top of page
mmu_circStxbp4_478
Basic information of circular RNA
PanCircBase ID:
mmu_circStxbp4_478
mm39_Chr. Position ID:
chr11|90426305|90439813|-
Gene name:
Stxbp4
Transcript:
ENSMUST00000143203.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
16,15,14,13
Exon/intron offsets:
0,2431,4686,13331
Genomic length:
13508
Exon/intron sizes in nt:
13,45,01,17,177
Flanking exon/introns:
chr11:90385485-90426305|chr11:90439813-90462547
Splice length:
478
Other database IDs:
circBase: mmu_circ_0003544, CIRCpedia: MMU_CIRCpedia_222854, circAtlas: mmu-Stxbp4_0009
circBase: hsa_circ_0044699, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_21485
Human Ortholog IDs:
Mature spliced Sequence:
GAAGCCAAAGCTGTAGCTGAGGAAACCCGAGCTCTGCGAAGCCGGATTCATCTCGCAGAAGCTGCACAGCGGCAGGCACACGGGATGGAAATGGATTATGAAGAGGTGATCCGTCTGCTAGAGGCTGAGGTCTCAGAACTAAAGGCTCAGCTCGCTGATTATTCTGACCAAAATAAAGAAAGTGTCCAGGACTTGAGAAAAAGAGTCACCGTTCTTGACTGCCAATTGCGAAAATCAGAAATGGCTCGGAAAGCATTCAAGGCGTCCACTGAAAGGCTCCTTGGTTTCATAGAGGCTATTCAAGAAGTTCTTTTGGATAGTTCTGCTCCTTTATCAACTTTAAGTGAAAGAAGAGCTGTGCTCGCATCTCAGACTTCGCTTCCACTGCTGGCAAGGAACGGACGCAGCTTCCCAGCAACCCTGCTTCTGGAATCCAAGGAGCTTGTCAGATCTGTCCGTGCCATACTTGATATGGACT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTTCCACTGCTGGCAAGGAA
60.54
GATGAATCCGGCTTCGCAGA
60.53
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTTCCACTGCTGGCAAGGAA
60.54
GAGATGAATCCGGCTTCGCA
60.53
154
PCR template sequence:
CTTCCACTGCTGGCAAGGAACGGACGCAGCTTCCCAGCAACCCTGCTTCTGGAATCCAAGGAGCTTGTCAGATCTGTCCGTGCCATACTTGATATGGACTGAAGCCAAAGCTGTAGCTGAGGAAACCCGAGCTCTGCGAAGCCGGATTCATCTCGCAGAAGCTGCACAGCGGCAGGCACACGGGATGGAAATGGATTATG
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-26a-5p(1), mmu-miR-26b-5p(1), mmu-miR-183-5p(1), mmu-miR-666-5p(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTTGATATGGACTGAAGCCAAAGCTG
siRNA sets
TTTGGCTTCAGTCCATATC, TTGGCTTCAGTCCATATCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSTXBP4_478_ORF_1
1.0037
0.122187926
0.489577628
396
ORF sequence:
ATGGAAATGGATTATGAAGAGGTGATCCGTCTGCTAGAGGCTGAGGTCTCAGAACTAAAGGCTCAGCTCGCTGATTATTCTGACCAAAATAAAGAAAGTGTCCAGGACTTGAGAAAAAGAGTCACCGTTCTTGACTGCCAATTGCGAAAATCAGAAATGGCTCGGAAAGCATTCAAGGCGTCCACTGAAAGGCTCCTTGGTTTCATAGAGGCTATTCAAGAAGTTCTTTTGGATAGTTCTGCTCCTTTATCAACTTTAAGTGAAAGAAGAGCTGTGCTCGCATCTCAGACTTCGCTTCCACTGCTGGCAAGGAACGGACGCAGCTTCCCAGCAACCCTGCTTCTGGAATCCAAGGAGCTTGTCAGATCTGTCCGTGCCATACTTGATATGGACTGA
Peptide sequence:
MEMDYEEVIRLLEAEVSELKAQLADYSDQNKESVQDLRKRVTVLDCQLRKSEMARKAFKASTERLLGFIEAIQEVLLDSSAPLSTLSERRAVLASQTSLPLLARNGRSFPATLLLESKELVRSVRAILDMD
IRESfinder result
IRESfinder score
0.571198436
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page