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mmu_circHlcs_272
Basic information of circular RNA
PanCircBase ID:
mmu_circHlcs_272
mm39_Chr. Position ID:
chr16|94031922|94032194|-
Gene name:
Hlcs
Transcript:
ENSMUST00000228910.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
1
Exon/intron indexes:
2
Exon/intron offsets:
0
Genomic length:
272
Exon/intron sizes in nt:
272
Flanking exon/introns:
chr16:93942275-94031922|chr16:94032194-94046708
Splice length:
272
Other database IDs:
CIRCpedia: MMU_CIRCpedia_34733, circAtlas: mmu-Hlcs_0008
circBase: hsa_circ_0061651, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_35426
Human Ortholog IDs:
Mature spliced Sequence:
GAAACCCAGGATCCGTTCATGCAGTGGCTCGGGAGGCACACAGATCCTGAAGGAATCATAAAATCCAGCAAGCTCTCCCTTCAGTTTGTTTCCTCCTACACATCTGAAGCGGAGATCACCCCGTCTTCCATGCCTGTGGTCACTGACCCAGAAGCCTTTTCATCAGAGCACTTCAGCCTAGAGACCTATCGACAGAATCTGCAGACCACGCGCCTTGGGAAAGTGATTCTGTTTGCAGAAGTGACCTCCACCACCATGAGTCTCCTGGATGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCGCCTTGGGAAAGTGATTC
59.83
ACTGAAGGGAGAGCTTGCTG
59.68
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCGCCTTGGGAAAGTGATTC
59.83
CTGAAGGGAGAGCTTGCTGG
60.39
147
PCR template sequence:
TCAGCCTAGAGACCTATCGACAGAATCTGCAGACCACGCGCCTTGGGAAAGTGATTCTGTTTGCAGAAGTGACCTCCACCACCATGAGTCTCCTGGATGGGAAACCCAGGATCCGTTCATGCAGTGGCTCGGGAGGCACACAGATCCTGAAGGAATCATAAAATCCAGCAAGCTCTCCCTTCAGTTTGTTTCCTCCTACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-7b-5p(1), mmu-miR-217-5p(1), mmu-miR-7a-5p(1), mmu-miR-511-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTCTCCTGGATGGGAAACCCAGGATC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHLCS_272_ORF_1
0.8188
0.233513534
0.376295743
315
ORF sequence:
ATGCAGTGGCTCGGGAGGCACACAGATCCTGAAGGAATCATAAAATCCAGCAAGCTCTCCCTTCAGTTTGTTTCCTCCTACACATCTGAAGCGGAGATCACCCCGTCTTCCATGCCTGTGGTCACTGACCCAGAAGCCTTTTCATCAGAGCACTTCAGCCTAGAGACCTATCGACAGAATCTGCAGACCACGCGCCTTGGGAAAGTGATTCTGTTTGCAGAAGTGACCTCCACCACCATGAGTCTCCTGGATGGGAAACCCAGGATCCGTTCATGCAGTGGCTCGGGAGGCACACAGATCCTGAAGGAATCATAA
Peptide sequence:
MQWLGRHTDPEGIIKSSKLSLQFVSSYTSEAEITPSSMPVVTDPEAFSSEHFSLETYRQNLQTTRLGKVILFAEVTSTTMSLLDGKPRIRSCSGSGGTQILKES
IRESfinder result
IRESfinder score
0.738535929
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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