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mmu_circSsh2_553
Basic information of circular RNA
PanCircBase ID:
mmu_circSsh2_553
mm39_Chr. Position ID:
chr11|77307240|77316477|+
Gene name:
Ssh2
Transcript:
ENSMUST00000037912.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,7,8,9,10
Exon/intron offsets:
0,1051,4801,8886,9108
Genomic length:
9237
Exon/intron sizes in nt:
6,96,61,95,94,129
Flanking exon/introns:
chr11:77299073-77307240|chr11:77316477-77320611
Splice length:
553
Other database IDs:
circAtlas: mmu-Ssh2_0012
circBase: hsa_circ_0042809, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_19978
Human Ortholog IDs:
Mature spliced Sequence:
TAGCACTTGTACCATGGGCTTGGTCTTGCCTCTCTGGAGTGACACCCTAATTCATTTGGATGGTGATGGTGGGTTCAGCGTATCAACAGATAACAGAGTTCACATATTCAAACCTGTATCTGTGCAAGCAATGTGGTCTGCACTACAGAGTTTGCACAAGGCTTGTGAAGTGGCCAGAATGCATAACTACTATCCAGGCAGCCTTTTTCTCACTTGGGTGAGTTATTACGAGAGCCATATCAACTCAGATCAGTCCTCAGTCAATGAGTGGAATGCTATGCAGGATGTGCAGTCTCATCGGCCTGACTCTCCAGCCCTCTTCACAGACATACCAACTGAACGTGAGCGAACAGAAAGGCTTATTAAGACTAAATTAAGGGAGATCATGATGCAAAAGGATTTGGAGAATATCACCTCCAAAGAGATACGCACGGAGCTGGAGATGCAGATGGTGTGCAACTTGCGAGAATTTAAGGAATTCATAGATAATGAAATGATCGTGATCCTTGGTCAGATGGACAGTCCCACACAGATATTTGAGCATGTATTCCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGTGATCCTTGGTCAGATGGA
59.52
TTGATACGCTGAACCCACCA
59.31
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCGTGATCCTTGGTCAGATGG
59.52
TTGATACGCTGAACCCACCA
59.31
142
PCR template sequence:
GTGCAACTTGCGAGAATTTAAGGAATTCATAGATAATGAAATGATCGTGATCCTTGGTCAGATGGACAGTCCCACACAGATATTTGAGCATGTATTCCTGTAGCACTTGTACCATGGGCTTGGTCTTGCCTCTCTGGAGTGACACCCTAATTCATTTGGATGGTGATGGTGGGTTCAGCGTATCAACAGATAACAGAGTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-19a-3p(1), mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
GCATGTATTCCTGTAGCACTTGTACC
siRNA sets
GTGCTACAGGAATACATGC, CAAGTGCTACAGGAATACA, AAGTGCTACAGGAATACAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSSH2_553_ORF_1
0.9361
0.161103936
0.768619738
564
ORF sequence:
ATGTATTCCTGTAGCACTTGTACCATGGGCTTGGTCTTGCCTCTCTGGAGTGACACCCTAATTCATTTGGATGGTGATGGTGGGTTCAGCGTATCAACAGATAACAGAGTTCACATATTCAAACCTGTATCTGTGCAAGCAATGTGGTCTGCACTACAGAGTTTGCACAAGGCTTGTGAAGTGGCCAGAATGCATAACTACTATCCAGGCAGCCTTTTTCTCACTTGGGTGAGTTATTACGAGAGCCATATCAACTCAGATCAGTCCTCAGTCAATGAGTGGAATGCTATGCAGGATGTGCAGTCTCATCGGCCTGACTCTCCAGCCCTCTTCACAGACATACCAACTGAACGTGAGCGAACAGAAAGGCTTATTAAGACTAAATTAAGGGAGATCATGATGCAAAAGGATTTGGAGAATATCACCTCCAAAGAGATACGCACGGAGCTGGAGATGCAGATGGTGTGCAACTTGCGAGAATTTAAGGAATTCATAGATAATGAAATGATCGTGATCCTTGGTCAGATGGACAGTCCCACACAGATATTTGAGCATGTATTCCTG
Peptide sequence:
MYSCSTCTMGLVLPLWSDTLIHLDGDGGFSVSTDNRVHIFKPVSVQAMWSALQSLHKACEVARMHNYYPGSLFLTWVSYYESHINSDQSSVNEWNAMQDVQSHRPDSPALFTDIPTERERTERLIKTKLREIMMQKDLENITSKEIRTELEMQMVCNLREFKEFIDNEMIVILGQMDSPTQIFEHVFL
IRESfinder result
IRESfinder score
0.671459258
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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