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mmu_circAtf1_200
Basic information of circular RNA
PanCircBase ID:
mmu_circAtf1_200
mm39_Chr. Position ID:
chr15|100130613|100143226|+
Gene name:
Atf1
Transcript:
ENSMUST00000023769.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
2,3
Exon/intron offsets:
0,12512
Genomic length:
12613
Exon/intron sizes in nt:
99,101
Flanking exon/introns:
chr15:100125963-100130613|chr15:100143226-100149949
Splice length:
200
Other database IDs:
circBase: hsa_circ_0007241, circAtlas: hsa-ATF1_0005, CIRCpedia: HSA_CIRCpedia_8749
Human Ortholog IDs:
Mature spliced Sequence:
TTGATTATGGAAGATTCCCACAAGAGTAACACGACAGAGACTGCATCTCAGCCTGGTTCAACCGTTGCGGGGCCTCACGTTTCTCAGATAGTACATCAGGTGTCATCGTTATCAGAAAGTGAGGAGTCTCAGGACTCATCTGACAGCATAGGCTCCTCACAGAAAGCTCACGGGATCCTGGCCCGGCGCCCATCCTACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGCTCCTCACAGAAAGCTC
59.39
ATCTGAGAAACGTGAGGCCC
59.75
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCTCCTCACAGAAAGCTCA
59.68
TATCTGAGAAACGTGAGGCCC
59.52
140
PCR template sequence:
TGTCATCGTTATCAGAAAGTGAGGAGTCTCAGGACTCATCTGACAGCATAGGCTCCTCACAGAAAGCTCACGGGATCCTGGCCCGGCGCCCATCCTACAGTTGATTATGGAAGATTCCCACAAGAGTAACACGACAGAGACTGCATCTCAGCCTGGTTCAACCGTTGCGGGGCCTCACGTTTCTCAGATAGTACATCAGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-125b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCCCATCCTACAGTTGATTATGGAAG
siRNA sets
TAATCAACTGTAGGATGGG, ATAATCAACTGTAGGATGG, AATCAACTGTAGGATGGGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATF1_200_ORF_1
0.9123
0.127991924
0.167452832
198
ORF sequence:
ATGGAAGATTCCCACAAGAGTAACACGACAGAGACTGCATCTCAGCCTGGTTCAACCGTTGCGGGGCCTCACGTTTCTCAGATAGTACATCAGGTGTCATCGTTATCAGAAAGTGAGGAGTCTCAGGACTCATCTGACAGCATAGGCTCCTCACAGAAAGCTCACGGGATCCTGGCCCGGCGCCCATCCTACAGTTGA
Peptide sequence:
MEDSHKSNTTETASQPGSTVAGPHVSQIVHQVSSLSESEESQDSSDSIGSSQKAHGILARRPSYS
IRESfinder result
IRESfinder score
0.66618418
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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