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mmu_circGsk3b_531
Basic information of circular RNA
PanCircBase ID:
mmu_circGsk3b_531
mm39_Chr. Position ID:
chr16|37991025|38014356|+
Gene name:
Gsk3b
Transcript:
ENSMUST00000023507.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
3,4,5,6,7
Exon/intron offsets:
0,13771,17147,20864,23233
Genomic length:
23331
Exon/intron sizes in nt:
84,111,131,107,98
Flanking exon/introns:
chr16:37964815-37991025|chr16:38014356-38028356
Splice length:
531
Other database IDs:
circBase: mmu_circ_0006260, CIRCpedia: MMU_CIRCpedia_18824, circAtlas: mmu-Gsk3b_0003
circBase: hsa_circ_0007926, circAtlas: hsa-GSK3B_0003, CIRCpedia: HSA_CIRCpedia_43097
Human Ortholog IDs:
Mature spliced Sequence:
AACCGAGAGCTCCAGATCATGAGAAAGCTAGACCACTGTAACATAGTCCGACTGCGGTATTTCTTCTACTCGAGTGGTGAGAAGAAAGATGAGGTCTACCTTAACCTGGTGCTGGACTATGTTCCGGAGACAGTGTACAGAGTCGCCAGACACTATAGTCGAGCCAAGCAGACACTCCCTGTGATCTATGTCAAGTTGTATATGTATCAGCTGTTCAGAAGTCTAGCCTATATCCATTCCTTTGGAATCTGCCATCGAGACATTAAACCACAGAACCTCTTGTTGGATCCTGATACAGCTGTATTAAAACTCTGTGACTTTGGAAGTGCAAAGCAGCTGGTCCGAGGAGAGCCCAATGTTTCATATATCTGTTCTCGGTACTACAGGGCACCAGAGTTGATCTTTGGAGCCACTGATTACACGTCCAGTATAGATGTATGGTCTGCAGGCTGTGTGTTGGCTGAATTGTTGCTAGGACAACCAATATTTCCTGGGGACAGTGGTGTGGATCAGTTGGTGGAAATAATAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTATGGTCTGCAGGCTGTGT
60.04
CGCAGTCGGACTATGTTACAGT
60.16
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TATGGTCTGCAGGCTGTGTG
60.04
CGCAGTCGGACTATGTTACAGT
60.16
151
PCR template sequence:
AGATGTATGGTCTGCAGGCTGTGTGTTGGCTGAATTGTTGCTAGGACAACCAATATTTCCTGGGGACAGTGGTGTGGATCAGTTGGTGGAAATAATAAAGAACCGAGAGCTCCAGATCATGAGAAAGCTAGACCACTGTAACATAGTCCGACTGCGGTATTTCTTCTACTCGAGTGGTGAGAAGAAAGATGAGGTCTACC
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-10b-5p(1), mmu-miR-434-5p(1), mmu-miR-433-3p(1), mmu-miR-466d-3p(1), mmu-miR-224-5p(1), mmu-miR-190b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGAAATAATAAAGAACCGAGAGCTCC
siRNA sets
TCGGTTCTTTATTATTTCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGSK3B_531_ORF_1
0.8324
0.179108675
0.989503473
1044
ORF sequence:
ATGAGAAAGCTAGACCACTGTAACATAGTCCGACTGCGGTATTTCTTCTACTCGAGTGGTGAGAAGAAAGATGAGGTCTACCTTAACCTGGTGCTGGACTATGTTCCGGAGACAGTGTACAGAGTCGCCAGACACTATAGTCGAGCCAAGCAGACACTCCCTGTGATCTATGTCAAGTTGTATATGTATCAGCTGTTCAGAAGTCTAGCCTATATCCATTCCTTTGGAATCTGCCATCGAGACATTAAACCACAGAACCTCTTGTTGGATCCTGATACAGCTGTATTAAAACTCTGTGACTTTGGAAGTGCAAAGCAGCTGGTCCGAGGAGAGCCCAATGTTTCATATATCTGTTCTCGGTACTACAGGGCACCAGAGTTGATCTTTGGAGCCACTGATTACACGTCCAGTATAGATGTATGGTCTGCAGGCTGTGTGTTGGCTGAATTGTTGCTAGGACAACCAATATTTCCTGGGGACAGTGGTGTGGATCAGTTGGTGGAAATAATAAAGAACCGAGAGCTCCAGATCATGAGAAAGCTAGACCACTGTAACATAGTCCGACTGCGGTATTTCTTCTACTCGAGTGGTGAGAAGAAAGATGAGGTCTACCTTAACCTGGTGCTGGACTATGTTCCGGAGACAGTGTACAGAGTCGCCAGACACTATAGTCGAGCCAAGCAGACACTCCCTGTGATCTATGTCAAGTTGTATATGTATCAGCTGTTCAGAAGTCTAGCCTATATCCATTCCTTTGGAATCTGCCATCGAGACATTAAACCACAGAACCTCTTGTTGGATCCTGATACAGCTGTATTAAAACTCTGTGACTTTGGAAGTGCAAAGCAGCTGGTCCGAGGAGAGCCCAATGTTTCATATATCTGTTCTCGGTACTACAGGGCACCAGAGTTGATCTTTGGAGCCACTGATTACACGTCCAGTATAGATGTATGGTCTGCAGGCTGTGTGTTGGCTGAATTGTTGCTAGGACAACCAATATTTCCTGGGGACAGTGGTGTGGATCAGTTGGTGGAAATAATAAAG
Peptide sequence:
MRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIK
IRESfinder result
IRESfinder score
0.58506022
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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