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mmu_circGspt1_414
Basic information of circular RNA
PanCircBase ID:
mmu_circGspt1_414
mm39_Chr. Position ID:
chr16|11048700|11053307|-
Gene name:
Gspt1
Transcript:
ENSMUST00000167571.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
8,7,6
Exon/intron offsets:
0,1695,4529
Genomic length:
4607
Exon/intron sizes in nt:
155,181,78
Flanking exon/introns:
chr16:11048514-11048700|chr16:11053307-11055394
Splice length:
414
Other database IDs:
CIRCpedia: MMU_CIRCpedia_220424, circAtlas: mmu-Gspt1_0024
Human Ortholog IDs:
Mature spliced Sequence:
GTATTTGACTGGAATGGTCGACAAAAGGACACTTGAGAAGTATGAACGAGAAGCTAAAGAAAAAAACAGAGAAACTTGGTACTTGTCTTGGGCCTTAGACACGAATCAGGAAGAACGAGACAAGGGCAAAACCGTGGAGGTGGGTCGTGCCTATTTTGAAACGGAAAAGAAGCATTTTACAATTCTAGATGCTCCTGGCCATAAGAGTTTTGTCCCAAATATGATTGGTGGTGCCTCTCAAGCTGACTTGGCTGTACTGGTAATCTCAGCCAGGAAAGGAGAGTTTGAAACTGGATTTGAAAAAGGAGGACAGACAAGAGAACATGCAATGTTGGCAAAGACAGCAGGTGTCAAACACTTAATTGTGCTTATTAATAAGATGGATGATCCAACGGTAAACTGGAGCAACGAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTTGGCAAAGACAGCAGGTG
59.97
AGGCCCAAGACAAGTACCAAG
59.93
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTTGGCAAAGACAGCAGGTG
59.97
AGGCCCAAGACAAGTACCAA
58.85
179
PCR template sequence:
CAAGAGAACATGCAATGTTGGCAAAGACAGCAGGTGTCAAACACTTAATTGTGCTTATTAATAAGATGGATGATCCAACGGTAAACTGGAGCAACGAGAGGTATTTGACTGGAATGGTCGACAAAAGGACACTTGAGAAGTATGAACGAGAAGCTAAAGAAAAAAACAGAGAAACTTGGTACTTGTCTTGGGCCTTAGAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-544-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGAGCAACGAGAGGTATTTGACTGGA
siRNA sets
CAAATACCTCTCGTTGCTC, GTCAAATACCTCTCGTTGC, TCAAATACCTCTCGTTGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGSPT1_414_ORF_1
1.0219
0.17718279
0.961918431
813
ORF sequence:
ATGGTCGACAAAAGGACACTTGAGAAGTATGAACGAGAAGCTAAAGAAAAAAACAGAGAAACTTGGTACTTGTCTTGGGCCTTAGACACGAATCAGGAAGAACGAGACAAGGGCAAAACCGTGGAGGTGGGTCGTGCCTATTTTGAAACGGAAAAGAAGCATTTTACAATTCTAGATGCTCCTGGCCATAAGAGTTTTGTCCCAAATATGATTGGTGGTGCCTCTCAAGCTGACTTGGCTGTACTGGTAATCTCAGCCAGGAAAGGAGAGTTTGAAACTGGATTTGAAAAAGGAGGACAGACAAGAGAACATGCAATGTTGGCAAAGACAGCAGGTGTCAAACACTTAATTGTGCTTATTAATAAGATGGATGATCCAACGGTAAACTGGAGCAACGAGAGGTATTTGACTGGAATGGTCGACAAAAGGACACTTGAGAAGTATGAACGAGAAGCTAAAGAAAAAAACAGAGAAACTTGGTACTTGTCTTGGGCCTTAGACACGAATCAGGAAGAACGAGACAAGGGCAAAACCGTGGAGGTGGGTCGTGCCTATTTTGAAACGGAAAAGAAGCATTTTACAATTCTAGATGCTCCTGGCCATAAGAGTTTTGTCCCAAATATGATTGGTGGTGCCTCTCAAGCTGACTTGGCTGTACTGGTAATCTCAGCCAGGAAAGGAGAGTTTGAAACTGGATTTGAAAAAGGAGGACAGACAAGAGAACATGCAATGTTGGCAAAGACAGCAGGTGTCAAACACTTAATTGTGCTTATTAATAAGATGGATGATCCAACGGTAAACTGGAGCAACGAG
Peptide sequence:
MVDKRTLEKYEREAKEKNRETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISARKGEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSNERYLTGMVDKRTLEKYEREAKEKNRETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISARKGEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSNE
IRESfinder result
IRESfinder score
0.524836468
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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