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mmu_circAtf6_397
Basic information of circular RNA
PanCircBase ID:
mmu_circAtf6_397
mm39_Chr. Position ID:
chr1|170614914|170622339|-
Gene name:
Atf6
Transcript:
ENSMUST00000027974.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
14,13,12,11
Exon/intron offsets:
0,1262,6611,7311
Genomic length:
7425
Exon/intron sizes in nt:
11,56,81,00,114
Flanking exon/introns:
chr1:170574759-170614914|chr1:170622339-170627182
Splice length:
397
Other database IDs:
CIRCpedia: MMU_CIRCpedia_11812, circAtlas: mmu-Atf6_0022
circBase: hsa_circ_0110996, circAtlas: hsa-ATF6_0010, CIRCpedia: HSA_CIRCpedia_140040
Human Ortholog IDs:
Mature spliced Sequence:
CTATGATCACTCTGTGTCCAATGACAAAGCTTTAATGGTGCTAAGTGAAGAGCCATTGCTTTATATGCCTCCACCTCCATGTCAACCCCTGATTAACACAACAGAGTCTCTCAGGTTGAACCATGAACTTCGAGGCTGGGTTCATAGACATGAAGTGGAAAGGACCAAATCTAGAAGAATGACAAATAGCCAACAGAAAGCCCGCATTCTCCAGGGTGCTCTGGAACAGGGCTCTAATTCTCAGCTGATGGCTGTCCAGTACACAGAAACCACTAGCATCAGTAGGAATTCTGGGAGTGAGCTGCAAGTGTATTACGCCTCCCCTGGAAGTTACCAAGGCTTCTTTGACGCCATCCGCAGGAGGGGAGATACGTTTTACGTTGTCTCATTTCGAAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTATTACGCCTCCCCTGGA
60.03
GGTTGACATGGAGGTGGAGG
60.04
176
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTATTACGCCTCCCCTGGA
60.03
GGGTTGACATGGAGGTGGAG
60.04
177
PCR template sequence:
TGAGCTGCAAGTGTATTACGCCTCCCCTGGAAGTTACCAAGGCTTCTTTGACGCCATCCGCAGGAGGGGAGATACGTTTTACGTTGTCTCATTTCGAAGGCTATGATCACTCTGTGTCCAATGACAAAGCTTTAATGGTGCTAAGTGAAGAGCCATTGCTTTATATGCCTCCACCTCCATGTCAACCCCTGATTAACACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-140-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-340-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTCATTTCGAAGGCTATGATCACTCT
siRNA sets
AGAGTGATCATAGCCTTCG,GAGTGATCATAGCCTTCGA,GATCATAGCCTTCGAAATG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATF6_397_ORF_1
0.7407
0.086894014
0.296053799
369
ORF sequence:
ATGGTGCTAAGTGAAGAGCCATTGCTTTATATGCCTCCACCTCCATGTCAACCCCTGATTAACACAACAGAGTCTCTCAGGTTGAACCATGAACTTCGAGGCTGGGTTCATAGACATGAAGTGGAAAGGACCAAATCTAGAAGAATGACAAATAGCCAACAGAAAGCCCGCATTCTCCAGGGTGCTCTGGAACAGGGCTCTAATTCTCAGCTGATGGCTGTCCAGTACACAGAAACCACTAGCATCAGTAGGAATTCTGGGAGTGAGCTGCAAGTGTATTACGCCTCCCCTGGAAGTTACCAAGGCTTCTTTGACGCCATCCGCAGGAGGGGAGATACGTTTTACGTTGTCTCATTTCGAAGGCTATGA
Peptide sequence:
MVLSEEPLLYMPPPPCQPLINTTESLRLNHELRGWVHRHEVERTKSRRMTNSQQKARILQGALEQGSNSQLMAVQYTETTSISRNSGSELQVYYASPGSYQGFFDAIRRRGDTFYVVSFRRL
IRESfinder result
IRESfinder score
0.499639634
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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