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mmu_circRalgapa2_1064
Basic information of circular RNA
PanCircBase ID:
mmu_circRalgapa2_1064
mm39_Chr. Position ID:
chr2|146229147|146254788|-
Gene name:
Ralgapa2
Transcript:
ENSMUST00000109986.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
24,23,22,21,20,19,18,17
Exon/intron offsets:
0,379,1263,17635,19114,22945,24818,25506
Genomic length:
25641
Exon/intron sizes in nt:
156,99,194,177,91,98,114,135
Flanking exon/introns:
chr2:146203439-146229147|chr2:146254788-146263512
Splice length:
1064
Other database IDs:
circBase: mmu_circ_0009413, CIRCpedia: MMU_CIRCpedia_9664, circAtlas: mmu-Ralgapa2_0003
Human Ortholog IDs:
Mature spliced Sequence:
AAGTGGAGGAGTTCCAGCAGGCAGAGAGCACCGCCGCAGCCGACTGTGACTATCTTGTGGTAGGACAGCAGCAGGTGCCCCGGAGCAGCAGCACCTCTGACATCACTGAGCGCTTGTACTCAGACTCCTCTCAAGGTTACAGCCCCATGTTGCCTCATCCTGCTTTTTCCACGACTTCTGGGGATCAGAGCTCTGGTCCTCATGCTTGCACAGCTGGCCCTTTACCTTTGAGCCGTCTCCCCAGTGCAGGTCAAAAGGTAGAACATTCGCAGAATTTAAGCTCTTCAGAACCCAAGTCTGTTCAAGAGAGTAAAGGACATGTGACTCATGAACATGAAGGAATAACAATGTTGGTTCGAAGGAGCAGCAGTCCCGCTGAGCTGGAGCTGAAGGATGATTTACAGCAGGCACATGGAAGATGCAGGCAGAGACAGACAAGTGAAAGTACTGGTAGTGACACAGTTGTGGGCTACAGCAATGAAGCAGAGCTACCTGTGAGCCCGTGGCAGGCCTGTGAGGAGGACCCGGACCTGAGCACTCCCACAGATGCTGTGGCTGACTCTGATGCCCGCCACTGGTTACAACTGAGTCCTACTGATGCTTCAAACTTAACAGACAGCAGAGAATGCCTTGCAGACGACTGTAGCATTATTGCTGGAGGAAACCTCACTGGTTGGCACCCAGACTCCGCTGCTGTGTTATGGCGAAGAGTCTTGGGAATCCTTGGAGATGTGAATAACATCCAGTCGCCGAAGATCCATGCCAAAGTTTTTGGCTATCTCTATGAACTGTGGTATAAACTGGCCAAGATACGAGATAATTTAGCAATAAGCCTGGATAACCAGTCGTCTCCATCTCCTCCTCTCTTGATCCCACCACTCAGAATGTTTGCATCATGGCTATTTAAGGCTACAACTCTGCCAAATGAATATAAAGAAGGCAAACTGCAAGCCTACAAACTGATCTGTGCCATGATGACCAGACGCCAGGATGTTCTGCCAAACTCTGACTTCCTGGTGCATTTTTACCTTGTGATGCACCTGGGACTAACCAGCGAGGACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCCAGGATGTTCTGCCAAAC
59.76
TGCTGCTGTCCTACCACAAG
59.96
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCCAGGATGTTCTGCCAAAC
59.76
CTGCTGCTGTCCTACCACAA
59.96
154
PCR template sequence:
CTGTGCCATGATGACCAGACGCCAGGATGTTCTGCCAAACTCTGACTTCCTGGTGCATTTTTACCTTGTGATGCACCTGGGACTAACCAGCGAGGACCAGAAGTGGAGGAGTTCCAGCAGGCAGAGAGCACCGCCGCAGCCGACTGTGACTATCTTGTGGTAGGACAGCAGCAGGTGCCCCGGAGCAGCAGCACCTCTGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-137-3p(1), mmu-miR-23b-3p(1), mmu-miR-155-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-205-5p(1), mmu-miR-23a-3p(1), mmu-miR-501-3p(1), mmu-miR-370-3p(1), mmu-miR-183-5p(1), mmu-miR-666-5p(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
CAGCGAGGACCAGAAGTGGAGGAGTT
siRNA sets
CTCCACTTCTGGTCCTCGC, AACTCCTCCACTTCTGGTC, ACTCCTCCACTTCTGGTCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRALGAPA2_1064_ORF_1
0.7905
0.119911879
0.976947839
981
ORF sequence:
ATGTTGCCTCATCCTGCTTTTTCCACGACTTCTGGGGATCAGAGCTCTGGTCCTCATGCTTGCACAGCTGGCCCTTTACCTTTGAGCCGTCTCCCCAGTGCAGGTCAAAAGGTAGAACATTCGCAGAATTTAAGCTCTTCAGAACCCAAGTCTGTTCAAGAGAGTAAAGGACATGTGACTCATGAACATGAAGGAATAACAATGTTGGTTCGAAGGAGCAGCAGTCCCGCTGAGCTGGAGCTGAAGGATGATTTACAGCAGGCACATGGAAGATGCAGGCAGAGACAGACAAGTGAAAGTACTGGTAGTGACACAGTTGTGGGCTACAGCAATGAAGCAGAGCTACCTGTGAGCCCGTGGCAGGCCTGTGAGGAGGACCCGGACCTGAGCACTCCCACAGATGCTGTGGCTGACTCTGATGCCCGCCACTGGTTACAACTGAGTCCTACTGATGCTTCAAACTTAACAGACAGCAGAGAATGCCTTGCAGACGACTGTAGCATTATTGCTGGAGGAAACCTCACTGGTTGGCACCCAGACTCCGCTGCTGTGTTATGGCGAAGAGTCTTGGGAATCCTTGGAGATGTGAATAACATCCAGTCGCCGAAGATCCATGCCAAAGTTTTTGGCTATCTCTATGAACTGTGGTATAAACTGGCCAAGATACGAGATAATTTAGCAATAAGCCTGGATAACCAGTCGTCTCCATCTCCTCCTCTCTTGATCCCACCACTCAGAATGTTTGCATCATGGCTATTTAAGGCTACAACTCTGCCAAATGAATATAAAGAAGGCAAACTGCAAGCCTACAAACTGATCTGTGCCATGATGACCAGACGCCAGGATGTTCTGCCAAACTCTGACTTCCTGGTGCATTTTTACCTTGTGATGCACCTGGGACTAACCAGCGAGGACCAGAAGTGGAGGAGTTCCAGCAGGCAGAGAGCACCGCCGCAGCCGACTGTGACTATCTTGTGGTAG
Peptide sequence:
MLPHPAFSTTSGDQSSGPHACTAGPLPLSRLPSAGQKVEHSQNLSSSEPKSVQESKGHVTHEHEGITMLVRRSSSPAELELKDDLQQAHGRCRQRQTSESTGSDTVVGYSNEAELPVSPWQACEEDPDLSTPTDAVADSDARHWLQLSPTDASNLTDSRECLADDCSIIAGGNLTGWHPDSAAVLWRRVLGILGDVNNIQSPKIHAKVFGYLYELWYKLAKIRDNLAISLDNQSSPSPPLLIPPLRMFASWLFKATTLPNEYKEGKLQAYKLICAMMTRRQDVLPNSDFLVHFYLVMHLGLTSEDQKWRSSSRQRAPPQPTVTILW
IRESfinder result
IRESfinder score
0.503007315
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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