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mmu_circLin7c_401
Basic information of circular RNA
PanCircBase ID:
mmu_circLin7c_401
mm39_Chr. Position ID:
chr2|109724809|109726790|+
Gene name:
Lin7c
Transcript:
ENSMUST00000028583.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
2,3,4
Exon/intron offsets:
0,643,1771
Genomic length:
1981
Exon/intron sizes in nt:
1,19,72,210
Flanking exon/introns:
chr2:109721266-109724809|chr2:109726790-109727590
Splice length:
401
Other database IDs:
circAtlas: mmu-Lin7c_0001
circBase: hsa_circ_0095646, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_151829
Human Ortholog IDs:
Mature spliced Sequence:
ATATCTGCAGAGCAATTGAATTGTTGGAGAAATTACAGAGGAGTGGAGAGGTGCCGCCACAGAAACTTCAGGCTTTGCAAAGAGTCCTTCAGAGTGAGTTCTGCAATGCTGTAAGAGAGGTATACGAACATGTTTATGAGACGGTGGACATCAGCAGCAGCCCTGAAGTGAGAGCCAATGCAACTGCAAAGGCTACTGTTGCTGCATTTGCTGCCAGTGAAGGACACTCTCATCCCCGAGTTGTTGAGCTACCCAAAACAGAAGAGGGCCTTGGATTCAATATTATGGGAGGCAAAGAGCAAAACTCACCAATCTATATATCGCGGATAATTCCAGGTGGAATTGCTGACAGACATGGGGGCCTCAAACGAGGAGATCAGCTACTTTCTGTTAATGGAGTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGCGGATAATTCCAGGTGGA
59.89
AGCCTGAAGTTTCTGTGGCG
60.89
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCGCGGATAATTCCAGGTGG
59.89
AGCCTGAAGTTTCTGTGGCG
60.89
155
PCR template sequence:
AAACTCACCAATCTATATATCGCGGATAATTCCAGGTGGAATTGCTGACAGACATGGGGGCCTCAAACGAGGAGATCAGCTACTTTCTGTTAATGGAGTGATATCTGCAGAGCAATTGAATTGTTGGAGAAATTACAGAGGAGTGGAGAGGTGCCGCCACAGAAACTTCAGGCTTTGCAAAGAGTCCTTCAGAGTGAGTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-3087-3p(1), mmu-miR-542-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGTTAATGGAGTGATATCTGCAGAGC
siRNA sets
GCTCTGCAGATATCACTCC, CTCTGCAGATATCACTCCA, AGATATCACTCCATTAACA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCLIN7C_401_ORF_1
0.4984
-0.094964466
0.044944337
231
ORF sequence:
ATGGGAGGCAAAGAGCAAAACTCACCAATCTATATATCGCGGATAATTCCAGGTGGAATTGCTGACAGACATGGGGGCCTCAAACGAGGAGATCAGCTACTTTCTGTTAATGGAGTGATATCTGCAGAGCAATTGAATTGTTGGAGAAATTACAGAGGAGTGGAGAGGTGCCGCCACAGAAACTTCAGGCTTTGCAAAGAGTCCTTCAGAGTGAGTTCTGCAATGCTGTAA
Peptide sequence:
MGGKEQNSPIYISRIIPGGIADRHGGLKRGDQLLSVNGVISAEQLNCWRNYRGVERCRHRNFRLCKESFRVSSAML
IRESfinder result
IRESfinder score
0.511836884
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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