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mmu_circSlc12a2_611
Basic information of circular RNA
PanCircBase ID:
mmu_circSlc12a2_611
mm39_Chr. Position ID:
chr18|58045908|58054958|+
Gene name:
Slc12a2
Transcript:
ENSMUST00000115366.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
13,14,15,16,17
Exon/intron offsets:
0,1269,2572,6619,8909
Genomic length:
9050
Exon/intron sizes in nt:
10,21,56,10,01,12,141
Flanking exon/introns:
chr18:58045085-58045908|chr18:58054958-58059478
Splice length:
611
Other database IDs:
CIRCpedia: MMU_CIRCpedia_216043, circAtlas: mmu-Slc12a2_0034
Human Ortholog IDs:
Mature spliced Sequence:
CTGAATTGAACGTTATTGCTCCAATTATCTCTAATTTCTTCCTTGCATCGTATGCCTTAATCAACTTTTCAGTATTCCATGCATCACTTGCAAAATCTCCAGGATGGCGTCCTGCATTCAAATACTACAACATGTGGATCTCCCTTATTGGAGCAATTCTTTGTTGCATAGTGATGTTTGTCATTAACTGGTGGGCTGCGTTGCTCACATATGTGATAGTCCTTGGGCTGTACATTTATGTTACTTACAAAAAACCAGATGTGAACTGGGGATCCTCCACACAAGCGCTGACTTACCTCAGTGCACTGCAGCATTCAATCCGTCTTTCTGGGGTGGAGGACCATGTGAAAAACTTCAGACCACAGTGCCTTGTAATGACAGGTTCTCCAAACTCACGGCCTGCTTTACTTCATCTTGTTCATGACTTCACGAAAAATGTTGGTTTAATGATCTGTGGCCATGTGCATATGGGCCCCAGAAGACAAGCTATGAAAGAGATGTCCATTGATCAAGCCAGATATCAGCGATGGCTCATTAAAAACAAAATGAAGGCTTTCTATGCTCCGGTTCACGCAGATGACTTGCGAGAAGGTGCACAATACTTGATGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTATGCTCCGGTTCACGC
60.46
CAAGTGATGCATGGAATACTGA
56.5
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTATGCTCCGGTTCACGC
60.46
CAAGTGATGCATGGAATACTGAA
57.18
147
PCR template sequence:
AGCCAGATATCAGCGATGGCTCATTAAAAACAAAATGAAGGCTTTCTATGCTCCGGTTCACGCAGATGACTTGCGAGAAGGTGCACAATACTTGATGCAGCTGAATTGAACGTTATTGCTCCAATTATCTCTAATTTCTTCCTTGCATCGTATGCCTTAATCAACTTTTCAGTATTCCATGCATCACTTGCAAAATCTCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-124-3p(1), mmu-miR-200c-3p(1), mmu-miR-152-3p(1), mmu-miR-148a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATACTTGATGCAGCTGAATTGAACGT
siRNA sets
GTTCAATTCAGCTGCATCA, AATTCAGCTGCATCAAGTA, CAATTCAGCTGCATCAAGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSLC12A2_611_ORF_1
0.7562
-0.005805703
0.41086783
489
ORF sequence:
ATGTGGATCTCCCTTATTGGAGCAATTCTTTGTTGCATAGTGATGTTTGTCATTAACTGGTGGGCTGCGTTGCTCACATATGTGATAGTCCTTGGGCTGTACATTTATGTTACTTACAAAAAACCAGATGTGAACTGGGGATCCTCCACACAAGCGCTGACTTACCTCAGTGCACTGCAGCATTCAATCCGTCTTTCTGGGGTGGAGGACCATGTGAAAAACTTCAGACCACAGTGCCTTGTAATGACAGGTTCTCCAAACTCACGGCCTGCTTTACTTCATCTTGTTCATGACTTCACGAAAAATGTTGGTTTAATGATCTGTGGCCATGTGCATATGGGCCCCAGAAGACAAGCTATGAAAGAGATGTCCATTGATCAAGCCAGATATCAGCGATGGCTCATTAAAAACAAAATGAAGGCTTTCTATGCTCCGGTTCACGCAGATGACTTGCGAGAAGGTGCACAATACTTGATGCAGCTGAATTGA
Peptide sequence:
MWISLIGAILCCIVMFVINWWAALLTYVIVLGLYIYVTYKKPDVNWGSSTQALTYLSALQHSIRLSGVEDHVKNFRPQCLVMTGSPNSRPALLHLVHDFTKNVGLMICGHVHMGPRRQAMKEMSIDQARYQRWLIKNKMKAFYAPVHADDLREGAQYLMQLN
IRESfinder result
IRESfinder score
0.644604606
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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