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mmu_circSlain1_648
Basic information of circular RNA
PanCircBase ID:
mmu_circSlain1_648
mm39_Chr. Position ID:
chr14|103923104|103932759|+
Gene name:
Slain1
Transcript:
ENSMUST00000069443.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
3,4,5
Exon/intron offsets:
0,2393,9499
Genomic length:
9655
Exon/intron sizes in nt:
15,03,42,156
Flanking exon/introns:
chr14:103894508-103923104|chr14:103932759-103939952
Splice length:
648
Other database IDs:
CIRCpedia: MMU_CIRCpedia_217401
circBase: hsa_circ_0100935, circAtlas: hsa-SLAIN1_0007, CIRCpedia: HSA_CIRCpedia_11149
Human Ortholog IDs:
Mature spliced Sequence:
GTTATACCTCCAGGGGCTCTCCACTTAGTCCGCAGTCATCCATCGACAGTGAGCTGAGTACCTCGGAGTTGGAGGATGACTCTATATCCATGGGATATAAATTACAGGACCTTACTGATGTTCAGATCATGGCTCGTCTGCAAGAAGAGAGTCTCAGGCAAGACTACGCTTCCACGTCAGCATCAGTGTCCAGAAACAGTTCCAGTGTATCCCTGAGTTCAGGGAAAAAGGGGACATGCAGTGATCAAGAGTATGATCGCTACAGCCTGGAGGACGAGGAAGAGTTTGACCATCTGCCGCCACCCCAGCCCCGTCTTCCGAGGTGTTCACCTTTCCAAAGAGGGATCCCCCACTCACAGACTTTCTCCAGCATCCGGGATTGCAGGAGGAGCCCCAGTACCCAGTATTTCCCCTCAAATAACTTCCAGCAGCCACAGTATTACCCACCTCAAGCCCAGACTGCAGACCAGCAACCAAATAGGACCAATGGAGATAAGCTACGAAGAAGCATGCCTAATCTGGCCCGGATGCCGAGCACCGCTGCGGCCAGCAGCAACCTCAGCTCTCCTGTGACAGTGAGGAGCAGTCAGAGCTTTGACTCCAGCTTGCATGGAGCTGGAAGTGGGGTTTCTCGGGTACCGTCCTGCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTGTGACAGTGAGGAGCAG
60.04
TCATCCTCCAACTCCGAGGT
59.96
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGTGAGGAGCAGTCAGAGC
60.11
TCATCCTCCAACTCCGAGGT
59.96
154
PCR template sequence:
AGCAGCAACCTCAGCTCTCCTGTGACAGTGAGGAGCAGTCAGAGCTTTGACTCCAGCTTGCATGGAGCTGGAAGTGGGGTTTCTCGGGTACCGTCCTGCAGTTATACCTCCAGGGGCTCTCCACTTAGTCCGCAGTCATCCATCGACAGTGAGCTGAGTACCTCGGAGTTGGAGGATGACTCTATATCCATGGGATATAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-200c-3p(1), mmu-miR-136-5p(1), mmu-miR-431-5p(1), mmu-miR-300-3p(1), mmu-miR-670-5p(1), mmu-miR-202-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTACCGTCCTGCAGTTATACCTCCAG
siRNA sets
AGGTATAACTGCAGGACGG, GAGGTATAACTGCAGGACG, TATAACTGCAGGACGGTAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSLAIN1_648_ORF_1
0.6998
0.219038882
0.996411376
1206
ORF sequence:
ATGGGATATAAATTACAGGACCTTACTGATGTTCAGATCATGGCTCGTCTGCAAGAAGAGAGTCTCAGGCAAGACTACGCTTCCACGTCAGCATCAGTGTCCAGAAACAGTTCCAGTGTATCCCTGAGTTCAGGGAAAAAGGGGACATGCAGTGATCAAGAGTATGATCGCTACAGCCTGGAGGACGAGGAAGAGTTTGACCATCTGCCGCCACCCCAGCCCCGTCTTCCGAGGTGTTCACCTTTCCAAAGAGGGATCCCCCACTCACAGACTTTCTCCAGCATCCGGGATTGCAGGAGGAGCCCCAGTACCCAGTATTTCCCCTCAAATAACTTCCAGCAGCCACAGTATTACCCACCTCAAGCCCAGACTGCAGACCAGCAACCAAATAGGACCAATGGAGATAAGCTACGAAGAAGCATGCCTAATCTGGCCCGGATGCCGAGCACCGCTGCGGCCAGCAGCAACCTCAGCTCTCCTGTGACAGTGAGGAGCAGTCAGAGCTTTGACTCCAGCTTGCATGGAGCTGGAAGTGGGGTTTCTCGGGTACCGTCCTGCAGTTATACCTCCAGGGGCTCTCCACTTAGTCCGCAGTCATCCATCGACAGTGAGCTGAGTACCTCGGAGTTGGAGGATGACTCTATATCCATGGGATATAAATTACAGGACCTTACTGATGTTCAGATCATGGCTCGTCTGCAAGAAGAGAGTCTCAGGCAAGACTACGCTTCCACGTCAGCATCAGTGTCCAGAAACAGTTCCAGTGTATCCCTGAGTTCAGGGAAAAAGGGGACATGCAGTGATCAAGAGTATGATCGCTACAGCCTGGAGGACGAGGAAGAGTTTGACCATCTGCCGCCACCCCAGCCCCGTCTTCCGAGGTGTTCACCTTTCCAAAGAGGGATCCCCCACTCACAGACTTTCTCCAGCATCCGGGATTGCAGGAGGAGCCCCAGTACCCAGTATTTCCCCTCAAATAACTTCCAGCAGCCACAGTATTACCCACCTCAAGCCCAGACTGCAGACCAGCAACCAAATAGGACCAATGGAGATAAGCTACGAAGAAGCATGCCTAATCTGGCCCGGATGCCGAGCACCGCTGCGGCCAGCAGCAACCTCAGCTCTCCTGTGACAGTGAGGAGCAGTCAGAGCTTTGACTCCAGCTTGCATGGAGCTGGAAGTGGGGTTTCTCGGGTACCGTCCTGC
Peptide sequence:
MGYKLQDLTDVQIMARLQEESLRQDYASTSASVSRNSSSVSLSSGKKGTCSDQEYDRYSLEDEEEFDHLPPPQPRLPRCSPFQRGIPHSQTFSSIRDCRRSPSTQYFPSNNFQQPQYYPPQAQTADQQPNRTNGDKLRRSMPNLARMPSTAAASSNLSSPVTVRSSQSFDSSLHGAGSGVSRVPSCSYTSRGSPLSPQSSIDSELSTSELEDDSISMGYKLQDLTDVQIMARLQEESLRQDYASTSASVSRNSSSVSLSSGKKGTCSDQEYDRYSLEDEEEFDHLPPPQPRLPRCSPFQRGIPHSQTFSSIRDCRRSPSTQYFPSNNFQQPQYYPPQAQTADQQPNRTNGDKLRRSMPNLARMPSTAAASSNLSSPVTVRSSQSFDSSLHGAGSGVSRVPSC
IRESfinder result
IRESfinder score
0.459131487
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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