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mmu_ciMalat1_787
Basic information of circular RNA
PanCircBase ID:
mmu_ciMalat1_787
mm39_Chr. Position ID:
chr19|5846244|5847031|-
Gene name:
Malat1
Transcript:
ENSMUST00000173314.2
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
1
Exon/intron offsets:
0
Genomic length:
787
Exon/intron sizes in nt:
787
Flanking exon/introns:
chr19:5845813-5847031
Splice length:
787
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGAACGAGCCTTTTCTTGTTTAAGATTAGCTACTGGTAATCTAGTGTTGAATCCTCTCCAGCTTCATGCTGGAGCAGCTAGCATGTGATGTAATGTTGGCCTTGGGGTGGAGGGGTGAGGTGGGCGCTAAGCCTTTTTTTAAGATTTTTCAGGTACCCCTCACTAAAGGCACTGAAGGCTTAATGTAGGACAGCGGAGCCTTCCTGTGTGGCAAGAATCAAGCAAGCAGTATTGTATCGAGACCAAAGTGGTATCATGGTCGGTTTTGATTAGCAGTGGGGACTACCCTACCGTAACACCTTGTTGGAATTGAAGCATCCAAAGAAAATACTTGAGAGGCCCTGGGCTTGTTTTAACATCTGGAAAAAAGGCTGTTTTTATAGCAGCGGTTACCAGCCCAAACCTCAAGTTGTGCTTGCAGGGGAGGGAAAAGGGGGAAAGCGGGCAACCAGTTTCCCCAGCTTTTCCAGAATCCTGTTACAAGGTCTCCCCACAAGTGATTTCTCTGCCACATCGCCACCATGGGCCTTTGGCCTAATCACAGACCCTTCACCCCTCACCTTGATGCAGCCAGTAGCTGGATCCTTGAGGTCACGTTGCATATCGGTTTCAAGGTAACCATGGTGCCAAGGTCCTGTGGGTTGCACCAGAAAAGGCCATCAATTTTCCCCTTGCCTGTAATTTAACATTAAAACCATAGCTAAGATGTTTTATACATAGCACCTATGCAGAGTAAACAAACCAGTATGGGTATAGTATGTTTGATACCAGTGCTGGGTGGGAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACCTATGCAGAGTAAACAAACCA
59.24
TCACATGCTAGCTGCTCCAG
59.82
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCAGAGTAAACAAACCAGT
55.11
TCACATGCTAGCTGCTCCAG
59.82
149
PCR template sequence:
CATTAAAACCATAGCTAAGATGTTTTATACATAGCACCTATGCAGAGTAAACAAACCAGTATGGGTATAGTATGTTTGATACCAGTGCTGGGTGGGAATGGTGAACGAGCCTTTTCTTGTTTAAGATTAGCTACTGGTAATCTAGTGTTGAATCCTCTCCAGCTTCATGCTGGAGCAGCTAGCATGTGATGTAATGTTGG
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-9-5p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-200c-3p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-320-3p(1), mmu-miR-127-5p(1), mmu-miR-96-5p(1), mmu-miR-5101(1), mmu-miR-539-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGGGTGGGAATGGTGAACGAGCCTT
siRNA sets
TCGTTCACCATTCCCACCC, CTCGTTCACCATTCCCACC, GTTCACCATTCCCACCCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIMALAT1_787_ORF_3
0.9301
-0.249202083
0.029694178
150
ORF sequence:
ATGCAGAGTAAACAAACCAGTATGGGTATAGTATGTTTGATACCAGTGCTGGGTGGGAATGGTGAACGAGCCTTTTCTTGTTTAAGATTAGCTACTGGTAATCTAGTGTTGAATCCTCTCCAGCTTCATGCTGGAGCAGCTAGCATGTGA
Peptide sequence:
MQSKQTSMGIVCLIPVLGGNGERAFSCLRLATGNLVLNPLQLHAGAASM
IRESfinder result
IRESfinder score
0.761462675
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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