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mmu_circMgat5_673
Basic information of circular RNA
PanCircBase ID:
mmu_circMgat5_673
mm39_Chr. Position ID:
chr1|127310657|127325377|+
Gene name:
Mgat5
Transcript:
ENSMUST00000038361.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
7,8,9,10,11
Exon/intron offsets:
0,1847,4422,7823,14586
Genomic length:
14720
Exon/intron sizes in nt:
7,21,62,17,01,35,134
Flanking exon/introns:
chr1:127294229-127310657|chr1:127325377-127339863
Splice length:
673
Other database IDs:
CIRCpedia: MMU_CIRCpedia_6916, circAtlas: mmu-Mgat5_0001
circBase: hsa_circ_0117321, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_37915
Human Ortholog IDs:
Mature spliced Sequence:
GTTGAAAATTGGTGTCCTCGTTTACCTTGGAGAGCAAAAAATCCCTATGAAGAAGCTGATCATAACTCATTGGCGGAAATCCGTACGGATTTTAACATTCTCTACGGCATGATGAAGAAGCACGAGGAGTTCCGTTGGATGAGGCTTCGGATCCGGCGAATGGCTGACGCGTGGATCCAAGCTATCAAGTCTCTGGCGGAGAAACAAAACCTTGAGAAGAGGAAACGGAAGAAAATCCTTGTTCACCTGGGGCTCCTGACCAAGGAATCGGGCTTCAAGATTGCGGAGACAGCATTCAGCGGTGGCCCTCTGGGTGAACTCGTTCAGTGGAGTGACTTAATCACATCTCTGTACCTGCTGGGCCATGACATCCGGATCTCGGCCTCACTGGCTGAGCTCAAGGAGATAATGAAGAAGGTTGTTGGAAACCGGTCTGGCTGTCCAACTGTAGGAGACAGAATCGTTGAGCTGATTTATATCGATATTGTGGGACTTGCTCAATTTAAGAAAACACTAGGGCCATCCTGGGTTCATTACCAGTGCATGCTCCGGGTGCTAGACTCCTTTGGAACAGAACCTGAGTTCAATCATGCGAGCTATGCCCAGTCAAAAGGCCACAAGACCCCCTGGGGAAAGTGGAATCTGAACCCGCAGCAGTTTTACACCATGTTCC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AATCATGCGAGCTATGCCCA
59.89
CCGCCAATGAGTTATGATCAGC
59.77
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATCATGCGAGCTATGCCCAG
60.32
CCGCCAATGAGTTATGATCAGC
59.77
163
PCR template sequence:
GAACCTGAGTTCAATCATGCGAGCTATGCCCAGTCAAAAGGCCACAAGACCCCCTGGGGAAAGTGGAATCTGAACCCGCAGCAGTTTTACACCATGTTCCGTTGAAAATTGGTGTCCTCGTTTACCTTGGAGAGCAAAAAATCCCTATGAAGAAGCTGATCATAACTCATTGGCGGAAATCCGTACGGATTTTAACATTC
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-214-3p(1), mmu-miR-127-3p(1), mmu-miR-541-5p(1), mmu-miR-129-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TACACCATGTTCCGTTGAAAATTGGT
siRNA sets
ATTTTCAACGGAACATGGT, TTTCAACGGAACATGGTGT, TTTTCAACGGAACATGGTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMGAT5_673_ORF_1
1.1287
0.293519951
0.894522567
570
ORF sequence:
ATGATGAAGAAGCACGAGGAGTTCCGTTGGATGAGGCTTCGGATCCGGCGAATGGCTGACGCGTGGATCCAAGCTATCAAGTCTCTGGCGGAGAAACAAAACCTTGAGAAGAGGAAACGGAAGAAAATCCTTGTTCACCTGGGGCTCCTGACCAAGGAATCGGGCTTCAAGATTGCGGAGACAGCATTCAGCGGTGGCCCTCTGGGTGAACTCGTTCAGTGGAGTGACTTAATCACATCTCTGTACCTGCTGGGCCATGACATCCGGATCTCGGCCTCACTGGCTGAGCTCAAGGAGATAATGAAGAAGGTTGTTGGAAACCGGTCTGGCTGTCCAACTGTAGGAGACAGAATCGTTGAGCTGATTTATATCGATATTGTGGGACTTGCTCAATTTAAGAAAACACTAGGGCCATCCTGGGTTCATTACCAGTGCATGCTCCGGGTGCTAGACTCCTTTGGAACAGAACCTGAGTTCAATCATGCGAGCTATGCCCAGTCAAAAGGCCACAAGACCCCCTGGGGAAAGTGGAATCTGAACCCGCAGCAGTTTTACACCATGTTCCGTTGA
Peptide sequence:
MMKKHEEFRWMRLRIRRMADAWIQAIKSLAEKQNLEKRKRKKILVHLGLLTKESGFKIAETAFSGGPLGELVQWSDLITSLYLLGHDIRISASLAELKEIMKKVVGNRSGCPTVGDRIVELIYIDIVGLAQFKKTLGPSWVHYQCMLRVLDSFGTEPEFNHASYAQSKGHKTPWGKWNLNPQQFYTMFR
IRESfinder result
IRESfinder score
0.443058093
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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