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mmu_circMast4_396
Basic information of circular RNA
PanCircBase ID:
mmu_circMast4_396
mm39_Chr. Position ID:
chr13|102934553|102990427|-
Gene name:
Mast4
Transcript:
ENSMUST00000166726.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
8,7,6,5
Exon/intron offsets:
0,6596,12455,55785
Genomic length:
55874
Exon/intron sizes in nt:
158,79,70,89
Flanking exon/introns:
chr13:102932669-102934553|chr13:102990427-103162029
Splice length:
396
Other database IDs:
CIRCpedia: MMU_CIRCpedia_217773
circAtlas: hsa-MAST4_0049, CIRCpedia: HSA_CIRCpedia_175540
Human Ortholog IDs:
Mature spliced Sequence:
TTGCCGAACAAGCAACCGGAAGAGTTTGATAGGCAATGGCCAGTCTCCAGCACTGCCTCGACCACACTCACCTCTCTCTGCTCATGCAGGAAATAGCCCTCAAGACAGTCCAAGGAATTTCTCCCCCAGTGCCTCAGCCCATTTCTCATTTGCGAGGAGAACGGATGGGCGCCGCTGGTCTCTGGCTTCTCTCCCTTCCTCAGGCTATGGGACAAATACCCCAAGCTCCACCGTCTCCTCATCCTGTTCTTCCCAGGAGAAGTTGCACCAGCTACCATACCAGCCAACCCCAGATGAATTACACTTCTTATCCAAACACTTCTGCACAACAGAAAGTATCGCCACTGAGAACCGGTGCAGAAACACACCCATGCGTCCACGTTCCCGGAGTCTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTATCGCCACTGAGAACCG
59.54
GCAGAGAGAGGTGAGTGTGG
59.75
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTATCGCCACTGAGAACCGG
60.53
GCAGAGAGAGGTGAGTGTGG
59.75
142
PCR template sequence:
AATTACACTTCTTATCCAAACACTTCTGCACAACAGAAAGTATCGCCACTGAGAACCGGTGCAGAAACACACCCATGCGTCCACGTTCCCGGAGTCTCAGTTGCCGAACAAGCAACCGGAAGAGTTTGATAGGCAATGGCCAGTCTCCAGCACTGCCTCGACCACACTCACCTCTCTCTGCTCATGCAGGAAATAGCCCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-709(1), mmu-miR-185-5p(1), mmu-miR-207(1), mmu-miR-539-5p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCCGGAGTCTCAGTTGCCGAACAAGC
siRNA sets
GTTCGGCAACTGAGACTCC, TGTTCGGCAACTGAGACTC, CTTGTTCGGCAACTGAGAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMAST4_396_ORF_1
0.8607
0.091312053
0.436138217
420
ORF sequence:
ATGCGTCCACGTTCCCGGAGTCTCAGTTGCCGAACAAGCAACCGGAAGAGTTTGATAGGCAATGGCCAGTCTCCAGCACTGCCTCGACCACACTCACCTCTCTCTGCTCATGCAGGAAATAGCCCTCAAGACAGTCCAAGGAATTTCTCCCCCAGTGCCTCAGCCCATTTCTCATTTGCGAGGAGAACGGATGGGCGCCGCTGGTCTCTGGCTTCTCTCCCTTCCTCAGGCTATGGGACAAATACCCCAAGCTCCACCGTCTCCTCATCCTGTTCTTCCCAGGAGAAGTTGCACCAGCTACCATACCAGCCAACCCCAGATGAATTACACTTCTTATCCAAACACTTCTGCACAACAGAAAGTATCGCCACTGAGAACCGGTGCAGAAACACACCCATGCGTCCACGTTCCCGGAGTCTC
Peptide sequence:
MRPRSRSLSCRTSNRKSLIGNGQSPALPRPHSPLSAHAGNSPQDSPRNFSPSASAHFSFARRTDGRRWSLASLPSSGYGTNTPSSTVSSSCSSQEKLHQLPYQPTPDELHFLSKHFCTTESIATENRCRNTPMRPRSRSL
IRESfinder result
IRESfinder score
0.564086411
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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