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mmu_circSpats2l_402
Basic information of circular RNA
PanCircBase ID:
mmu_circSpats2l_402
mm39_Chr. Position ID:
chr1|57939792|57962583|+
Gene name:
Spats2l
Transcript:
ENSMUST00000163239.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
6,7,8
Exon/intron offsets:
0,1455,22732
Genomic length:
22791
Exon/intron sizes in nt:
207,136,59
Flanking exon/introns:
chr1:57925108-57939792|chr1:57962583-57977070
Splice length:
402
Other database IDs:
circBase: mmu_circ_0000043, circAtlas: mmu-Spats2l_0009
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
AAGGCGGCAGACTACTGCAGCAGAAAATGTCCTTAGATGGGAACCCCAGAGCGATTCATGGACCATCAGAGAGGTCAGATGGCCCACAGTGGTCAGCTGGGCAGCCTTGTAACCCAAGCAAGCCTAAGGCAAAAACATCTCCTGTTAAGTCCAATGCCCCTGCAGCTCATCTTGAAATAAAGCCAGATGAGCTGGCAAAGAAAAGAGGCCCAAATATTGAGAAATCGGTGAAGGATCTGCAGCGCTGCACTGTTTCTCTGACGAGATACCGCGTCATGATCAAGGAAGAAGTGGACAGTTCCGTGAAGAAGATCAAAGCAGCATTTGCTGAGCTACACAACTGCATCATTGACAAAGAAGTTTCACTGATGGCAGAAATGGACAAAGTTAAAGAAGAAGCCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTGAGCTACACAACTGCA
59.89
TGGTCCATGAATCGCTCTGG
59.82
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTGAGCTACACAACTGCA
59.89
GTCCATGAATCGCTCTGGGG
60.53
140
PCR template sequence:
GTGAAGAAGATCAAAGCAGCATTTGCTGAGCTACACAACTGCATCATTGACAAAGAAGTTTCACTGATGGCAGAAATGGACAAAGTTAAAGAAGAAGCCAAAGGCGGCAGACTACTGCAGCAGAAAATGTCCTTAGATGGGAACCCCAGAGCGATTCATGGACCATCAGAGAGGTCAGATGGCCCACAGTGGTCAGCTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-129-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAAGAAGAAGCCAAAGGCGGCAGACT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSPATS2L_402_ORF_1
0.9586
0.289155196
0.964772023
777
ORF sequence:
ATGTCCTTAGATGGGAACCCCAGAGCGATTCATGGACCATCAGAGAGGTCAGATGGCCCACAGTGGTCAGCTGGGCAGCCTTGTAACCCAAGCAAGCCTAAGGCAAAAACATCTCCTGTTAAGTCCAATGCCCCTGCAGCTCATCTTGAAATAAAGCCAGATGAGCTGGCAAAGAAAAGAGGCCCAAATATTGAGAAATCGGTGAAGGATCTGCAGCGCTGCACTGTTTCTCTGACGAGATACCGCGTCATGATCAAGGAAGAAGTGGACAGTTCCGTGAAGAAGATCAAAGCAGCATTTGCTGAGCTACACAACTGCATCATTGACAAAGAAGTTTCACTGATGGCAGAAATGGACAAAGTTAAAGAAGAAGCCAAAGGCGGCAGACTACTGCAGCAGAAAATGTCCTTAGATGGGAACCCCAGAGCGATTCATGGACCATCAGAGAGGTCAGATGGCCCACAGTGGTCAGCTGGGCAGCCTTGTAACCCAAGCAAGCCTAAGGCAAAAACATCTCCTGTTAAGTCCAATGCCCCTGCAGCTCATCTTGAAATAAAGCCAGATGAGCTGGCAAAGAAAAGAGGCCCAAATATTGAGAAATCGGTGAAGGATCTGCAGCGCTGCACTGTTTCTCTGACGAGATACCGCGTCATGATCAAGGAAGAAGTGGACAGTTCCGTGAAGAAGATCAAAGCAGCATTTGCTGAGCTACACAACTGCATCATTGACAAAGAAGTTTCACTGATGGCAGAAATGGACAAAGTTAAAGAAGAAGCC
Peptide sequence:
MSLDGNPRAIHGPSERSDGPQWSAGQPCNPSKPKAKTSPVKSNAPAAHLEIKPDELAKKRGPNIEKSVKDLQRCTVSLTRYRVMIKEEVDSSVKKIKAAFAELHNCIIDKEVSLMAEMDKVKEEAKGGRLLQQKMSLDGNPRAIHGPSERSDGPQWSAGQPCNPSKPKAKTSPVKSNAPAAHLEIKPDELAKKRGPNIEKSVKDLQRCTVSLTRYRVMIKEEVDSSVKKIKAAFAELHNCIIDKEVSLMAEMDKVKEEA
IRESfinder result
IRESfinder score
0.2820648
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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