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mmu_circGnpat_394
Basic information of circular RNA
PanCircBase ID:
mmu_circGnpat_394
mm39_Chr. Position ID:
chr8|125612533|125614558|+
Gene name:
Gnpat
Transcript:
ENSMUST00000034466.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
12,13,14,15
Exon/intron offsets:
0,888,1058,1963
Genomic length:
2025
Exon/intron sizes in nt:
141,97,94,62
Flanking exon/introns:
chr8:125611783-125612533|chr8:125614558-125616010
Splice length:
394
Other database IDs:
circAtlas: mmu-Gnpat_0016
Human Ortholog IDs:
Mature spliced Sequence:
GACTTTGAGGAAGGCTGTTACTTGCTGTGTAAAGCTGAGGCTATGCAGATGGCTGGGAAGGACATCATCCTCACAGACAAAGGAACTGCTGTGTTACAGTTCCTCACAAGCCTCTTTAAGCCTTTTGTGGAATCATATCAGTTACTTTGCAGATACCTTTTGCATGAAGAGGACTACTTCGGTGAGAAGGAATACTTGGTTGCAGCCAGGAAGTTCACCCGTCAGCTTCTGGATCAAGGCTCCTCTCAGTGTTACGATGCGCTGTCTTCTGAACTGCAGAAAAATGCCTTAGCAGCTTTCGTGAGACTGGGGGTGGTGGAAAAGAAGAAGGTAGATAGTAAGTATGTGTATTATGTGAACGGGCCTGCCACAAGCAAGTTAGAAGAAATGCTCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGGGGTGGTGGAAAAGAAG
59.81
CAGCCATCTGCATAGCCTCA
59.89
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGGGGTGGTGGAAAAGAA
59.81
CAGCCATCTGCATAGCCTCA
59.89
143
PCR template sequence:
GCTTTCGTGAGACTGGGGGTGGTGGAAAAGAAGAAGGTAGATAGTAAGTATGTGTATTATGTGAACGGGCCTGCCACAAGCAAGTTAGAAGAAATGCTCGGACTTTGAGGAAGGCTGTTACTTGCTGTGTAAAGCTGAGGCTATGCAGATGGCTGGGAAGGACATCATCCTCACAGACAAAGGAACTGCTGTGTTACAGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-153-3p(1), mmu-miR-194-5p(1), mmu-miR-27a-5p(1), mmu-miR-369-3p(1), mmu-miR-452-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAAGAAATGCTCGGACTTTGAGGAAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGNPAT_394_ORF_1
1.0447
0.231874355
0.55654333
360
ORF sequence:
ATGCAGATGGCTGGGAAGGACATCATCCTCACAGACAAAGGAACTGCTGTGTTACAGTTCCTCACAAGCCTCTTTAAGCCTTTTGTGGAATCATATCAGTTACTTTGCAGATACCTTTTGCATGAAGAGGACTACTTCGGTGAGAAGGAATACTTGGTTGCAGCCAGGAAGTTCACCCGTCAGCTTCTGGATCAAGGCTCCTCTCAGTGTTACGATGCGCTGTCTTCTGAACTGCAGAAAAATGCCTTAGCAGCTTTCGTGAGACTGGGGGTGGTGGAAAAGAAGAAGGTAGATAGTAAGTATGTGTATTATGTGAACGGGCCTGCCACAAGCAAGTTAGAAGAAATGCTCGGACTTTGA
Peptide sequence:
MQMAGKDIILTDKGTAVLQFLTSLFKPFVESYQLLCRYLLHEEDYFGEKEYLVAARKFTRQLLDQGSSQCYDALSSELQKNALAAFVRLGVVEKKKVDSKYVYYVNGPATSKLEEMLGL
IRESfinder result
IRESfinder score
0.448834175
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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