top of page
mmu_circAbca5_367
Basic information of circular RNA
PanCircBase ID:
mmu_circAbca5_367
mm39_Chr. Position ID:
chr11|110217385|110218762|-
Gene name:
Abca5
Transcript:
ENSMUST00000043961.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
4,3
Exon/intron offsets:
0,1172
Genomic length:
1377
Exon/intron sizes in nt:
162,205
Flanking exon/introns:
chr11:110210708-110217385|chr11:110218762-110219962
Splice length:
367
Other database IDs:
circAtlas: mmu-Abca5_0020
Human Ortholog IDs:
Mature spliced Sequence:
GAAATTCTTTTTCCTCTATTTTTCTTATTTTGGCTGATATTAGTTAGCATGATGCATCCAAATAAGAAATATGAAGAGGTATCTGATATAGAGCTCAGCCCTATGGACAAATTCAGCCTTTCCAACGTTATTCTTGGATACACTCCCGTGACTAACATTACAAGCAGCATTATGCAGAGGGTTTCTACCGATCATCTTCCCAAGGTTATAGTTACTGAAGAATACGCAAATGAGAAAGAACTGGTAGCCGCAAGTCTTTCTAAGTCCAGCAACTTCGTAGGTGTGGTTTTCAAAGACACCATGTCCTATGAACTTCGTTTTTTTCCTGAAATGATTCCAGTGTCTTCTATTTATATGAATTCAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCAACTTCGTAGGTGTGGT
59.24
TTGGATGCATCATGCTAACT
55.09
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCAACTTCGTAGGTGTGGT
59.24
TTTGGATGCATCATGCTAACT
55.91
162
PCR template sequence:
AGCAACTTCGTAGGTGTGGTTTTCAAAGACACCATGTCCTATGAACTTCGTTTTTTTCCTGAAATGATTCCAGTGTCTTCTATTTATATGAATTCAAGAGGAAATTCTTTTTCCTCTATTTTTCTTATTTTGGCTGATATTAGTTAGCATGATGCATCCAAATAAGAAATATGAAGAGGTATCTGATATAGAGCTCAGCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-155-5p(1), mmu-miR-122-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATGAATTCAAGAGGAAATTCTTTTTC
siRNA sets
AAAAAGAATTTCCTCTTGA, AAAAGAATTTCCTCTTGAA, GAAAAAGAATTTCCTCTTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCABCA5_367_ORF_1
1.0642
-0.032172777
0.31613529
366
ORF sequence:
ATGATGCATCCAAATAAGAAATATGAAGAGGTATCTGATATAGAGCTCAGCCCTATGGACAAATTCAGCCTTTCCAACGTTATTCTTGGATACACTCCCGTGACTAACATTACAAGCAGCATTATGCAGAGGGTTTCTACCGATCATCTTCCCAAGGTTATAGTTACTGAAGAATACGCAAATGAGAAAGAACTGGTAGCCGCAAGTCTTTCTAAGTCCAGCAACTTCGTAGGTGTGGTTTTCAAAGACACCATGTCCTATGAACTTCGTTTTTTTCCTGAAATGATTCCAGTGTCTTCTATTTATATGAATTCAAGAGGAAATTCTTTTTCCTCTATTTTTCTTATTTTGGCTGATATTAGTTAG
Peptide sequence:
MMHPNKKYEEVSDIELSPMDKFSLSNVILGYTPVTNITSSIMQRVSTDHLPKVIVTEEYANEKELVAASLSKSSNFVGVVFKDTMSYELRFFPEMIPVSSIYMNSRGNSFSSIFLILADIS
IRESfinder result
IRESfinder score
0.841541889
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page