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mmu_circTdrd3_1548
Basic information of circular RNA
PanCircBase ID:
mmu_circTdrd3_1548
mm39_Chr. Position ID:
chr14|87718169|87749206|+
Gene name:
Tdrd3
Transcript:
ENSMUST00000168275.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
7,8,9,10,11,12
Exon/intron offsets:
0,4825,5458,6428,25025,30911
Genomic length:
31037
Exon/intron sizes in nt:
1,50,14,11,57,12,68,48,000
Flanking exon/introns:
chr14:87714897-87718169|chr14:87749206-87776832
Splice length:
1548
Other database IDs:
CIRCpedia: MMU_CIRCpedia_39270, circAtlas: mmu-Tdrd3_0015
circAtlas: hsa-TDRD3_0026
Human Ortholog IDs:
Mature spliced Sequence:
AAGTGTGCATCTAACGTCCAAGTGGATAGCAGAGAGCTTGATCGAAGAAAGACATTACAAGTTTCCCTGCCTGCCAAGCCTGCAAATGATAATGATGAATTTGAAAAGCAAAGAACTGCTGCCATTGCAGAGGTTGCAAAGAGCAAAGAGACCAAGACATTTGGAGGAGGTGGAGGTGGTGCCAGAAGTAATCTCAATATTGGTGCTGCTGGTCACCGAAATAGGGAGGTTTTACAGAAGGAAAAGGCTTCCAAGTCAGAGAGCAAGAACGAAGGTGTCTATAGAGAATTGGTTGATGAGAAAGCCCTGAAACACATAACAGAAATGGGCTTCAGTAAGGAGGCCTCAAGGCAAGCGCTGATGGATAATGCCAACAACTTAGAAGCAGCACTGAATGTCCTTCTGAACAGCAGTAAACAGAAGCCTGCTGTGGGCCCTCCTGCTAGAGGAAGAGGGAAAGGCAGGGGTCGAGGACGATCAGAAGATGAGGAAGACCTGGGAACCGCAAGACCGTCAGCACCAAGCACGTTATTTGATTTCTTGGAGTCTAAAATGGGAACTCTGAATGTGGAAGAACCTAAGTCACAGCCACAGCACCTTCATCAAGGACAGCACAGAGGATGGAATGCCGAGCAAAATGGGATGAAGGACGGCACTCAGTCAAGACATCTTCCTCGAAACGATACCAGGCAGCCAAGAAATGAGAGGCCACCTCGCTTTCAAAAAGACACCCCAACTTCCAAGTCAACTGTAGAAAACAGCGTATTATCTAGAAATAGAGGCTCCGAAAGGCCGAGTAGTTCCTCAGGTTCTGATGTATGGGCAGAAGAGAGGATCAAGTGTGACAGGCCATATTCTAGGTATGACAGAACTAAAGACGCTTCACATCCTCTAGGCCTTCAGCACAACGATGGTGCTTTTAAAAAGAGAGAGAACTCTATGCAAAACAGACCAGGAAGAGGCCCTTTGTATGCAGAGGCCAAAGAAAACCCACTTCCTCCAGAATTCGTAGATTACAATAATCAAAGACGTGGGAGAAGAGAAAACCAAACAGGTCATCCTGATCACTGTTATGAGAGGAAACCACGGACAATGAATAGTGAAGCTGTTAGTGGTCTAAAAATTGAGAAACATTTTAGTGTAAACACTGATTACCCGAGGCCTGTGCAGAGCAATAGTCTTGGTGTTCCAAATGGAGAGACAGCTCCGCCTCTGAAAGGAAGGCGCGTAGGACCGATTAAGTCAGCAGGACCTGTCACAGCTGTGCCCTACGATGATAAAATATTTTATAATAGTGGGCCCAAAAGAAGGTCTGGGCCAATTAAGCCTGAAAAGGTGATAGAATCATCTATTCCTGTGGAGTATGCAAAAGTGTGGAAACCTGGCGATGAATGTTTTGCACTTTATTGGGAAGACAACAAGTTTTACCGAGCAGAAGTTGAAGCCTTGCATTCTTCGGGTATGACAGCGGTCGTTAAGTTCACGGACTACGGCAACTATGAAGAGGTGCTACTGAGCAATATCAAGCCTGTTCAGACAGAGGCATGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTTCGGGTATGACAGCGG
59.83
GGCAGGCAGGGAAACTTGTA
60.25
172
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCGGTCGTTAAGTTCACG
59.57
GGCAGGCAGGGAAACTTGTA
60.25
158
PCR template sequence:
GCATTCTTCGGGTATGACAGCGGTCGTTAAGTTCACGGACTACGGCAACTATGAAGAGGTGCTACTGAGCAATATCAAGCCTGTTCAGACAGAGGCATGGAAGTGTGCATCTAACGTCCAAGTGGATAGCAGAGAGCTTGATCGAAGAAAGACATTACAAGTTTCCCTGCCTGCCAAGCCTGCAAATGATAATGATGAAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
28
Interacting miRNAs (#binding sites)
mmu-miR-181d-5p(3), mmu-miR-137-3p(2), mmu-miR-181a-5p(2), mmu-miR-181b-5p(2), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-19b-3p(1), mmu-miR-205-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-106b-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-19a-3p(1), mmu-miR-298-5p(1), mmu-miR-139-5p(1), mmu-miR-136-5p(1), mmu-miR-301b-3p(1), mmu-miR-382-5p(1), mmu-miR-301a-3p(1), mmu-miR-666-5p(1), mmu-miR-1198-5p(1), mmu-miR-207(1), mmu-miR-300-3p(1), mmu-miR-369-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GACAGAGGCATGGAAGTGTGCATCTA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTDRD3_1548_ORF_1
0.899
0.128179358
0.999999954
2772
ORF sequence:
ATGGGCTTCAGTAAGGAGGCCTCAAGGCAAGCGCTGATGGATAATGCCAACAACTTAGAAGCAGCACTGAATGTCCTTCTGAACAGCAGTAAACAGAAGCCTGCTGTGGGCCCTCCTGCTAGAGGAAGAGGGAAAGGCAGGGGTCGAGGACGATCAGAAGATGAGGAAGACCTGGGAACCGCAAGACCGTCAGCACCAAGCACGTTATTTGATTTCTTGGAGTCTAAAATGGGAACTCTGAATGTGGAAGAACCTAAGTCACAGCCACAGCACCTTCATCAAGGACAGCACAGAGGATGGAATGCCGAGCAAAATGGGATGAAGGACGGCACTCAGTCAAGACATCTTCCTCGAAACGATACCAGGCAGCCAAGAAATGAGAGGCCACCTCGCTTTCAAAAAGACACCCCAACTTCCAAGTCAACTGTAGAAAACAGCGTATTATCTAGAAATAGAGGCTCCGAAAGGCCGAGTAGTTCCTCAGGTTCTGATGTATGGGCAGAAGAGAGGATCAAGTGTGACAGGCCATATTCTAGGTATGACAGAACTAAAGACGCTTCACATCCTCTAGGCCTTCAGCACAACGATGGTGCTTTTAAAAAGAGAGAGAACTCTATGCAAAACAGACCAGGAAGAGGCCCTTTGTATGCAGAGGCCAAAGAAAACCCACTTCCTCCAGAATTCGTAGATTACAATAATCAAAGACGTGGGAGAAGAGAAAACCAAACAGGTCATCCTGATCACTGTTATGAGAGGAAACCACGGACAATGAATAGTGAAGCTGTTAGTGGTCTAAAAATTGAGAAACATTTTAGTGTAAACACTGATTACCCGAGGCCTGTGCAGAGCAATAGTCTTGGTGTTCCAAATGGAGAGACAGCTCCGCCTCTGAAAGGAAGGCGCGTAGGACCGATTAAGTCAGCAGGACCTGTCACAGCTGTGCCCTACGATGATAAAATATTTTATAATAGTGGGCCCAAAAGAAGGTCTGGGCCAATTAAGCCTGAAAAGGTGATAGAATCATCTATTCCTGTGGAGTATGCAAAAGTGTGGAAACCTGGCGATGAATGTTTTGCACTTTATTGGGAAGACAACAAGTTTTACCGAGCAGAAGTTGAAGCCTTGCATTCTTCGGGTATGACAGCGGTCGTTAAGTTCACGGACTACGGCAACTATGAAGAGGTGCTACTGAGCAATATCAAGCCTGTTCAGACAGAGGCATGGAAGTGTGCATCTAACGTCCAAGTGGATAGCAGAGAGCTTGATCGAAGAAAGACATTACAAGTTTCCCTGCCTGCCAAGCCTGCAAATGATAATGATGAATTTGAAAAGCAAAGAACTGCTGCCATTGCAGAGGTTGCAAAGAGCAAAGAGACCAAGACATTTGGAGGAGGTGGAGGTGGTGCCAGAAGTAATCTCAATATTGGTGCTGCTGGTCACCGAAATAGGGAGGTTTTACAGAAGGAAAAGGCTTCCAAGTCAGAGAGCAAGAACGAAGGTGTCTATAGAGAATTGGTTGATGAGAAAGCCCTGAAACACATAACAGAAATGGGCTTCAGTAAGGAGGCCTCAAGGCAAGCGCTGATGGATAATGCCAACAACTTAGAAGCAGCACTGAATGTCCTTCTGAACAGCAGTAAACAGAAGCCTGCTGTGGGCCCTCCTGCTAGAGGAAGAGGGAAAGGCAGGGGTCGAGGACGATCAGAAGATGAGGAAGACCTGGGAACCGCAAGACCGTCAGCACCAAGCACGTTATTTGATTTCTTGGAGTCTAAAATGGGAACTCTGAATGTGGAAGAACCTAAGTCACAGCCACAGCACCTTCATCAAGGACAGCACAGAGGATGGAATGCCGAGCAAAATGGGATGAAGGACGGCACTCAGTCAAGACATCTTCCTCGAAACGATACCAGGCAGCCAAGAAATGAGAGGCCACCTCGCTTTCAAAAAGACACCCCAACTTCCAAGTCAACTGTAGAAAACAGCGTATTATCTAGAAATAGAGGCTCCGAAAGGCCGAGTAGTTCCTCAGGTTCTGATGTATGGGCAGAAGAGAGGATCAAGTGTGACAGGCCATATTCTAGGTATGACAGAACTAAAGACGCTTCACATCCTCTAGGCCTTCAGCACAACGATGGTGCTTTTAAAAAGAGAGAGAACTCTATGCAAAACAGACCAGGAAGAGGCCCTTTGTATGCAGAGGCCAAAGAAAACCCACTTCCTCCAGAATTCGTAGATTACAATAATCAAAGACGTGGGAGAAGAGAAAACCAAACAGGTCATCCTGATCACTGTTATGAGAGGAAACCACGGACAATGAATAGTGAAGCTGTTAGTGGTCTAAAAATTGAGAAACATTTTAGTGTAAACACTGATTACCCGAGGCCTGTGCAGAGCAATAGTCTTGGTGTTCCAAATGGAGAGACAGCTCCGCCTCTGAAAGGAAGGCGCGTAGGACCGATTAAGTCAGCAGGACCTGTCACAGCTGTGCCCTACGATGATAAAATATTTTATAATAGTGGGCCCAAAAGAAGGTCTGGGCCAATTAAGCCTGAAAAGGTGATAGAATCATCTATTCCTGTGGAGTATGCAAAAGTGTGGAAACCTGGCGATGAATGTTTTGCACTTTATTGGGAAGACAACAAGTTTTACCGAGCAGAAGTTGAAGCCTTGCATTCTTCGGGTATGACAGCGGTCGTTAAGTTCACGGACTACGGCAACTATGAAGAGGTGCTACTGAGCAATATCAAGCCTGTTCAGACAGAGGCATGG
Peptide sequence:
MGFSKEASRQALMDNANNLEAALNVLLNSSKQKPAVGPPARGRGKGRGRGRSEDEEDLGTARPSAPSTLFDFLESKMGTLNVEEPKSQPQHLHQGQHRGWNAEQNGMKDGTQSRHLPRNDTRQPRNERPPRFQKDTPTSKSTVENSVLSRNRGSERPSSSSGSDVWAEERIKCDRPYSRYDRTKDASHPLGLQHNDGAFKKRENSMQNRPGRGPLYAEAKENPLPPEFVDYNNQRRGRRENQTGHPDHCYERKPRTMNSEAVSGLKIEKHFSVNTDYPRPVQSNSLGVPNGETAPPLKGRRVGPIKSAGPVTAVPYDDKIFYNSGPKRRSGPIKPEKVIESSIPVEYAKVWKPGDECFALYWEDNKFYRAEVEALHSSGMTAVVKFTDYGNYEEVLLSNIKPVQTEAWKCASNVQVDSRELDRRKTLQVSLPAKPANDNDEFEKQRTAAIAEVAKSKETKTFGGGGGGARSNLNIGAAGHRNREVLQKEKASKSESKNEGVYRELVDEKALKHITEMGFSKEASRQALMDNANNLEAALNVLLNSSKQKPAVGPPARGRGKGRGRGRSEDEEDLGTARPSAPSTLFDFLESKMGTLNVEEPKSQPQHLHQGQHRGWNAEQNGMKDGTQSRHLPRNDTRQPRNERPPRFQKDTPTSKSTVENSVLSRNRGSERPSSSSGSDVWAEERIKCDRPYSRYDRTKDASHPLGLQHNDGAFKKRENSMQNRPGRGPLYAEAKENPLPPEFVDYNNQRRGRRENQTGHPDHCYERKPRTMNSEAVSGLKIEKHFSVNTDYPRPVQSNSLGVPNGETAPPLKGRRVGPIKSAGPVTAVPYDDKIFYNSGPKRRSGPIKPEKVIESSIPVEYAKVWKPGDECFALYWEDNKFYRAEVEALHSSGMTAVVKFTDYGNYEEVLLSNIKPVQTEAW
IRESfinder result
IRESfinder score
0.411582716
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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