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mmu_circCspp1_328
Basic information of circular RNA
PanCircBase ID:
mmu_circCspp1_328
mm39_Chr. Position ID:
chr1|10196564|10200257|+
Gene name:
Cspp1
Transcript:
ENSMUST00000071087.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
24,25,26
Exon/intron offsets:
0,1083,3646
Genomic length:
3693
Exon/intron sizes in nt:
140,141,47
Flanking exon/introns:
chr1:10186956-10196564|chr1:10200257-10202678
Splice length:
328
Other database IDs:
circAtlas: mmu-Cspp1_0050
circBase: hsa_circ_0136976, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_141508
Human Ortholog IDs:
Mature spliced Sequence:
GAAAAGAGAGAGGAACCCAATGGATATATTTGACATGGCTAGACATCGGGTACAAGCCCCTGTCAGAAGACCATCGCCTAAGGGCTTAGATGCTACTACTTTTCAGAATATTCATGACTTTAATGAGCTGAGAGAGAGAGATTCAGATACTCGAGTGGATCTGAGATTAATGTACCCAGATCCTCCCCGCGATCATCACACCTTGGAGATTCAGCAGCAGGCCCTACTCCGAGAGCAGCAGAAGAGGCTTAATAGAATAAAGATGCGGAGAGATGCAGGAGCTGATTTGGACACCATCTGCACTGATAATGCACAAGGGCGCAGAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGATGCGGAGAGATGCAGG
59.89
GATGGTCTTCTGACAGGGGC
60.11
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGATGCGGAGAGATGCAGG
59.89
CGATGGTCTTCTGACAGGGG
59.82
145
PCR template sequence:
CCGAGAGCAGCAGAAGAGGCTTAATAGAATAAAGATGCGGAGAGATGCAGGAGCTGATTTGGACACCATCTGCACTGATAATGCACAAGGGCGCAGAATGGAAAAGAGAGAGGAACCCAATGGATATATTTGACATGGCTAGACATCGGGTACAAGCCCCTGTCAGAAGACCATCGCCTAAGGGCTTAGATGCTACTACT
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-216a-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
AGGGCGCAGAATGGAAAAGAGAGAGG
siRNA sets
TCTCTTTTCCATTCTGCGC, CTCTTTTCCATTCTGCGCC, TCTCTCTTTTCCATTCTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCSPP1_328_ORF_1
1.0167
0.1786161
0.533350804
384
ORF sequence:
ATGCAGGAGCTGATTTGGACACCATCTGCACTGATAATGCACAAGGGCGCAGAATGGAAAAGAGAGAGGAACCCAATGGATATATTTGACATGGCTAGACATCGGGTACAAGCCCCTGTCAGAAGACCATCGCCTAAGGGCTTAGATGCTACTACTTTTCAGAATATTCATGACTTTAATGAGCTGAGAGAGAGAGATTCAGATACTCGAGTGGATCTGAGATTAATGTACCCAGATCCTCCCCGCGATCATCACACCTTGGAGATTCAGCAGCAGGCCCTACTCCGAGAGCAGCAGAAGAGGCTTAATAGAATAAAGATGCGGAGAGATGCAGGAGCTGATTTGGACACCATCTGCACTGATAATGCACAAGGGCGCAGAATG
Peptide sequence:
MQELIWTPSALIMHKGAEWKRERNPMDIFDMARHRVQAPVRRPSPKGLDATTFQNIHDFNELRERDSDTRVDLRLMYPDPPRDHHTLEIQQQALLREQQKRLNRIKMRRDAGADLDTICTDNAQGRRM
IRESfinder result
IRESfinder score
0.487156929
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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