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mmu_circGpd2_1173
Basic information of circular RNA
PanCircBase ID:
mmu_circGpd2_1173
mm39_Chr. Position ID:
chr2|57157984|57235436|+
Gene name:
Gpd2
Transcript:
ENSMUST00000169687.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
2,3,4,5,6,7,8,9
Exon/intron offsets:
0,21872,36388,37835,38959,70874,72091,77258
Genomic length:
77452
Exon/intron sizes in nt:
11,01,72,12,59,81,64,10,00,00,000
Flanking exon/introns:
chr2:57128000-57157984|chr2:57235436-57245471
Splice length:
1173
Other database IDs:
CIRCpedia: MMU_CIRCpedia_226137, circAtlas: mmu-Gpd2_0005
circBase: hsa_circ_0117729, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_92922
Human Ortholog IDs:
Mature spliced Sequence:
GCTGAGCAATGGCGTTTCAAAAGGCAGTGAAGGGGACTATTCTTGTGGGTGGAGGAGCTCTGGCCACTGTTTTGGGACTCTCTCCGTTTGCTCATTACAGAAGGAAGCAAGTGAGCCTGGCATATGTGGAAGCAGCAGGATACCTCACGGAGCCTGTGAACAGGGAACCTCCCTCCAGAGAAGCTCAGCTCATGACTTTGAAGAACACACCCGAATTTGACATCCTTGTTATCGGAGGCGGAGCCACAGGGTGTGGCTGTGCACTAGATGCCGTCACCAGAGGACTGAAAACAGCCCTTGTAGAGAGAGATGACTTCTCATCGGGGACTAGCAGTAGAAGCACTAAATTGATCCACGGTGGTGTGCGATACCTCCAGAAGGCTATCATGAACTTGGATGTTGAGCAGTATAGGATGGTGAAAGAAGCCCTTCACGAACGTGCCAACTTACTAGAAATCGCTCCTCATTTATCAGCTCCGTTGCCTATCATGCTTCCACTTTACAAGTGGTGGCAGTTACCTTATTACTGGGTGGGAATCAAGATGTATGACCTGGTTGCAGGGAGTCAATGCCTGAAGAGCAGTTACGTCCTCAGCAAATCCCGAGCCCTGGAGCATTTTCCCATGCTCCAGAAGGACAAGCTGGTAGGCGCCATTGTCTACTATGACGGACAACACAACGATGCACGGATGAACCTCGCCATCGCCCTCACTGCTGCCAGGTACGGGGCTGCCACGGCCAATTACATGGAGGTGGTGAGCTTGCTCAAGAAGACAGACCCTGAAACCGGCAAAGAGCGAGTGAGCGGTGCGCGGTGCAAGGATGTGCTCACAGGGCAGGAATTTGACGTGAGAGCCAAATGCGTTATCAATGCCTCCGGCCCTTTCACAGACTCCGTGCGCAAAATGGATGATAAAAACGTTGTTCCCATCTGCCAGCCCAGTGCCGGGGTCCATATTGTGATGCCCGGATACTACAGCCCTGAGAACATGGGACTTCTTGATCCTGCAACCAGTGATGGCAGAGTGATTTTCTTCTTGCCTTGGGAGAAGATGACAATTGCTGGCACCACTGATACGCCAACGGACGTCACGCACCATCCTATTCCTTCAGAAGAAGACATTAACTTCATCCTGAATGAAGTGCGGAACTACCTGAGTTCTGACGTTGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GACGTCACGCACCATCCTAT
59.9
GCAAACGGAGAGAGTCCCAA
59.97
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GACGTCACGCACCATCCTAT
59.9
AGAGTCCCAAAACAGTGGCC
60.18
169
PCR template sequence:
GATACGCCAACGGACGTCACGCACCATCCTATTCCTTCAGAAGAAGACATTAACTTCATCCTGAATGAAGTGCGGAACTACCTGAGTTCTGACGTTGAAGGCTGAGCAATGGCGTTTCAAAAGGCAGTGAAGGGGACTATTCTTGTGGGTGGAGGAGCTCTGGCCACTGTTTTGGGACTCTCTCCGTTTGCTCATTACAG
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-196a-5p(1), 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-697(1), mmu-miR-202-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCTGACGTTGAAGGCTGAGCAATGGC
siRNA sets
ATTGCTCAGCCTTCAACGT, TTGCTCAGCCTTCAACGTC, CATTGCTCAGCCTTCAACG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGPD2_1173_ORF_1
1.1435
0.28305141
0.998388457
1170
ORF sequence:
ATGGCGTTTCAAAAGGCAGTGAAGGGGACTATTCTTGTGGGTGGAGGAGCTCTGGCCACTGTTTTGGGACTCTCTCCGTTTGCTCATTACAGAAGGAAGCAAGTGAGCCTGGCATATGTGGAAGCAGCAGGATACCTCACGGAGCCTGTGAACAGGGAACCTCCCTCCAGAGAAGCTCAGCTCATGACTTTGAAGAACACACCCGAATTTGACATCCTTGTTATCGGAGGCGGAGCCACAGGGTGTGGCTGTGCACTAGATGCCGTCACCAGAGGACTGAAAACAGCCCTTGTAGAGAGAGATGACTTCTCATCGGGGACTAGCAGTAGAAGCACTAAATTGATCCACGGTGGTGTGCGATACCTCCAGAAGGCTATCATGAACTTGGATGTTGAGCAGTATAGGATGGTGAAAGAAGCCCTTCACGAACGTGCCAACTTACTAGAAATCGCTCCTCATTTATCAGCTCCGTTGCCTATCATGCTTCCACTTTACAAGTGGTGGCAGTTACCTTATTACTGGGTGGGAATCAAGATGTATGACCTGGTTGCAGGGAGTCAATGCCTGAAGAGCAGTTACGTCCTCAGCAAATCCCGAGCCCTGGAGCATTTTCCCATGCTCCAGAAGGACAAGCTGGTAGGCGCCATTGTCTACTATGACGGACAACACAACGATGCACGGATGAACCTCGCCATCGCCCTCACTGCTGCCAGGTACGGGGCTGCCACGGCCAATTACATGGAGGTGGTGAGCTTGCTCAAGAAGACAGACCCTGAAACCGGCAAAGAGCGAGTGAGCGGTGCGCGGTGCAAGGATGTGCTCACAGGGCAGGAATTTGACGTGAGAGCCAAATGCGTTATCAATGCCTCCGGCCCTTTCACAGACTCCGTGCGCAAAATGGATGATAAAAACGTTGTTCCCATCTGCCAGCCCAGTGCCGGGGTCCATATTGTGATGCCCGGATACTACAGCCCTGAGAACATGGGACTTCTTGATCCTGCAACCAGTGATGGCAGAGTGATTTTCTTCTTGCCTTGGGAGAAGATGACAATTGCTGGCACCACTGATACGCCAACGGACGTCACGCACCATCCTATTCCTTCAGAAGAAGACATTAACTTCATCCTGAATGAAGTGCGGAACTACCTGAGTTCTGACGTTGAAGGCTGA
Peptide sequence:
MAFQKAVKGTILVGGGALATVLGLSPFAHYRRKQVSLAYVEAAGYLTEPVNREPPSREAQLMTLKNTPEFDILVIGGGATGCGCALDAVTRGLKTALVERDDFSSGTSSRSTKLIHGGVRYLQKAIMNLDVEQYRMVKEALHERANLLEIAPHLSAPLPIMLPLYKWWQLPYYWVGIKMYDLVAGSQCLKSSYVLSKSRALEHFPMLQKDKLVGAIVYYDGQHNDARMNLAIALTAARYGAATANYMEVVSLLKKTDPETGKERVSGARCKDVLTGQEFDVRAKCVINASGPFTDSVRKMDDKNVVPICQPSAGVHIVMPGYYSPENMGLLDPATSDGRVIFFLPWEKMTIAGTTDTPTDVTHHPIPSEEDINFILNEVRNYLSSDVEG
IRESfinder result
IRESfinder score
0.308231594
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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