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mmu_circAtrn_394
Basic information of circular RNA
PanCircBase ID:
mmu_circAtrn_394
mm39_Chr. Position ID:
chr2|130841065|130855588|+
Gene name:
Atrn
Transcript:
ENSMUST00000028781.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
22,23,24,25
Exon/intron offsets:
0,3616,5302,14461
Genomic length:
14523
Exon/intron sizes in nt:
95,79,158,62
Flanking exon/introns:
chr2:130837003-130841065|chr2:130855588-130860532
Splice length:
394
Other database IDs:
CIRCpedia: MMU_CIRCpedia_226209, circAtlas: mmu-Atrn_0003
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_168492
Human Ortholog IDs:
Mature spliced Sequence:
ATACCCTTCTCATTGACTATCAGTTCACCTTTAGCCTGTCCCAGGAAGACGACCGCTACTACACAGCCATCAACTTTGTGGCTACTCCTGATGAACAAAACAGGGATTTGGACATGTTCATCAATGCCTCCAAAAACTTCAACCTCAACATCACCTGGGCCACCAGCTTCCCAGCCGGAACCCAGACTGGAGAAGAGGTGCCTGTTGTTTCAAAAACCAACATCAAGGAATACAAAGATAGCTTCTCTAATGAGAAATTTGATTTTCGCAACCATCCAAACATCACTTTCTTTGTTTATGTCAGTAATTTCACTTGGCCCATCAAAATTCAGATTGCCTTCTCCCAGCACAGCAACTTCATGGACCTGGTACAGTTCTTCGTGACTTTCTTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGATTGCCTTCTCCCAGCAC
60.03
GCCACAAAGTTGATGGCTGT
59.32
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGATTGCCTTCTCCCAGCA
60.03
GCCACAAAGTTGATGGCTGT
59.32
147
PCR template sequence:
TTTATGTCAGTAATTTCACTTGGCCCATCAAAATTCAGATTGCCTTCTCCCAGCACAGCAACTTCATGGACCTGGTACAGTTCTTCGTGACTTTCTTCAGATACCCTTCTCATTGACTATCAGTTCACCTTTAGCCTGTCCCAGGAAGACGACCGCTACTACACAGCCATCAACTTTGTGGCTACTCCTGATGAACAAAA
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-207(1)
siRNAs for circular RNA silencing
Junction sequence
TGACTTTCTTCAGATACCCTTCTCAT
siRNA sets
AAGGGTATCTGAAGAAAGT, ATGAGAAGGGTATCTGAAG, GAAGGGTATCTGAAGAAAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATRN_394_ORF_1
0.8956
0.26691046
0.410590532
297
ORF sequence:
ATGTTCATCAATGCCTCCAAAAACTTCAACCTCAACATCACCTGGGCCACCAGCTTCCCAGCCGGAACCCAGACTGGAGAAGAGGTGCCTGTTGTTTCAAAAACCAACATCAAGGAATACAAAGATAGCTTCTCTAATGAGAAATTTGATTTTCGCAACCATCCAAACATCACTTTCTTTGTTTATGTCAGTAATTTCACTTGGCCCATCAAAATTCAGATTGCCTTCTCCCAGCACAGCAACTTCATGGACCTGGTACAGTTCTTCGTGACTTTCTTCAGATACCCTTCTCATTGA
Peptide sequence:
MFINASKNFNLNITWATSFPAGTQTGEEVPVVSKTNIKEYKDSFSNEKFDFRNHPNITFFVYVSNFTWPIKIQIAFSQHSNFMDLVQFFVTFFRYPSH
IRESfinder result
IRESfinder score
0.838621005
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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