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mmu_circLta4h_479
Basic information of circular RNA
PanCircBase ID:
mmu_circLta4h_479
mm39_Chr. Position ID:
chr10|93295678|93303026|+
Gene name:
Lta4h
Transcript:
ENSMUST00000016033.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
2,3,4,5,6
Exon/intron offsets:
0,1493,4628,6132,7295
Genomic length:
7348
Exon/intron sizes in nt:
131,121,69,105,53
Flanking exon/introns:
chr10:93289530-93295678|chr10:93303026-93304617
Splice length:
479
Other database IDs:
circAtlas: mmu-Lta4h_0004
Human Ortholog IDs:
Mature spliced Sequence:
ACTTTGGACACAAAAGACCTCACAATAGAAAAAGTGGTGATCAATGGACAAGAAGTCAAATACACCCTTGGAGAAAGTCAAGGTTACAAAGGGTCACCGATGGAAATCTCTCTTCCCATCGCCCTGAGCAAAAATCAAGAGATCGTTATAGAAATTTCCTTTGAGACATCTCCCAAATCCTCTGCGCTTCAGTGGCTCACTCCTGAACAGACGTCAGGGAAGCAGCATCCGTATCTCTTCAGTCAGTGCCAGGCCATCCACTGCAGGGCCATCCTCCCTTGCCAAGACACTCCTTCCGTGAAATTAACGTACACCGCAGAGGTGTCTGTCCCGAAAGAACTGGTGGCTCTCATGAGTGCCATCCGTGATGGAGAAGCCCCTGACCCAGAAGACCCCAGCAGGAAGATTTACAGATTCAACCAGAGGGTTCCCATACCATGCTACCTGATTGCTTTGGTTGTTGGAGCTTTAGAAAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGGGTTCCCATACCATGCT
59.15
TCGGTGACCCTTTGTAACCT
58.57
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGAGGGTTCCCATACCATGC
59.15
TCGGTGACCCTTTGTAACCT
58.57
158
PCR template sequence:
CTGACCCAGAAGACCCCAGCAGGAAGATTTACAGATTCAACCAGAGGGTTCCCATACCATGCTACCTGATTGCTTTGGTTGTTGGAGCTTTAGAAAGCAGACTTTGGACACAAAAGACCTCACAATAGAAAAAGTGGTGATCAATGGACAAGAAGTCAAATACACCCTTGGAGAAAGTCAAGGTTACAAAGGGTCACCGA
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-298-5p(1), mmu-miR-182-5p(1), mmu-miR-370-3p(1), mmu-miR-183-5p(1), mmu-miR-129-5p(1), mmu-miR-670-5p(1), mmu-miR-3061-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTTTAGAAAGCAGACTTTGGACACAA
siRNA sets
TGTCCAAAGTCTGCTTTCT,TTGTGTCCAAAGTCTGCTT,CAAAGTCTGCTTTCTAAAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCLTA4H_479_ORF_1
0.7892
0.167670393
0.653148805
519
ORF sequence:
ATGCTACCTGATTGCTTTGGTTGTTGGAGCTTTAGAAAGCAGACTTTGGACACAAAAGACCTCACAATAGAAAAAGTGGTGATCAATGGACAAGAAGTCAAATACACCCTTGGAGAAAGTCAAGGTTACAAAGGGTCACCGATGGAAATCTCTCTTCCCATCGCCCTGAGCAAAAATCAAGAGATCGTTATAGAAATTTCCTTTGAGACATCTCCCAAATCCTCTGCGCTTCAGTGGCTCACTCCTGAACAGACGTCAGGGAAGCAGCATCCGTATCTCTTCAGTCAGTGCCAGGCCATCCACTGCAGGGCCATCCTCCCTTGCCAAGACACTCCTTCCGTGAAATTAACGTACACCGCAGAGGTGTCTGTCCCGAAAGAACTGGTGGCTCTCATGAGTGCCATCCGTGATGGAGAAGCCCCTGACCCAGAAGACCCCAGCAGGAAGATTTACAGATTCAACCAGAGGGTTCCCATACCATGCTACCTGATTGCTTTGGTTGTTGGAGCTTTAGAAAGC
Peptide sequence:
MLPDCFGCWSFRKQTLDTKDLTIEKVVINGQEVKYTLGESQGYKGSPMEISLPIALSKNQEIVIEISFETSPKSSALQWLTPEQTSGKQHPYLFSQCQAIHCRAILPCQDTPSVKLTYTAEVSVPKELVALMSAIRDGEAPDPEDPSRKIYRFNQRVPIPCYLIALVVGALES
IRESfinder result
IRESfinder score
0.710116574
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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