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mmu_circAtrn_674
Basic information of circular RNA
PanCircBase ID:
mmu_circAtrn_674
mm39_Chr. Position ID:
chr2|130798940|130803594|+
Gene name:
Atrn
Transcript:
ENSMUST00000028781.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
7,8,9,10
Exon/intron offsets:
0,884,3364,4499
Genomic length:
4654
Exon/intron sizes in nt:
91,24,41,84,155
Flanking exon/introns:
chr2:130789647-130798940|chr2:130803594-130806763
Splice length:
674
Other database IDs:
CIRCpedia: MMU_CIRCpedia_216850, circAtlas: mmu-Atrn_0028
Human Ortholog IDs:
Mature spliced Sequence:
GTATGACCTGACTTCTAGGGAATGGCTTCCACTAAACCATTCTGTGAACAGTGTGGTTGTAAGATATGGTCATTCTTTGGCATTACATAAGGATAAAATCTACATGTATGGAGGAAAAATTGATTCAACAGGGAACGTGACCAATGAGCTGAGAGTATTTCATATTCATAATGAATCATGGGTATTGTTAACTCCGAAAGCTAAGGATCAGTATGCAGTGGTTGGACACTCAGCACACATTGTTACACTGGCATCTGGCCGTGTGGTCATGTTGGTCATCTTCGGTCATTGCCCACTCTATGGATATATAAGCGTTGTGCAGGAATATGACTTGGAAAAGAACACATGGAGTATATTACATACTCAGGGTGCTCTTGTGCAAGGGGGTTATGGCCACAGTAGTGTTTATGATGACAGGACCAAGGCTCTGTACGTTCATGGTGGCTACAAGGCTTTCAGCGCCAACAAATACCGGCTTGCAGATGACCTCTACAGATACGATGTGGATACTCAGATGTGGACCATTCTTAAGGACAGCCGATTTTTCCGTTACTTGCATACAGCTGTGATAGTGAGTGGAACCATGCTGGTGTTTGGAGGGAACACACACAATGACACTTCCATGAGCCACGGTGCCAAATGCTTCTCCTCAGACTTCATGGCTTATGACATTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CATGCTGGTGTTTGGAGGGA
60.25
CCACACTGTTCACAGAATGGT
58.42
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CATGCTGGTGTTTGGAGGGA
60.25
ACAACCACACTGTTCACAGA
57.22
152
PCR template sequence:
AGTGGAACCATGCTGGTGTTTGGAGGGAACACACACAATGACACTTCCATGAGCCACGGTGCCAAATGCTTCTCCTCAGACTTCATGGCTTATGACATTGGTATGACCTGACTTCTAGGGAATGGCTTCCACTAAACCATTCTGTGAACAGTGTGGTTGTAAGATATGGTCATTCTTTGGCATTACATAAGGATAAAATC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-10b-5p(1), mmu-miR-96-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-1198-5p(1), mmu-miR-3061-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCTTATGACATTGGTATGACCTGACT
siRNA sets
AGTCAGGTCATACCAATGT, TCAGGTCATACCAATGTCA, GTCAGGTCATACCAATGTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATRN_674_ORF_1
0.8785
0.158757362
0.769955315
582
ORF sequence:
ATGTATGGAGGAAAAATTGATTCAACAGGGAACGTGACCAATGAGCTGAGAGTATTTCATATTCATAATGAATCATGGGTATTGTTAACTCCGAAAGCTAAGGATCAGTATGCAGTGGTTGGACACTCAGCACACATTGTTACACTGGCATCTGGCCGTGTGGTCATGTTGGTCATCTTCGGTCATTGCCCACTCTATGGATATATAAGCGTTGTGCAGGAATATGACTTGGAAAAGAACACATGGAGTATATTACATACTCAGGGTGCTCTTGTGCAAGGGGGTTATGGCCACAGTAGTGTTTATGATGACAGGACCAAGGCTCTGTACGTTCATGGTGGCTACAAGGCTTTCAGCGCCAACAAATACCGGCTTGCAGATGACCTCTACAGATACGATGTGGATACTCAGATGTGGACCATTCTTAAGGACAGCCGATTTTTCCGTTACTTGCATACAGCTGTGATAGTGAGTGGAACCATGCTGGTGTTTGGAGGGAACACACACAATGACACTTCCATGAGCCACGGTGCCAAATGCTTCTCCTCAGACTTCATGGCTTATGACATTGGTATGACCTGA
Peptide sequence:
MYGGKIDSTGNVTNELRVFHIHNESWVLLTPKAKDQYAVVGHSAHIVTLASGRVVMLVIFGHCPLYGYISVVQEYDLEKNTWSILHTQGALVQGGYGHSSVYDDRTKALYVHGGYKAFSANKYRLADDLYRYDVDTQMWTILKDSRFFRYLHTAVIVSGTMLVFGGNTHNDTSMSHGAKCFSSDFMAYDIGMT
IRESfinder result
IRESfinder score
0.412126619
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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