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mmu_circStambpl1_1204
Basic information of circular RNA
PanCircBase ID:
mmu_circStambpl1_1204
mm39_Chr. Position ID:
chr19|34197586|34216288|+
Gene name:
Stambpl1
Transcript:
ENSMUST00000054956.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
2,3,4,5,6,7,8,9
Exon/intron offsets:
0,6355,9906,11244,13774,15023,16089,18589
Genomic length:
18702
Exon/intron sizes in nt:
80,21,87,69,63,58,12,50,00,000
Flanking exon/introns:
chr19:34170031-34197586|chr19:34216288-34216902
Splice length:
1204
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATGAAGTGACTGAGAAGGAGTGAGCACCTTGCCTTTGCAGACAGGACAGCATGGAGCAGCCATTCACTGTGAATTCACTGAAAAAGTTAGCTGCTATGCCTGACCATACAGATGTTTCTCTAAGTCCAGAGGAGCGGGTCCGCGCCCTAAGCAAACTTGGTTGTAATATCTCCATTAATGAAGATATCACCCCACGCCGTTACTTCAGGTCCGGAGTGGAAATGGAAAGGATGGCATCTGTGTATTTGGAAGAAGGAAACCTGGAAAATGCCTTTGTTCTTTATAACAAATTTATAACGTTATTTGTAGAAAAACTTCCCAGCCACCGAGATTACCAGCAGTGTGCAGTTCCAGAGAAGCAGGATATTATGAAGAAACTGAAGGAGATTGCGTTCCCAAGGACAGACGAATTGAAAACGGACCTGCTAAGGAAATATAACATAGAATACCAAGAGTATTTGCAAAGTAAAAACAAATATAAAGCCGAAATTCTCAAAAAGTTGGAACATCAGAGACTGATAGAGGCAGAGCGCCAGCGGATAGCTCAGATGCGCCAGCAGCAACTAGAGTCTGAACAGTTCCTGTTTTTTGAAGACCAACTCAAGAAGCAGGAGTTGGCTCGAGGCCAGATTCGAGGTCAGGACTCTCCGGTGTTGTCTGAGCAGACTGACGGAAGTGCGCTGTCCTGCTTTTCCACCCACCAGAGCAACTCTCTGAGGAACGCATTTGCAGATCACCCTCATAAAAGTGATGGAAGCAATTTCGCTAACTACTCTCCTCCCGTGAACAGGGCCCTAAAGCCAGCAGCCACCCTGAGTGCTGTTCAGAATTTGGTGGTTGAAGGGCTGAGGTGTGTAGTTTTATCAAGAGATCTTTGCCATAAATTTCTGCTGCTGGCTGACTCTAACACAGTGAGAGGAATAGAGACCTGTGGGATCCTCTGTGGAAAACTGACACACAATGAATTCACCATTACTCATGTGGTTGTGCCAAAGCAGTCTGCTGGCCCAGACTATTGCGATGTGGAGAACGTCGAAGAATTATTCAATGTTCAGGATCAACATGGTCTCCTCACACTGGGATGGATCCATACACACCCCACGCAAACGGCATTCCTGTCCAGTGTGGATCTCCACACTCACTGCTCCTACCAGCTTATGTTGCCAGAGGCCATTGCCATTGTGTGTTCCCCAAAGCATAAAGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCATTCCTGTCCAGTGTGGA
59.96
TCACAGTGAATGGCTGCTCC
60.32
167
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CACTCACTGCTCCTACCAGC
60.11
TCACAGTGAATGGCTGCTCC
60.32
141
PCR template sequence:
AAACGGCATTCCTGTCCAGTGTGGATCTCCACACTCACTGCTCCTACCAGCTTATGTTGCCAGAGGCCATTGCCATTGTGTGTTCCCCAAAGCATAAAGAATGAAGTGACTGAGAAGGAGTGAGCACCTTGCCTTTGCAGACAGGACAGCATGGAGCAGCCATTCACTGTGAATTCACTGAAAAAGTTAGCTGCTATGCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-223-3p(2), mmu-miR-16-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-199a-5p(1), mmu-miR-322-5p(1), mmu-miR-128-3p(1), mmu-miR-96-5p(1), mmu-miR-335-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
CAAAGCATAAAGAATGAAGTGACTGA
siRNA sets
TCACTTCATTCTTTATGCT, GTCACTTCATTCTTTATGC, CTTCATTCTTTATGCTTTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSTAMBPL1_1204_ORF_1
1.0314
0.172020845
0.996592897
1158
ORF sequence:
ATGGAGCAGCCATTCACTGTGAATTCACTGAAAAAGTTAGCTGCTATGCCTGACCATACAGATGTTTCTCTAAGTCCAGAGGAGCGGGTCCGCGCCCTAAGCAAACTTGGTTGTAATATCTCCATTAATGAAGATATCACCCCACGCCGTTACTTCAGGTCCGGAGTGGAAATGGAAAGGATGGCATCTGTGTATTTGGAAGAAGGAAACCTGGAAAATGCCTTTGTTCTTTATAACAAATTTATAACGTTATTTGTAGAAAAACTTCCCAGCCACCGAGATTACCAGCAGTGTGCAGTTCCAGAGAAGCAGGATATTATGAAGAAACTGAAGGAGATTGCGTTCCCAAGGACAGACGAATTGAAAACGGACCTGCTAAGGAAATATAACATAGAATACCAAGAGTATTTGCAAAGTAAAAACAAATATAAAGCCGAAATTCTCAAAAAGTTGGAACATCAGAGACTGATAGAGGCAGAGCGCCAGCGGATAGCTCAGATGCGCCAGCAGCAACTAGAGTCTGAACAGTTCCTGTTTTTTGAAGACCAACTCAAGAAGCAGGAGTTGGCTCGAGGCCAGATTCGAGGTCAGGACTCTCCGGTGTTGTCTGAGCAGACTGACGGAAGTGCGCTGTCCTGCTTTTCCACCCACCAGAGCAACTCTCTGAGGAACGCATTTGCAGATCACCCTCATAAAAGTGATGGAAGCAATTTCGCTAACTACTCTCCTCCCGTGAACAGGGCCCTAAAGCCAGCAGCCACCCTGAGTGCTGTTCAGAATTTGGTGGTTGAAGGGCTGAGGTGTGTAGTTTTATCAAGAGATCTTTGCCATAAATTTCTGCTGCTGGCTGACTCTAACACAGTGAGAGGAATAGAGACCTGTGGGATCCTCTGTGGAAAACTGACACACAATGAATTCACCATTACTCATGTGGTTGTGCCAAAGCAGTCTGCTGGCCCAGACTATTGCGATGTGGAGAACGTCGAAGAATTATTCAATGTTCAGGATCAACATGGTCTCCTCACACTGGGATGGATCCATACACACCCCACGCAAACGGCATTCCTGTCCAGTGTGGATCTCCACACTCACTGCTCCTACCAGCTTATGTTGCCAGAGGCCATTGCCATTGTGTGTTCCCCAAAGCATAAAGAATGA
Peptide sequence:
MEQPFTVNSLKKLAAMPDHTDVSLSPEERVRALSKLGCNISINEDITPRRYFRSGVEMERMASVYLEEGNLENAFVLYNKFITLFVEKLPSHRDYQQCAVPEKQDIMKKLKEIAFPRTDELKTDLLRKYNIEYQEYLQSKNKYKAEILKKLEHQRLIEAERQRIAQMRQQQLESEQFLFFEDQLKKQELARGQIRGQDSPVLSEQTDGSALSCFSTHQSNSLRNAFADHPHKSDGSNFANYSPPVNRALKPAATLSAVQNLVVEGLRCVVLSRDLCHKFLLLADSNTVRGIETCGILCGKLTHNEFTITHVVVPKQSAGPDYCDVENVEELFNVQDQHGLLTLGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSPKHKE
IRESfinder result
IRESfinder score
0.563852054
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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