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mmu_circRalgapa2_717
Basic information of circular RNA
PanCircBase ID:
mmu_circRalgapa2_717
mm39_Chr. Position ID:
chr2|146229147|146248352|-
Gene name:
Ralgapa2
Transcript:
ENSMUST00000109986.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
24,23,22,21,20
Exon/intron offsets:
0,379,1263,17635,19114
Genomic length:
19205
Exon/intron sizes in nt:
156,99,194,177,91
Flanking exon/introns:
chr2:146203439-146229147|chr2:146248352-146252092
Splice length:
717
Other database IDs:
circBase: mmu_circ_0009412, CIRCpedia: MMU_CIRCpedia_9663, circAtlas: mmu-Ralgapa2_0025
Human Ortholog IDs:
Mature spliced Sequence:
ATGTTGGTTCGAAGGAGCAGCAGTCCCGCTGAGCTGGAGCTGAAGGATGATTTACAGCAGGCACATGGAAGATGCAGGCAGAGACAGACAAGTGAAAGTACTGGTAGTGACACAGTTGTGGGCTACAGCAATGAAGCAGAGCTACCTGTGAGCCCGTGGCAGGCCTGTGAGGAGGACCCGGACCTGAGCACTCCCACAGATGCTGTGGCTGACTCTGATGCCCGCCACTGGTTACAACTGAGTCCTACTGATGCTTCAAACTTAACAGACAGCAGAGAATGCCTTGCAGACGACTGTAGCATTATTGCTGGAGGAAACCTCACTGGTTGGCACCCAGACTCCGCTGCTGTGTTATGGCGAAGAGTCTTGGGAATCCTTGGAGATGTGAATAACATCCAGTCGCCGAAGATCCATGCCAAAGTTTTTGGCTATCTCTATGAACTGTGGTATAAACTGGCCAAGATACGAGATAATTTAGCAATAAGCCTGGATAACCAGTCGTCTCCATCTCCTCCTCTCTTGATCCCACCACTCAGAATGTTTGCATCATGGCTATTTAAGGCTACAACTCTGCCAAATGAATATAAAGAAGGCAAACTGCAAGCCTACAAACTGATCTGTGCCATGATGACCAGACGCCAGGATGTTCTGCCAAACTCTGACTTCCTGGTGCATTTTTACCTTGTGATGCACCTGGGACTAACCAGCGAGGACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCCAGGATGTTCTGCCAAAC
59.76
CTTGTCTGTCTCTGCCTGCA
59.97
172
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCCAGGATGTTCTGCCAAAC
59.76
ACTTGTCTGTCTCTGCCTGC
59.97
173
PCR template sequence:
CTGTGCCATGATGACCAGACGCCAGGATGTTCTGCCAAACTCTGACTTCCTGGTGCATTTTTACCTTGTGATGCACCTGGGACTAACCAGCGAGGACCAGATGTTGGTTCGAAGGAGCAGCAGTCCCGCTGAGCTGGAGCTGAAGGATGATTTACAGCAGGCACATGGAAGATGCAGGCAGAGACAGACAAGTGAAAGTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-137-3p(1), mmu-miR-23b-3p(1), mmu-miR-155-5p(1), mmu-miR-23a-3p(1), mmu-miR-501-3p(1), mmu-miR-183-5p(1), mmu-miR-666-5p(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
CAGCGAGGACCAGATGTTGGTTCGAA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRALGAPA2_717_ORF_1
0.8386
0.198906951
0.999415583
1434
ORF sequence:
ATGTTGGTTCGAAGGAGCAGCAGTCCCGCTGAGCTGGAGCTGAAGGATGATTTACAGCAGGCACATGGAAGATGCAGGCAGAGACAGACAAGTGAAAGTACTGGTAGTGACACAGTTGTGGGCTACAGCAATGAAGCAGAGCTACCTGTGAGCCCGTGGCAGGCCTGTGAGGAGGACCCGGACCTGAGCACTCCCACAGATGCTGTGGCTGACTCTGATGCCCGCCACTGGTTACAACTGAGTCCTACTGATGCTTCAAACTTAACAGACAGCAGAGAATGCCTTGCAGACGACTGTAGCATTATTGCTGGAGGAAACCTCACTGGTTGGCACCCAGACTCCGCTGCTGTGTTATGGCGAAGAGTCTTGGGAATCCTTGGAGATGTGAATAACATCCAGTCGCCGAAGATCCATGCCAAAGTTTTTGGCTATCTCTATGAACTGTGGTATAAACTGGCCAAGATACGAGATAATTTAGCAATAAGCCTGGATAACCAGTCGTCTCCATCTCCTCCTCTCTTGATCCCACCACTCAGAATGTTTGCATCATGGCTATTTAAGGCTACAACTCTGCCAAATGAATATAAAGAAGGCAAACTGCAAGCCTACAAACTGATCTGTGCCATGATGACCAGACGCCAGGATGTTCTGCCAAACTCTGACTTCCTGGTGCATTTTTACCTTGTGATGCACCTGGGACTAACCAGCGAGGACCAGATGTTGGTTCGAAGGAGCAGCAGTCCCGCTGAGCTGGAGCTGAAGGATGATTTACAGCAGGCACATGGAAGATGCAGGCAGAGACAGACAAGTGAAAGTACTGGTAGTGACACAGTTGTGGGCTACAGCAATGAAGCAGAGCTACCTGTGAGCCCGTGGCAGGCCTGTGAGGAGGACCCGGACCTGAGCACTCCCACAGATGCTGTGGCTGACTCTGATGCCCGCCACTGGTTACAACTGAGTCCTACTGATGCTTCAAACTTAACAGACAGCAGAGAATGCCTTGCAGACGACTGTAGCATTATTGCTGGAGGAAACCTCACTGGTTGGCACCCAGACTCCGCTGCTGTGTTATGGCGAAGAGTCTTGGGAATCCTTGGAGATGTGAATAACATCCAGTCGCCGAAGATCCATGCCAAAGTTTTTGGCTATCTCTATGAACTGTGGTATAAACTGGCCAAGATACGAGATAATTTAGCAATAAGCCTGGATAACCAGTCGTCTCCATCTCCTCCTCTCTTGATCCCACCACTCAGAATGTTTGCATCATGGCTATTTAAGGCTACAACTCTGCCAAATGAATATAAAGAAGGCAAACTGCAAGCCTACAAACTGATCTGTGCCATGATGACCAGACGCCAGGATGTTCTGCCAAACTCTGACTTCCTGGTGCATTTTTACCTTGTGATGCACCTGGGACTAACCAGCGAGGACCAG
Peptide sequence:
MLVRRSSSPAELELKDDLQQAHGRCRQRQTSESTGSDTVVGYSNEAELPVSPWQACEEDPDLSTPTDAVADSDARHWLQLSPTDASNLTDSRECLADDCSIIAGGNLTGWHPDSAAVLWRRVLGILGDVNNIQSPKIHAKVFGYLYELWYKLAKIRDNLAISLDNQSSPSPPLLIPPLRMFASWLFKATTLPNEYKEGKLQAYKLICAMMTRRQDVLPNSDFLVHFYLVMHLGLTSEDQMLVRRSSSPAELELKDDLQQAHGRCRQRQTSESTGSDTVVGYSNEAELPVSPWQACEEDPDLSTPTDAVADSDARHWLQLSPTDASNLTDSRECLADDCSIIAGGNLTGWHPDSAAVLWRRVLGILGDVNNIQSPKIHAKVFGYLYELWYKLAKIRDNLAISLDNQSSPSPPLLIPPLRMFASWLFKATTLPNEYKEGKLQAYKLICAMMTRRQDVLPNSDFLVHFYLVMHLGLTSEDQ
IRESfinder result
IRESfinder score
0.424960283
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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