top of page
mmu_ciStambpl1_941
Basic information of circular RNA
PanCircBase ID:
mmu_ciStambpl1_941
mm39_Chr. Position ID:
chr19|34212734|34213675|+
Gene name:
Stambpl1
Transcript:
ENSMUST00000054956.15
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
7
Exon/intron offsets:
0
Genomic length:
941
Exon/intron sizes in nt:
941
Flanking exon/introns:
chr19:34212734-34213675
Splice length:
941
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTATGATCTTATTCCATCTCTCAATAGGGTCCATTGAGTAGTACTGGCTTCCCTGTGATAGGAAGAGCAGTGTAGATGGGGGCTGGGCAGGGGTAAATATTATGAAGTTACTATTAACTCTTACATATCCTTAAACTACTGACATTATTCATGGATTTGGTATTCTTAAAAAAAATGAGCTCTAAAATTTCAGAAACATTGTAAAACTCCTTAAACAAACTATTTAGAAAATGGTAAAATAGGAGGCAAGATGTAAAGAATAGTACTCAACACATTAGAGGGCCCTGAGGCTGGAGACAGGATGGTATTTTAGAAGGGTGGGAGGTCCCCAGGTCTGGAAGAGGACAGCAACTCACAACCCAGTGACCTAAATAAATCTCTTTACTTCAAGACCCCTTCTTTTCCATACTTACCTTTTCCCCAAGGAGAGCAATATGTTTCTTCTTACTAGATTCTAAAAGCTGTATCATTTTCATTTTGGAAGACACTGGAGACTCTTAGAGGAAAAGTCCTAATTCTTTCATAATTACATACAATTAATAAAAACAAGACATCAGCCCTGACAACTCATAGGCATACCTTTTAGTAGCATCAGGCATTTGGGAAATTAGTCTGTCTCTCTAAAGAATGCTGGTCTTGCTGTGTGAAGACATTTTCCATTGTAGGTCAAGTACGCAAAGAAATCATTTGTTAACTATGTATCAATTACCCATTGTTCACCCTGATACTAATTCCTTTCTACTTTCTATAGCAGCAATGGGATTCAAGACCCAAATAATGGATGTCCAAAACCTTTTAGTAGAGTCAGTTTTTCTGCTTGGTTTTGGATTGTGAGAGAGTGTAGTGAGATACAAGGGGTGAGGTCTGCTGGCTGATGACATCCTGTCCAGATGTCTCTTCTCTCAGAGGCTTGTTACTTTTTGTTTTGTTTTGTTTTCTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGGCTGATGACATCCTGT
60.11
ATATTTACCCCTGCCCAGCC
59.52
175
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGTCTGCTGGCTGATGACAT
60.11
ATATTTACCCCTGCCCAGCC
59.52
180
PCR template sequence:
TAGTGAGATACAAGGGGTGAGGTCTGCTGGCTGATGACATCCTGTCCAGATGTCTCTTCTCTCAGAGGCTTGTTACTTTTTGTTTTGTTTTGTTTTCTAGGTATGATCTTATTCCATCTCTCAATAGGGTCCATTGAGTAGTACTGGCTTCCCTGTGATAGGAAGAGCAGTGTAGATGGGGGCTGGGCAGGGGTAAATAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-153-3p(1), mmu-miR-192-5p(1), mmu-miR-541-5p(1), mmu-miR-215-5p(1), mmu-miR-377-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTTGTTTTCTAGGTATGATCTTATT
siRNA sets
AATAAGATCATACCTAGAA, AAGATCATACCTAGAAAAC, AGATCATACCTAGAAAACA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CISTAMBPL1_941_ORF_3
0.7238
-0.566861274
0.004154673
108
ORF sequence:
ATGACATCCTGTCCAGATGTCTCTTCTCTCAGAGGCTTGTTACTTTTTGTTTTGTTTTGTTTTCTAGGTATGATCTTATTCCATCTCTCAATAGGGTCCATTGAGTAG
Peptide sequence:
MTSCPDVSSLRGLLLFVLFCFLGMILFHLSIGSIE
IRESfinder result
IRESfinder score
0.856326558
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page