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mmu_circGpd2_407
Basic information of circular RNA
PanCircBase ID:
mmu_circGpd2_407
mm39_Chr. Position ID:
chr2|57157984|57194497|+
Gene name:
Gpd2
Transcript:
ENSMUST00000141536.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
2,3,4
Exon/intron offsets:
0,21872,36388
Genomic length:
36513
Exon/intron sizes in nt:
11,01,72,125
Flanking exon/introns:
chr2:57128000-57157984|chr2:57194497-57195819
Splice length:
407
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GCTGAGCAATGGCGTTTCAAAAGGCAGTGAAGGGGACTATTCTTGTGGGTGGAGGAGCTCTGGCCACTGTTTTGGGACTCTCTCCGTTTGCTCATTACAGAAGGAAGCAAGTGAGCCTGGCATATGTGGAAGCAGCAGGATACCTCACGGAGCCTGTGAACAGGGAACCTCCCTCCAGAGAAGCTCAGCTCATGACTTTGAAGAACACACCCGAATTTGACATCCTTGTTATCGGAGGCGGAGCCACAGGGTGTGGCTGTGCACTAGATGCCGTCACCAGAGGACTGAAAACAGCCCTTGTAGAGAGAGATGACTTCTCATCGGGGACTAGCAGTAGAAGCACTAAATTGATCCACGGTGGTGTGCGATACCTCCAGAAGGCTATCATGAACTTGGATGTTGAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGGGGACTAGCAGTAGAAGC
59.61
GCAAACGGAGAGAGTCCCAA
59.97
177
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTCATCGGGGACTAGCAGT
59.74
AGAGTCCCAAAACAGTGGCC
60.18
173
PCR template sequence:
AGATGACTTCTCATCGGGGACTAGCAGTAGAAGCACTAAATTGATCCACGGTGGTGTGCGATACCTCCAGAAGGCTATCATGAACTTGGATGTTGAGCAGGCTGAGCAATGGCGTTTCAAAAGGCAGTGAAGGGGACTATTCTTGTGGGTGGAGGAGCTCTGGCCACTGTTTTGGGACTCTCTCCGTTTGCTCATTACAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-10b-5p(1), mmu-miR-10a-5p(1), mmu-miR-433-3p(1), mmu-miR-680(1), mmu-miR-484(1), mmu-miR-202-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGATGTTGAGCAGGCTGAGCAATGGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGPD2_407_ORF_1
0.8447
0.145805859
0.500156431
429
ORF sequence:
ATGGCGTTTCAAAAGGCAGTGAAGGGGACTATTCTTGTGGGTGGAGGAGCTCTGGCCACTGTTTTGGGACTCTCTCCGTTTGCTCATTACAGAAGGAAGCAAGTGAGCCTGGCATATGTGGAAGCAGCAGGATACCTCACGGAGCCTGTGAACAGGGAACCTCCCTCCAGAGAAGCTCAGCTCATGACTTTGAAGAACACACCCGAATTTGACATCCTTGTTATCGGAGGCGGAGCCACAGGGTGTGGCTGTGCACTAGATGCCGTCACCAGAGGACTGAAAACAGCCCTTGTAGAGAGAGATGACTTCTCATCGGGGACTAGCAGTAGAAGCACTAAATTGATCCACGGTGGTGTGCGATACCTCCAGAAGGCTATCATGAACTTGGATGTTGAGCAGGCTGAGCAATGGCGTTTCAAAAGGCAGTGA
Peptide sequence:
MAFQKAVKGTILVGGGALATVLGLSPFAHYRRKQVSLAYVEAAGYLTEPVNREPPSREAQLMTLKNTPEFDILVIGGGATGCGCALDAVTRGLKTALVERDDFSSGTSSRSTKLIHGGVRYLQKAIMNLDVEQAEQWRFKRQ
IRESfinder result
IRESfinder score
0.387749159
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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