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mmu_circStambpl1_470
Basic information of circular RNA
PanCircBase ID:
mmu_circStambpl1_470
mm39_Chr. Position ID:
chr19|34197586|34208926|+
Gene name:
Stambpl1
Transcript:
ENSMUST00000054956.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
2,3,4,5
Exon/intron offsets:
0,6355,9906,11244
Genomic length:
11340
Exon/intron sizes in nt:
80,218,76,96
Flanking exon/introns:
chr19:34170031-34197586|chr19:34208926-34211360
Splice length:
470
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
ATGAAGTGACTGAGAAGGAGTGAGCACCTTGCCTTTGCAGACAGGACAGCATGGAGCAGCCATTCACTGTGAATTCACTGAAAAAGTTAGCTGCTATGCCTGACCATACAGATGTTTCTCTAAGTCCAGAGGAGCGGGTCCGCGCCCTAAGCAAACTTGGTTGTAATATCTCCATTAATGAAGATATCACCCCACGCCGTTACTTCAGGTCCGGAGTGGAAATGGAAAGGATGGCATCTGTGTATTTGGAAGAAGGAAACCTGGAAAATGCCTTTGTTCTTTATAACAAATTTATAACGTTATTTGTAGAAAAACTTCCCAGCCACCGAGATTACCAGCAGTGTGCAGTTCCAGAGAAGCAGGATATTATGAAGAAACTGAAGGAGATTGCGTTCCCAAGGACAGACGAATTGAAAACGGACCTGCTAAGGAAATATAACATAGAATACCAAGAGTATTTGCAAAGTAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGTTCCCAAGGACAGACGAA
59.97
TCACAGTGAATGGCTGCTCC
60.32
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGAGATTGCGTTCCCAAGG
60.04
TCACAGTGAATGGCTGCTCC
60.32
161
PCR template sequence:
GAAGAAACTGAAGGAGATTGCGTTCCCAAGGACAGACGAATTGAAAACGGACCTGCTAAGGAAATATAACATAGAATACCAAGAGTATTTGCAAAGTAAAATGAAGTGACTGAGAAGGAGTGAGCACCTTGCCTTTGCAGACAGGACAGCATGGAGCAGCCATTCACTGTGAATTCACTGAAAAAGTTAGCTGCTATGCC
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-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-128-3p(1), mmu-miR-335-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
TTTGCAAAGTAAAATGAAGTGACTGA
siRNA sets
TCACTTCATTTTACTTTGC, CACTTCATTTTACTTTGCA, TCAGTCACTTCATTTTACT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSTAMBPL1_470_ORF_1
0.9278
0.158576312
0.550932165
429
ORF sequence:
ATGGAGCAGCCATTCACTGTGAATTCACTGAAAAAGTTAGCTGCTATGCCTGACCATACAGATGTTTCTCTAAGTCCAGAGGAGCGGGTCCGCGCCCTAAGCAAACTTGGTTGTAATATCTCCATTAATGAAGATATCACCCCACGCCGTTACTTCAGGTCCGGAGTGGAAATGGAAAGGATGGCATCTGTGTATTTGGAAGAAGGAAACCTGGAAAATGCCTTTGTTCTTTATAACAAATTTATAACGTTATTTGTAGAAAAACTTCCCAGCCACCGAGATTACCAGCAGTGTGCAGTTCCAGAGAAGCAGGATATTATGAAGAAACTGAAGGAGATTGCGTTCCCAAGGACAGACGAATTGAAAACGGACCTGCTAAGGAAATATAACATAGAATACCAAGAGTATTTGCAAAGTAAAATGAAGTGA
Peptide sequence:
MEQPFTVNSLKKLAAMPDHTDVSLSPEERVRALSKLGCNISINEDITPRRYFRSGVEMERMASVYLEEGNLENAFVLYNKFITLFVEKLPSHRDYQQCAVPEKQDIMKKLKEIAFPRTDELKTDLLRKYNIEYQEYLQSKMK
IRESfinder result
IRESfinder score
0.612468448
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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