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mmu_circGabpb1_795
Basic information of circular RNA
PanCircBase ID:
mmu_circGabpb1_795
mm39_Chr. Position ID:
chr2|126491987|126505008|-
Gene name:
Gabpb1
Transcript:
ENSMUST00000103227.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
7,6,5,4,3,2
Exon/intron offsets:
0,441,2165,3487,8402,12923
Genomic length:
13021
Exon/intron sizes in nt:
114,112,195,168,108,98
Flanking exon/introns:
chr2:126488665-126491987|chr2:126505008-126517275
Splice length:
795
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CAGCCCTCCTACCTGCTGACCAGCTCCCAGACTCTTGGGCATTTTCATTGTCTGGATGCAACTGAATTTCTCCCAGTCAGAATTCATTGTGTTTTCAGATGTCCCTGGTAGATTTGGGGAAGAAGCTTTTAGAAGCGGCACGAGCCGGTCAAGATGATGAAGTTCGCATTTTGATGGCAAATGGAGCTCCTTTTACTACAGACTGGTTGGGAACTTCTCCACTTCATCTGGCCGCACAGTATGGGCATTTCTCTACCACAGAGGTTCTTCTCCGAGCCGGTGTAAGTAGAGATGCCAGGACCAAAGTGGACCGGACACCACTGCACATGGCGGCTTCTGAGGGCCATGCCAACATAGTAGAAGTTTTGCTTAAGCATGGTGCTGACGTCAATGCAAAGGATATGTTAAAGATGACAGCTCTGCATTGGGCAACAGAACATAATCATCAAGAGGTGGTGGAGCTTTTAATCAAATATGGTGCTGATGTACACACGCAGAGTAAATTTTGTAAAACTGCATTTGATATTTCAATAGACAATGGAAATGAAGATTTAGCAGAGATATTACAGATTGCTATGCAGAACCAAATCAACACCAACCCGGAGAGTCCTGACACTGTGACAATACACGCTGCCACACCACAGTTCATCATTGGACCCGGAGGGGTGGTGAACCTCACAGATGAAACAGGAGTATCTGCTGTTCAGTTTGGAAACTCCTCTACGTCAGTATTAGCTACGTTAGCTGCCTTAGCTGAAGCTTCTGCCCCATTGTCCAATTCTTCAGAAACTCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTGTTCAGTTTGGAAACTCC
59.31
TGAAAATGCCCAAGAGTCTGG
58.48
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGTTCAGTTTGGAAACTCCT
59.05
TGAAAATGCCCAAGAGTCTGG
58.48
144
PCR template sequence:
TCTGCTGTTCAGTTTGGAAACTCCTCTACGTCAGTATTAGCTACGTTAGCTGCCTTAGCTGAAGCTTCTGCCCCATTGTCCAATTCTTCAGAAACTCCAGCAGCCCTCCTACCTGCTGACCAGCTCCCAGACTCTTGGGCATTTTCATTGTCTGGATGCAACTGAATTTCTCCCAGTCAGAATTCATTGTGTTTTCAGAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-29b-3p(2), mmu-miR-29c-3p(2), mmu-miR-9-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-29a-3p(1), mmu-miR-33-5p(1), mmu-miR-128-3p(1), mmu-miR-136-5p(1), mmu-miR-680(1), mmu-miR-539-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCAGAAACTCCAGCAGCCCTCCTACC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGABPB1_795_ORF_1
1.0559
0.117235872
0.934716251
762
ORF sequence:
ATGTCCCTGGTAGATTTGGGGAAGAAGCTTTTAGAAGCGGCACGAGCCGGTCAAGATGATGAAGTTCGCATTTTGATGGCAAATGGAGCTCCTTTTACTACAGACTGGTTGGGAACTTCTCCACTTCATCTGGCCGCACAGTATGGGCATTTCTCTACCACAGAGGTTCTTCTCCGAGCCGGTGTAAGTAGAGATGCCAGGACCAAAGTGGACCGGACACCACTGCACATGGCGGCTTCTGAGGGCCATGCCAACATAGTAGAAGTTTTGCTTAAGCATGGTGCTGACGTCAATGCAAAGGATATGTTAAAGATGACAGCTCTGCATTGGGCAACAGAACATAATCATCAAGAGGTGGTGGAGCTTTTAATCAAATATGGTGCTGATGTACACACGCAGAGTAAATTTTGTAAAACTGCATTTGATATTTCAATAGACAATGGAAATGAAGATTTAGCAGAGATATTACAGATTGCTATGCAGAACCAAATCAACACCAACCCGGAGAGTCCTGACACTGTGACAATACACGCTGCCACACCACAGTTCATCATTGGACCCGGAGGGGTGGTGAACCTCACAGATGAAACAGGAGTATCTGCTGTTCAGTTTGGAAACTCCTCTACGTCAGTATTAGCTACGTTAGCTGCCTTAGCTGAAGCTTCTGCCCCATTGTCCAATTCTTCAGAAACTCCAGCAGCCCTCCTACCTGCTGACCAGCTCCCAGACTCTTGGGCATTTTCATTGTCTGGATGCAACTGA
Peptide sequence:
MSLVDLGKKLLEAARAGQDDEVRILMANGAPFTTDWLGTSPLHLAAQYGHFSTTEVLLRAGVSRDARTKVDRTPLHMAASEGHANIVEVLLKHGADVNAKDMLKMTALHWATEHNHQEVVELLIKYGADVHTQSKFCKTAFDISIDNGNEDLAEILQIAMQNQINTNPESPDTVTIHAATPQFIIGPGGVVNLTDETGVSAVQFGNSSTSVLATLAALAEASAPLSNSSETPAALLPADQLPDSWAFSLSGCN
IRESfinder result
IRESfinder score
0.50581254
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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