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mmu_circGfpt1_1142
Basic information of circular RNA
PanCircBase ID:
mmu_circGfpt1_1142
mm39_Chr. Position ID:
chr6|87027902|87050461|+
Gene name:
Gfpt1
Transcript:
ENSMUST00000113658.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
2,3,4,5,6,7,8,9,10,11,12
Exon/intron offsets:
0,2830,3680,5223,6709,8459,9600,12884,15703,16763,22461
Genomic length:
22559
Exon/intron sizes in nt:
108,108,126,59,135,62,80,106,164,96,98
Flanking exon/introns:
chr6:87019987-87027902|chr6:87050461-87053238
Splice length:
1142
Other database IDs:
circAtlas: mmu-Gfpt1_0002
circAtlas: hsa-GFPT1_0004, CIRCpedia: HSA_CIRCpedia_372376
Human Ortholog IDs:
Mature spliced Sequence:
GTATATTTGCTTATTTAAATTACCATGTTCCTCGAACAAGACGAGAAATCTTGGAGACACTAATCAAAGGCCTTCAGAGACTGGAATACAGAGGATATGATTCTGCTGGTGTGGGACTTGACGGAGGCAATGACAAAGACTGGGAAGCCAACGCCTGCAAAATCCAGCTCATTAAGAAGAAAGGAAAAGTTAAGGCACTGGATGAAGAAGTTCACAAACAACAAGATATGGACTTGGATATAGAATTTGATGTGCATCTTGGAATAGCTCATACCCGTTGGGCGACACATGGAGAACCCAATCCTGTCAATAGTCACCCCCAGCGCTCTGATAAAAATAATGAATTCATTGTTATTCATAATGGAATCATCACCAACTACAAAGACTTGAAAAAGTTTCTGGAAAGCAAAGGCTATGACTTTGAATCTGAAACAGACACAGAAACCATTGCCAAGCTCGTCAAGTACATGTATGACAACTGGGAGAGCCAGGACGTCAGTTTTACCACCTTGGTGGAGAGAGTTATCCAACAATTGGAAGGCGCCTTTGCTCTTGTGTTTAAAAGTGTCCATTTTCCCGGGCAAGCAGTTGGCACAAGGCGAGGTAGCCCTCTCTTGATTGGTGTGCGGAGTGAACATAAGCTTTCTACAGATCACATTCCGATTCTGTACAGAACAGGCAAAGACAAGAAAGGAAGCTGCGGTCTTTCCCGTGTGGACAGCACGACATGCCTGTTCCCTGTTGAGGAAAAGGCAGTTGAATATTACTTTGCTTCTGATGCAAGTGCCGTGATAGAGCACACCAATCGTGTCATCTTTCTGGAAGATGATGATGTTGCAGCAGTGGTGGATGGCCGTCTCTCTATCCACCGAATTAAACGAACTGCAGGAGACCATCCTGGCCGAGCTGTGCAAACTCTCCAGATGGAGCTCCAGCAGATCATGAAGGGCAACTTTAGTTCATTTATGCAGAAGGAAATTTTTGAGCAGCCAGAATCTGTTGTGAACACAATGAGAGGAAGAGTCAATTTTGATGACTACACTGTGAATTTGGGAGGTTTGAAAGATCACATTAAGGAGATCCAGCGGTGTCGGCGGTTGATTCTTATTGCTTGTGGCACAAGTTACCACGCTGGTGTGGCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGTGTCGGCGGTTGATTCTT
60.95
CCAGTCTCTGAAGGCCTTTGA
59.65
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGTGTCGGCGGTTGATTCTT
60.95
TCCAGTCTCTGAAGGCCTTTG
59.65
141
PCR template sequence:
TGTGAATTTGGGAGGTTTGAAAGATCACATTAAGGAGATCCAGCGGTGTCGGCGGTTGATTCTTATTGCTTGTGGCACAAGTTACCACGCTGGTGTGGCAGTATATTTGCTTATTTAAATTACCATGTTCCTCGAACAAGACGAGAAATCTTGGAGACACTAATCAAAGGCCTTCAGAGACTGGAATACAGAGGATATGA
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-205-5p(1), mmu-miR-335-5p(1), mmu-miR-182-5p(1), mmu-miR-425-5p(1), mmu-miR-188-3p(1), mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
CGCTGGTGTGGCAGTATATTTGCTTA
siRNA sets
TAAGCAAATATACTGCCAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGFPT1_1142_ORF_1
1.2263
0.189562608
0.988924521
933
ORF sequence:
ATGGACTTGGATATAGAATTTGATGTGCATCTTGGAATAGCTCATACCCGTTGGGCGACACATGGAGAACCCAATCCTGTCAATAGTCACCCCCAGCGCTCTGATAAAAATAATGAATTCATTGTTATTCATAATGGAATCATCACCAACTACAAAGACTTGAAAAAGTTTCTGGAAAGCAAAGGCTATGACTTTGAATCTGAAACAGACACAGAAACCATTGCCAAGCTCGTCAAGTACATGTATGACAACTGGGAGAGCCAGGACGTCAGTTTTACCACCTTGGTGGAGAGAGTTATCCAACAATTGGAAGGCGCCTTTGCTCTTGTGTTTAAAAGTGTCCATTTTCCCGGGCAAGCAGTTGGCACAAGGCGAGGTAGCCCTCTCTTGATTGGTGTGCGGAGTGAACATAAGCTTTCTACAGATCACATTCCGATTCTGTACAGAACAGGCAAAGACAAGAAAGGAAGCTGCGGTCTTTCCCGTGTGGACAGCACGACATGCCTGTTCCCTGTTGAGGAAAAGGCAGTTGAATATTACTTTGCTTCTGATGCAAGTGCCGTGATAGAGCACACCAATCGTGTCATCTTTCTGGAAGATGATGATGTTGCAGCAGTGGTGGATGGCCGTCTCTCTATCCACCGAATTAAACGAACTGCAGGAGACCATCCTGGCCGAGCTGTGCAAACTCTCCAGATGGAGCTCCAGCAGATCATGAAGGGCAACTTTAGTTCATTTATGCAGAAGGAAATTTTTGAGCAGCCAGAATCTGTTGTGAACACAATGAGAGGAAGAGTCAATTTTGATGACTACACTGTGAATTTGGGAGGTTTGAAAGATCACATTAAGGAGATCCAGCGGTGTCGGCGGTTGATTCTTATTGCTTGTGGCACAAGTTACCACGCTGGTGTGGCAGTATATTTGCTTATTTAA
Peptide sequence:
MDLDIEFDVHLGIAHTRWATHGEPNPVNSHPQRSDKNNEFIVIHNGIITNYKDLKKFLESKGYDFESETDTETIAKLVKYMYDNWESQDVSFTTLVERVIQQLEGAFALVFKSVHFPGQAVGTRRGSPLLIGVRSEHKLSTDHIPILYRTGKDKKGSCGLSRVDSTTCLFPVEEKAVEYYFASDASAVIEHTNRVIFLEDDDVAAVVDGRLSIHRIKRTAGDHPGRAVQTLQMELQQIMKGNFSSFMQKEIFEQPESVVNTMRGRVNFDDYTVNLGGLKDHIKEIQRCRRLILIACGTSYHAGVAVYLLI
IRESfinder result
IRESfinder score
0.565627594
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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