTGGACTCAGACAGTGTTACAGCATCAACAAGGATTGATGCTGCTGCTGCTACTACTACTAATGCCAGTGATGGTAACATTAAGTGTTCAAAACCTGTGGCTGGTACTACTGCAGATAATGAAGTCATGCAGCAAGATTTTGTATTTGAGGATCAGAAAAATAATGAGTCTGTAGGTATACTGTTAGAGCCTTGTAGTGACCACGGGGATAGTGAAGATGGCTGTCCTGAGAGGAAGGAATATTTATTATGTGACAGTGATAAATTGCCGCACTTGATTCTGATTATAATAATGAAGATGAATTTGGAAGAAAGTTGA
Peptide sequence:
MKEQEIVSRIMAGLLENYYEFFENEEEDFSSNDLSSITEQVNELSEEEEEDEKLEHIEELPEEGVEKSAGMPEVLQLRMTENLLDSDSVTASTRIDAAAATTTNASDGNIKCSKPVAGTTADNEVMQQDFVFEDQKNNESVGILLEPCSDHGDSEDGCPERKEYLLCDSDKLPHLILIIIMKMNLEES
IRESfinder result
IRESfinder score
0.557562425
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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