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mmu_circKcnh1_393
Basic information of circular RNA
PanCircBase ID:
mmu_circKcnh1_393
mm39_Chr. Position ID:
chr1|191959005|191959398|+
Gene name:
Kcnh1
Transcript:
ENSMUST00000110844.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
1
Exon/intron indexes:
6
Exon/intron offsets:
0
Genomic length:
393
Exon/intron sizes in nt:
393
Flanking exon/introns:
chr1:191924345-191959005|chr1:191959398-192019707
Splice length:
393
Other database IDs:
circAtlas: mmu-Kcnh1_0007
circBase: hsa_circ_0111831, circAtlas: hsa-KCNH1_0008, CIRCpedia: HSA_CIRCpedia_29785
Human Ortholog IDs:
Mature spliced Sequence:
GTCCTGCAGCTGGGTTCAGACATCCTTCCCCAGTACAAGCAAGAGGCGCCAAAGACACCCCCTCACATCATCCTACACTACTGTGTCTTTAAGACCACGTGGGATTGGATCATCTTGATCCTGACCTTCTACACAGCCATCTTGGTCCCTTACAACGTCTCCTTTAAAACCAGGCAGAATAATGTGGCCTGGCTGGTGGTGGACAGCATCGTGGATGTCATCTTTTTGGTGGACATTGTTTTGAATTTTCACACCACCTTTGTCGGGCCAGCGGGGGAAGTGATATCTGACCCCAAACTTATCCGCATGAACTACCTGAAGACGTGGTTTGTGATCGACCTTCTGTCCTGTTTGCCGTATGACGTCATCAACGCTTTTGAGAACGTGGATGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACGTGGTTTGTGATCGACCT
59.61
GGATGATGTGAGGGGGTGTC
59.82
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACGTGGTTTGTGATCGACCT
59.61
AGGATGATGTGAGGGGGTGT
60.25
146
PCR template sequence:
CAAACTTATCCGCATGAACTACCTGAAGACGTGGTTTGTGATCGACCTTCTGTCCTGTTTGCCGTATGACGTCATCAACGCTTTTGAGAACGTGGATGAGGTCCTGCAGCTGGGTTCAGACATCCTTCCCCAGTACAAGCAAGAGGCGCCAAAGACACCCCCTCACATCATCCTACACTACTGTGTCTTTAAGACCACGT
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-221-3p(1), mmu-miR-196a-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-540-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAACGTGGATGAGGTCCTGCAGCTGG
siRNA sets
CAGCTGCAGGACCTCATCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKCNH1_393_ORF_1
1.2975
0.442301478
0.918611199
480
ORF sequence:
ATGAACTACCTGAAGACGTGGTTTGTGATCGACCTTCTGTCCTGTTTGCCGTATGACGTCATCAACGCTTTTGAGAACGTGGATGAGGTCCTGCAGCTGGGTTCAGACATCCTTCCCCAGTACAAGCAAGAGGCGCCAAAGACACCCCCTCACATCATCCTACACTACTGTGTCTTTAAGACCACGTGGGATTGGATCATCTTGATCCTGACCTTCTACACAGCCATCTTGGTCCCTTACAACGTCTCCTTTAAAACCAGGCAGAATAATGTGGCCTGGCTGGTGGTGGACAGCATCGTGGATGTCATCTTTTTGGTGGACATTGTTTTGAATTTTCACACCACCTTTGTCGGGCCAGCGGGGGAAGTGATATCTGACCCCAAACTTATCCGCATGAACTACCTGAAGACGTGGTTTGTGATCGACCTTCTGTCCTGTTTGCCGTATGACGTCATCAACGCTTTTGAGAACGTGGATGAG
Peptide sequence:
MNYLKTWFVIDLLSCLPYDVINAFENVDEVLQLGSDILPQYKQEAPKTPPHIILHYCVFKTTWDWIILILTFYTAILVPYNVSFKTRQNNVAWLVVDSIVDVIFLVDIVLNFHTTFVGPAGEVISDPKLIRMNYLKTWFVIDLLSCLPYDVINAFENVDE
IRESfinder result
IRESfinder score
0.708567602
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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