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mmu_circEpb41l3_1156
Basic information of circular RNA
PanCircBase ID:
mmu_circEpb41l3_1156
mm39_Chr. Position ID:
chr17|69517180|69566183|+
Gene name:
Epb41l3
Transcript:
ENSMUST00000239167.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
3,4,5,6,7,8,9,10,11
Exon/intron offsets:
0,28159,29561,33402,37350,38444,43210,47185,48827
Genomic length:
49003
Exon/intron sizes in nt:
198,105,43,76,219,88,153,98,176
Flanking exon/introns:
chr17:69515071-69517180|chr17:69566183-69569120
Splice length:
1156
Other database IDs:
circAtlas: hsa-EPB41L3_0027
Human Ortholog IDs:
Mature spliced Sequence:
ATCGGTGACAAAGACCGGGACTTTGCTGCTGCAGCTGCGAAACAGCTTGAATATCAGCAGTTTGAGGACGATAAGCTCTCTCAGAGATCATCCAGCAGCAAACTCTCACGGTCCCCGCTGAAGATCGTGAAAAGGCCTAAAAGCATGCAGTGCAAAGTGACGCTTCTGGATGGGTCAGAGTACGGCTGCGATGTGGACAAGCGCTCCCGAGGACAAGTGCTCTTTGACAAAGTGTGCGAACATCTGAACCTGCTAGAAAAAGACTACTTTGGCCTCACGTATCGAGACGCAGAGAATCAGAAGAACTGGTTGGACCCTGCTAAGGAAATTAAAAAGCAGATTCGGAGCGGTGCTTGGCATTTTTCATTTAATGTGAAGTTTTACCCACCAGACCCTGCCCAGCTATCAGAAGATATCACCAGGTACTACCTCTGCTTGCAGCTGCGAGATGATATTGTGTCTGGACGGCTACCCTGTTCCTTCGTGACTCTTGCCCTGCTGGGCTCCTACACGGTGCAGTCAGAGCTCGGGGACTACGATCCCGATGAATGTGGGAATGACTACATCAGTGAGTTCCGCTTTGCGCCAAACCACACGAAAGAACTGGAGGATAAAGTGATTGAGCTGCACAAGAGCCACAGAGGAATGACGCCAGCTGAAGCCGAGATGCACTTCCTCGAAAATGCCAAAAAGCTCTCCATGTACGGGGTGGACTTACACCATGCCAAGGATTCGGAAGGAGTGGAGATTATGTTAGGAGTCTGTGCCAGTGGTCTGTTGATATATCGTGACCGGCTTCGAATAAACAGATTTGCTTGGCCGAAGGTCTTAAAAATTTCTTATAAACGGAACAACTTTTACATTAAAATCCGGCCAGGAGAGTTTGAGCAATTTGAAAGCACCATTGGGTTCAAGTTGCCAAACCATAGGGCTGCCAAGCGCCTCTGGAAAGTGTGTGTGGAGCATCATACATTTTTCAGATTATTGCTACCAGAAGCACCTCCAAAGAAATTCTTGACCTTGGGCTCCAAGTTCCGCTACAGTGGCAGAACCCAGGCGCAAACAAGAAGAGCCAGTGCGTTGATAGACCGCCCGGCCCCTTACTTTGAACGCTCGTCCAGCAAACGATACACCATGTCTCGCAGCTTGGATGGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCCCCTTACTTTGAACGCT
60.61
TGCTGCTGGATGATCTCTGAG
59.59
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCCCCTTACTTTGAACGCT
60.61
TGCTGCTGGATGATCTCTGA
58.51
162
PCR template sequence:
GCGCAAACAAGAAGAGCCAGTGCGTTGATAGACCGCCCGGCCCCTTACTTTGAACGCTCGTCCAGCAAACGATACACCATGTCTCGCAGCTTGGATGGAGATCGGTGACAAAGACCGGGACTTTGCTGCTGCAGCTGCGAAACAGCTTGAATATCAGCAGTTTGAGGACGATAAGCTCTCTCAGAGATCATCCAGCAGCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
21
Interacting miRNAs (#binding sites)
mmu-let-7a-5p(1), mmu-miR-15a-5p(1), mmu-miR-181a-5p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-196a-5p(1), mmu-miR-181b-5p(1), mmu-miR-214-3p(1), mmu-let-7d-5p(1), mmu-miR-149-5p(1), mmu-miR-182-5p(1), mmu-miR-382-5p(1), mmu-miR-362-5p(1), mmu-miR-98-5p(1), mmu-miR-3087-3p(1), mmu-miR-188-3p(1), mmu-miR-1904(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGCTTGGATGGAGATCGGTGACAAAG
siRNA sets
TTGTCACCGATCTCCATCC, CACCGATCTCCATCCAAGC, TTTGTCACCGATCTCCATC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCEPB41L3_1156_ORF_1
0.8487
0.336334462
0.997610781
1161
ORF sequence:
ATGGAGATCGGTGACAAAGACCGGGACTTTGCTGCTGCAGCTGCGAAACAGCTTGAATATCAGCAGTTTGAGGACGATAAGCTCTCTCAGAGATCATCCAGCAGCAAACTCTCACGGTCCCCGCTGAAGATCGTGAAAAGGCCTAAAAGCATGCAGTGCAAAGTGACGCTTCTGGATGGGTCAGAGTACGGCTGCGATGTGGACAAGCGCTCCCGAGGACAAGTGCTCTTTGACAAAGTGTGCGAACATCTGAACCTGCTAGAAAAAGACTACTTTGGCCTCACGTATCGAGACGCAGAGAATCAGAAGAACTGGTTGGACCCTGCTAAGGAAATTAAAAAGCAGATTCGGAGCGGTGCTTGGCATTTTTCATTTAATGTGAAGTTTTACCCACCAGACCCTGCCCAGCTATCAGAAGATATCACCAGGTACTACCTCTGCTTGCAGCTGCGAGATGATATTGTGTCTGGACGGCTACCCTGTTCCTTCGTGACTCTTGCCCTGCTGGGCTCCTACACGGTGCAGTCAGAGCTCGGGGACTACGATCCCGATGAATGTGGGAATGACTACATCAGTGAGTTCCGCTTTGCGCCAAACCACACGAAAGAACTGGAGGATAAAGTGATTGAGCTGCACAAGAGCCACAGAGGAATGACGCCAGCTGAAGCCGAGATGCACTTCCTCGAAAATGCCAAAAAGCTCTCCATGTACGGGGTGGACTTACACCATGCCAAGGATTCGGAAGGAGTGGAGATTATGTTAGGAGTCTGTGCCAGTGGTCTGTTGATATATCGTGACCGGCTTCGAATAAACAGATTTGCTTGGCCGAAGGTCTTAAAAATTTCTTATAAACGGAACAACTTTTACATTAAAATCCGGCCAGGAGAGTTTGAGCAATTTGAAAGCACCATTGGGTTCAAGTTGCCAAACCATAGGGCTGCCAAGCGCCTCTGGAAAGTGTGTGTGGAGCATCATACATTTTTCAGATTATTGCTACCAGAAGCACCTCCAAAGAAATTCTTGACCTTGGGCTCCAAGTTCCGCTACAGTGGCAGAACCCAGGCGCAAACAAGAAGAGCCAGTGCGTTGATAGACCGCCCGGCCCCTTACTTTGAACGCTCGTCCAGCAAACGATACACCATGTCTCGCAGCTTGGATGGA
Peptide sequence:
MEIGDKDRDFAAAAAKQLEYQQFEDDKLSQRSSSSKLSRSPLKIVKRPKSMQCKVTLLDGSEYGCDVDKRSRGQVLFDKVCEHLNLLEKDYFGLTYRDAENQKNWLDPAKEIKKQIRSGAWHFSFNVKFYPPDPAQLSEDITRYYLCLQLRDDIVSGRLPCSFVTLALLGSYTVQSELGDYDPDECGNDYISEFRFAPNHTKELEDKVIELHKSHRGMTPAEAEMHFLENAKKLSMYGVDLHHAKDSEGVEIMLGVCASGLLIYRDRLRINRFAWPKVLKISYKRNNFYIKIRPGEFEQFESTIGFKLPNHRAAKRLWKVCVEHHTFFRLLLPEAPPKKFLTLGSKFRYSGRTQAQTRRASALIDRPAPYFERSSSKRYTMSRSLDG
IRESfinder result
IRESfinder score
0.402604833
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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