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mmu_circEfcab14_592
Basic information of circular RNA
PanCircBase ID:
mmu_circEfcab14_592
mm39_Chr. Position ID:
chr4|115616005|115623709|+
Gene name:
Efcab14
Transcript:
ENSMUST00000106525.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,7,8,9,10
Exon/intron offsets:
0,1061,3409,5763,7584
Genomic length:
7704
Exon/intron sizes in nt:
87,192,81,112,120
Flanking exon/introns:
chr4:115613740-115616005|chr4:115623709-115631034
Splice length:
592
Other database IDs:
circAtlas: mmu-Efcab14_0004
circAtlas: hsa-EFCAB14_0013
Human Ortholog IDs:
Mature spliced Sequence:
GAGAACAATGGAAGCAACCAGATCTTGCCATCACCTTCACCTCCATCAGAGCTTGACAATAAATCCCACAGTGAAAGTGCAAAACAGGATATCCTGTACCTGCACAACTCCTTAGAGGAAGTCAACAGTACTGTAGTGGAATACCAGAGACAGAATGACCTTAAACTCAAGGGAATGAGCGAGACCCTCAGTAACCTGACACAGAGACTCAGCCTGATAGAAAGCCATGTGGTTGCACTGAGCAAGGCAGAACAGAGAACAAACGTGAGCTCCAGCACGATGGAGAATAGGGCTGCCACTCTGAAAAGAGAGTCTTTGGTGACCAACAGAAGTGACACTGTACAGGCGCAAAGCATGAAGAAAGAAGATAATTCAAATTCTCAGGTATCCGAGCTTCGAGAAAAACTGCAGCTGATCAGTGCTCTCACAAACAAACCTGAAAGCAACAGGCCTCCGGAGACCACAGATGAAGAGCAAGTACAGAACTTCACATCAGATCCTTCAGCATTGCCAGAATTTTCACAGCTTCTTAGAAACCAAATTGAGACCCAAGTAAAACCTCTCTCCCTGCCTGGGATTTCTAGCATCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCAGATCCTTCAGCATTGCCA
59.72
GGAGGTGAAGGTGATGGCAA
59.96
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCAGATCCTTCAGCATTGCCA
59.72
ATGGAGGTGAAGGTGATGGC
59.74
146
PCR template sequence:
TCAGATCCTTCAGCATTGCCAGAATTTTCACAGCTTCTTAGAAACCAAATTGAGACCCAAGTAAAACCTCTCTCCCTGCCTGGGATTTCTAGCATCAAAGGAGAACAATGGAAGCAACCAGATCTTGCCATCACCTTCACCTCCATCAGAGCTTGACAATAAATCCCACAGTGAAAGTGCAAAACAGGATATCCTGTACC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(1), mmu-miR-31-5p(1), mmu-miR-101a-3p(1), mmu-miR-152-3p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-101b-3p(1), mmu-miR-139-5p(1), mmu-miR-301b-3p(1), mmu-miR-721(1), mmu-miR-301a-3p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCTAGCATCAAAGGAGAACAATGGAA
siRNA sets
GTTCTCCTTTGATGCTAGA, ATTGTTCTCCTTTGATGCT, TTGTTCTCCTTTGATGCTA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCEFCAB14_592_ORF_1
0.8739
0.188843
0.633434098
474
ORF sequence:
ATGAGCGAGACCCTCAGTAACCTGACACAGAGACTCAGCCTGATAGAAAGCCATGTGGTTGCACTGAGCAAGGCAGAACAGAGAACAAACGTGAGCTCCAGCACGATGGAGAATAGGGCTGCCACTCTGAAAAGAGAGTCTTTGGTGACCAACAGAAGTGACACTGTACAGGCGCAAAGCATGAAGAAAGAAGATAATTCAAATTCTCAGGTATCCGAGCTTCGAGAAAAACTGCAGCTGATCAGTGCTCTCACAAACAAACCTGAAAGCAACAGGCCTCCGGAGACCACAGATGAAGAGCAAGTACAGAACTTCACATCAGATCCTTCAGCATTGCCAGAATTTTCACAGCTTCTTAGAAACCAAATTGAGACCCAAGTAAAACCTCTCTCCCTGCCTGGGATTTCTAGCATCAAAGGAGAACAATGGAAGCAACCAGATCTTGCCATCACCTTCACCTCCATCAGAGCTTGA
Peptide sequence:
MSETLSNLTQRLSLIESHVVALSKAEQRTNVSSSTMENRAATLKRESLVTNRSDTVQAQSMKKEDNSNSQVSELREKLQLISALTNKPESNRPPETTDEEQVQNFTSDPSALPEFSQLLRNQIETQVKPLSLPGISSIKGEQWKQPDLAITFTSIRA
IRESfinder result
IRESfinder score
0.658240238
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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