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mmu_circYthdf3_1685
Basic information of circular RNA
PanCircBase ID:
mmu_circYthdf3_1685
mm39_Chr. Position ID:
chr3|16243641|16259588|+
Gene name:
Ythdf3
Transcript:
ENSMUST00000108345.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,4
Exon/intron offsets:
0,14348
Genomic length:
15947
Exon/intron sizes in nt:
8,61,599
Flanking exon/introns:
chr3:16238110-16243641|chr3:16259588-16268118
Splice length:
1685
Other database IDs:
circBase: mmu_circ_0010586, CIRCpedia: MMU_CIRCpedia_11241, circAtlas: mmu-Ythdf3_0001
circBase: hsa_circ_0136874, circAtlas: hsa-YTHDF3_0002, CIRCpedia: HSA_CIRCpedia_61453
Human Ortholog IDs:
Mature spliced Sequence:
TTTCAGTACAAAATGGTTCGATTCATCAAAAAGATGCTGTAAATGATGATGATTTTGAGCCATACTTAAGTAGCCAGACAAATCAGAATAACAGCTATCCACCAATGTCAGATCCATATATGCCTAGTTACTATGCTCCGTCCATTGGATTTCCATATTCTCTTGGGGAAGCAGCATGGTCCACGGCTGGAGATCAGCCTATGCCATATCTGACAACCTATGGACAAATGAGTAATGGAGAACATCATTATATACCAGATGGTGTTTTTAGTCAACCAGGGGCATTAGGAAATACCCCTCCATTTCTTGGTCAACATGGATTTAACTTTTTTCCTGGTAATGCTGATTTCTCTACATGGGGAACAAGTGGATCTCAGGGACAATCAACACAAAATTCTGCTTATAGTAGCAGTTACGGCTATCCACCTAGTTCTCTTGGGAGAGCTATTACTGATGGACAGGCCGGATTTGGCAATGATACTTTGAGTAAGGTGCCTGGCATTAGTAGTATTGAGCAAGGCATGACTGGACTGAAAATTGGTGGTGACCTGACAGCTGCGGTGACGAAAACTGTAGGTACAGCCTTGAGCAGCAGTGGTATGACTAGCATTGCAACCAATAATGTGCCCCCTGTTAGCAGTGCAGCACCTAAACCAACTTCTTGGGCTGCTATTGCCAGAAAGCCTGCAAAACCTCAGCCGAAACTTAAACCCAAGGGCAATGTGGGAATTGGGGGTTCTGCTGTGCCACCACCTCCTATAAAACACAACATGAATATTGGAACTTGGGATGAAAAGGGGTCAGTGGTAAAGGCTCCACCAACCCAACCAGTTCTGCCTCCTCAAACTATAATCCAGCAGCCTCAGCCATTAATTCAACCACCACCATTGGTGCAAAGCCAACTGCCTCAACAGCAGCCTCAGCCACCACAACCACAGCAGCAACAAGGACCTCAGCCACAGGCCCAGCCTCACCAAGTGCAGTCTCAACAGCCACAGTTGCAGAATCGTTGGGTAGCTCCTCGGAATAGGGGAACCGGCTTCAACCAGAACAATGGAACAGGCAGTGAAAACTTTGGTTTAGGTGTTGTGCCTGTTAGTGCTTCACCTTCTAGTGTAGAGGTGCATCCAGTGCTGGAAAAACTAAAGGCCATAAACAATTATAATCCCAAAGACTTTGATTGGAACCTGAAGAATGGACGTGTGTTTATAATTAAGAGCTATTCTGAGGATGATATACATCGTTCCATCAAGTACTCTATCTGGTGTAGTACTGAGCATGGTAATAAGCGTTTGGATGCAGCTTATCGTTCCCTGAATGGGAAAGGCCCACTCTATTTACTCTTCAGTGTGAATGGCAGTGGACATTTTTGTGGAGTGGCTGAAATGAAGTCTGTTGTAGACTATAATGCTTATGCTGGTGTCTGGTCTCAGGATAAGTGGAAGGGCAAATTTGAAGTTAAATGGATCTTTGTCAAAGATGTTCCCAATAACCAATTACGACATATTCGCTTAGAAAATAATGACAACAAACCAGTAACCAATTCAAGGGACACTCAAGAAGTACCCCTAGAAAAAGCAAAGCAAGTGCTTAAAATAATCGCTACTTTCAAGCATACCACCTCAATCTTTGATGACTTTGCACATTATGAAAAGCGTCAAGAGGAGGAGGAAGCCATGCGAAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGCTACTTTCAAGCATACCACC
59.65
TGTCTGGCTACTTAAGTATGGCT
58.97
165
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGCTACTTTCAAGCATACCACC
59.65
GTCTGGCTACTTAAGTATGGCTCA
59.9
164
PCR template sequence:
AGTGCTTAAAATAATCGCTACTTTCAAGCATACCACCTCAATCTTTGATGACTTTGCACATTATGAAAAGCGTCAAGAGGAGGAGGAAGCCATGCGAAGGTTTCAGTACAAAATGGTTCGATTCATCAAAAAGATGCTGTAAATGATGATGATTTTGAGCCATACTTAAGTAGCCAGACAAATCAGAATAACAGCTATCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
18
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-let-7b-5p(1), mmu-miR-135a-5p(1), mmu-miR-19b-3p(1), mmu-miR-204-5p(1), mmu-miR-19a-3p(1), mmu-miR-184-3p(1), mmu-miR-125b-5p(1), mmu-miR-136-5p(1), mmu-miR-351-5p(1), mmu-miR-125a-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-539-5p(1), mmu-miR-335-3p(1), mmu-miR-188-3p(1), mmu-miR-670-5p(1), mmu-miR-296-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGCCATGCGAAGGTTTCAGTACAAAA
siRNA sets
TTTGTACTGAAACCTTCGC, TTTTGTACTGAAACCTTCG, TTGTACTGAAACCTTCGCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCYTHDF3_1685_ORF_1
0.9373
0.078155379
0.999786749
1623
ORF sequence:
ATGTCAGATCCATATATGCCTAGTTACTATGCTCCGTCCATTGGATTTCCATATTCTCTTGGGGAAGCAGCATGGTCCACGGCTGGAGATCAGCCTATGCCATATCTGACAACCTATGGACAAATGAGTAATGGAGAACATCATTATATACCAGATGGTGTTTTTAGTCAACCAGGGGCATTAGGAAATACCCCTCCATTTCTTGGTCAACATGGATTTAACTTTTTTCCTGGTAATGCTGATTTCTCTACATGGGGAACAAGTGGATCTCAGGGACAATCAACACAAAATTCTGCTTATAGTAGCAGTTACGGCTATCCACCTAGTTCTCTTGGGAGAGCTATTACTGATGGACAGGCCGGATTTGGCAATGATACTTTGAGTAAGGTGCCTGGCATTAGTAGTATTGAGCAAGGCATGACTGGACTGAAAATTGGTGGTGACCTGACAGCTGCGGTGACGAAAACTGTAGGTACAGCCTTGAGCAGCAGTGGTATGACTAGCATTGCAACCAATAATGTGCCCCCTGTTAGCAGTGCAGCACCTAAACCAACTTCTTGGGCTGCTATTGCCAGAAAGCCTGCAAAACCTCAGCCGAAACTTAAACCCAAGGGCAATGTGGGAATTGGGGGTTCTGCTGTGCCACCACCTCCTATAAAACACAACATGAATATTGGAACTTGGGATGAAAAGGGGTCAGTGGTAAAGGCTCCACCAACCCAACCAGTTCTGCCTCCTCAAACTATAATCCAGCAGCCTCAGCCATTAATTCAACCACCACCATTGGTGCAAAGCCAACTGCCTCAACAGCAGCCTCAGCCACCACAACCACAGCAGCAACAAGGACCTCAGCCACAGGCCCAGCCTCACCAAGTGCAGTCTCAACAGCCACAGTTGCAGAATCGTTGGGTAGCTCCTCGGAATAGGGGAACCGGCTTCAACCAGAACAATGGAACAGGCAGTGAAAACTTTGGTTTAGGTGTTGTGCCTGTTAGTGCTTCACCTTCTAGTGTAGAGGTGCATCCAGTGCTGGAAAAACTAAAGGCCATAAACAATTATAATCCCAAAGACTTTGATTGGAACCTGAAGAATGGACGTGTGTTTATAATTAAGAGCTATTCTGAGGATGATATACATCGTTCCATCAAGTACTCTATCTGGTGTAGTACTGAGCATGGTAATAAGCGTTTGGATGCAGCTTATCGTTCCCTGAATGGGAAAGGCCCACTCTATTTACTCTTCAGTGTGAATGGCAGTGGACATTTTTGTGGAGTGGCTGAAATGAAGTCTGTTGTAGACTATAATGCTTATGCTGGTGTCTGGTCTCAGGATAAGTGGAAGGGCAAATTTGAAGTTAAATGGATCTTTGTCAAAGATGTTCCCAATAACCAATTACGACATATTCGCTTAGAAAATAATGACAACAAACCAGTAACCAATTCAAGGGACACTCAAGAAGTACCCCTAGAAAAAGCAAAGCAAGTGCTTAAAATAATCGCTACTTTCAAGCATACCACCTCAATCTTTGATGACTTTGCACATTATGAAAAGCGTCAAGAGGAGGAGGAAGCCATGCGAAGGTTTCAGTACAAAATGGTTCGATTCATCAAAAAGATGCTGTAA
Peptide sequence:
MSDPYMPSYYAPSIGFPYSLGEAAWSTAGDQPMPYLTTYGQMSNGEHHYIPDGVFSQPGALGNTPPFLGQHGFNFFPGNADFSTWGTSGSQGQSTQNSAYSSSYGYPPSSLGRAITDGQAGFGNDTLSKVPGISSIEQGMTGLKIGGDLTAAVTKTVGTALSSSGMTSIATNNVPPVSSAAPKPTSWAAIARKPAKPQPKLKPKGNVGIGGSAVPPPPIKHNMNIGTWDEKGSVVKAPPTQPVLPPQTIIQQPQPLIQPPPLVQSQLPQQQPQPPQPQQQQGPQPQAQPHQVQSQQPQLQNRWVAPRNRGTGFNQNNGTGSENFGLGVVPVSASPSSVEVHPVLEKLKAINNYNPKDFDWNLKNGRVFIIKSYSEDDIHRSIKYSIWCSTEHGNKRLDAAYRSLNGKGPLYLLFSVNGSGHFCGVAEMKSVVDYNAYAGVWSQDKWKGKFEVKWIFVKDVPNNQLRHIRLENNDNKPVTNSRDTQEVPLEKAKQVLKIIATFKHTTSIFDDFAHYEKRQEEEEAMRRFQYKMVRFIKKML
IRESfinder result
IRESfinder score
0.582867322
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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