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mmu_circSlc22a4_259
Basic information of circular RNA
PanCircBase ID:
mmu_circSlc22a4_259
mm39_Chr. Position ID:
chr11|53896219|53898697|-
Gene name:
Slc22a4
Transcript:
ENSMUST00000020586.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,2
Exon/intron offsets:
0,2374
Genomic length:
2478
Exon/intron sizes in nt:
1,55,104
Flanking exon/introns:
chr11:53888374-53896219|chr11:53898697-53918409
Splice length:
259
Other database IDs:
circAtlas: mmu-Slc22a4_0001
circBase: hsa_circ_0008869, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_68705
Human Ortholog IDs:
Mature spliced Sequence:
TGGAATCTGGTGTGTGAGGATGACTGGAAGACACCCCTCACCACCTCCCTGTTCTTCGTAGGCGTTCTCTGCGGCTCCTTCGTGTCTGGGCAGCTGTCAGACAGGTTTGGCAGGAAGAAAGTCCTCTTTGCAACCATGGCTGTGCAGACTGGATTCAGCTTCGTGCAGATTTTCTCAACCAACTGGGAGATGTTCACTGTGTTGTTTGCCATTGTGGGCATGGGCCAGATCTCCAACTACGTGGTGGCCTTCATACTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTTCACTGTGTTGTTTGCCA
59.11
GCAGAGAACGCCTACGAAGA
59.83
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGGGAGATGTTCACTGTGT
58.95
AACGCCTACGAAGAACAGGG
60.04
144
PCR template sequence:
TTCGTGCAGATTTTCTCAACCAACTGGGAGATGTTCACTGTGTTGTTTGCCATTGTGGGCATGGGCCAGATCTCCAACTACGTGGTGGCCTTCATACTAGTGGAATCTGGTGTGTGAGGATGACTGGAAGACACCCCTCACCACCTCCCTGTTCTTCGTAGGCGTTCTCTGCGGCTCCTTCGTGTCTGGGCAGCTGTCAG
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-128-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCCTTCATACTAGTGGAATCTGGTGT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSLC22A4_259_ORF_1
1.1483
0.341516193
0.330487071
141
ORF sequence:
ATGGCTGTGCAGACTGGATTCAGCTTCGTGCAGATTTTCTCAACCAACTGGGAGATGTTCACTGTGTTGTTTGCCATTGTGGGCATGGGCCAGATCTCCAACTACGTGGTGGCCTTCATACTAGTGGAATCTGGTGTGTGA
Peptide sequence:
MAVQTGFSFVQIFSTNWEMFTVLFAIVGMGQISNYVVAFILVESGV
IRESfinder result
IRESfinder score
0.587587544
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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