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mmu_circGpcpd1_400
Basic information of circular RNA
PanCircBase ID:
mmu_circGpcpd1_400
mm39_Chr. Position ID:
chr2|132395876|132414177|-
Gene name:
Gpcpd1
Transcript:
ENSMUST00000110136.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,2978,4650,10670,18228
Genomic length:
18301
Exon/intron sizes in nt:
124,42,76,85,73
Flanking exon/introns:
chr2:132392474-132395876|chr2:132414177-132419987
Splice length:
400
Other database IDs:
circAtlas: mmu-Gpcpd1_0028
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_95430
Human Ortholog IDs:
Mature spliced Sequence:
CAGAAATCCTAAAATTCCATCAGAATGACACCTTCTCAGGTCACTTTTGAAATAAGAGGAACTCTTTTACCAGTGTGTTGTGGAAAGCAGTGATTGCTCTCAATAGAGGAGTGTCAGTGAAGTACCGCTACTTCAGAGGCTGCTTTTTAGAACCAAAGACTATCGGTGGTCCATGTCAAGTCATAGTTCACAAGTGGGAGACTCATCTACAACCACGATCAATAACCCCTTTAGAAAGTGAAATCATTATTGACGATGGACAGTTTGGCATCCACAATGGTGTTGAAACACTGGATTCTGGATGGCTTACATGTCAGACTGAAATAAGATTGCGTCTGCATTTTTCTGAGAAACCTCCTGTTTCAATTAGCAAGAAAAAGTTCAAAAAATCGAGATTTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCGTCTGCATTTTTCTGAGA
56.74
CTGCTTTCCACAACACACTGG
59.93
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCGTCTGCATTTTTCTGAGA
56.74
TGCTTTCCACAACACACTGG
58.9
158
PCR template sequence:
GATGGCTTACATGTCAGACTGAAATAAGATTGCGTCTGCATTTTTCTGAGAAACCTCCTGTTTCAATTAGCAAGAAAAAGTTCAAAAAATCGAGATTTAGCAGAAATCCTAAAATTCCATCAGAATGACACCTTCTCAGGTCACTTTTGAAATAAGAGGAACTCTTTTACCAGTGTGTTGTGGAAAGCAGTGATTGCTCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-199a-5p(1), mmu-miR-192-5p(1), mmu-miR-215-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AATCGAGATTTAGCAGAAATCCTAAA
siRNA sets
TTTCTGCTAAATCTCGATT, ATTTCTGCTAAATCTCGAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.678365653
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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