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mmu_circKcnh1_360
Basic information of circular RNA
PanCircBase ID:
mmu_circKcnh1_360
mm39_Chr. Position ID:
chr1|191903640|191921161|+
Gene name:
Kcnh1
Transcript:
ENSMUST00000078470.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
2,3,4
Exon/intron offsets:
0,3512,17392
Genomic length:
17521
Exon/intron sizes in nt:
12,41,07,129
Flanking exon/introns:
chr1:191873394-191903640|chr1:191921161-191924226
Splice length:
360
Other database IDs:
CIRCpedia: MMU_CIRCpedia_12697, circAtlas: mmu-Kcnh1_0032
circBase: hsa_circ_0111834, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_148851
Human Ortholog IDs:
Mature spliced Sequence:
ACACTAATTTTGTGTTGGGGAATGCCCAGATAGTCGACTGGCCCATCGTGTACAGCAATGATGGATTCTGCAAGCTGTCTGGCTACCACCGGGCAGAAGTGATGCAGAAAAGCAGCGCCTGCAGTTTTATGTATGGAGAGCTGACTGACAAGGACACAGTTGAAAAGGTTCGCCAGACCTTTGAGAACTACGAGATGAATTCCTTCGAAATTCTGATGTACAAGAAGAACAGGACACCTGTGTGGTTTTTTGTGAAGATCGCTCCGATCAGGAACGAACAGGATAAAGTGGTCCTGTTCCTTTGCACTTTCAGCGACATAACTGCATTCAAGCAGCCCATCGAGGACGACTCCTGCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCGATCAGGAACGAACAGGA
59.47
CGATGGGCCAGTCGACTATC
60.04
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGTCCTGTTCCTTTGCACT
59.45
GTAGCCAGACAGCTTGCAGA
60.04
158
PCR template sequence:
GCTCCGATCAGGAACGAACAGGATAAAGTGGTCCTGTTCCTTTGCACTTTCAGCGACATAACTGCATTCAAGCAGCCCATCGAGGACGACTCCTGCAAAGACACTAATTTTGTGTTGGGGAATGCCCAGATAGTCGACTGGCCCATCGTGTACAGCAATGATGGATTCTGCAAGCTGTCTGGCTACCACCGGGCAGAAGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-130a-3p(1), mmu-miR-130b-3p(1), mmu-miR-301b-3p(1), mmu-miR-721(1), mmu-miR-350-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GACTCCTGCAAAGACACTAATTTTGT
siRNA sets
AAATTAGTGTCTTTGCAGG, AATTAGTGTCTTTGCAGGA, AAAATTAGTGTCTTTGCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKCNH1_360_ORF_1
1.1961
0.390603866
0.953517321
618
ORF sequence:
ATGCAGAAAAGCAGCGCCTGCAGTTTTATGTATGGAGAGCTGACTGACAAGGACACAGTTGAAAAGGTTCGCCAGACCTTTGAGAACTACGAGATGAATTCCTTCGAAATTCTGATGTACAAGAAGAACAGGACACCTGTGTGGTTTTTTGTGAAGATCGCTCCGATCAGGAACGAACAGGATAAAGTGGTCCTGTTCCTTTGCACTTTCAGCGACATAACTGCATTCAAGCAGCCCATCGAGGACGACTCCTGCAAAGACACTAATTTTGTGTTGGGGAATGCCCAGATAGTCGACTGGCCCATCGTGTACAGCAATGATGGATTCTGCAAGCTGTCTGGCTACCACCGGGCAGAAGTGATGCAGAAAAGCAGCGCCTGCAGTTTTATGTATGGAGAGCTGACTGACAAGGACACAGTTGAAAAGGTTCGCCAGACCTTTGAGAACTACGAGATGAATTCCTTCGAAATTCTGATGTACAAGAAGAACAGGACACCTGTGTGGTTTTTTGTGAAGATCGCTCCGATCAGGAACGAACAGGATAAAGTGGTCCTGTTCCTTTGCACTTTCAGCGACATAACTGCATTCAAGCAGCCCATCGAGGACGACTCCTGCAAA
Peptide sequence:
MQKSSACSFMYGELTDKDTVEKVRQTFENYEMNSFEILMYKKNRTPVWFFVKIAPIRNEQDKVVLFLCTFSDITAFKQPIEDDSCKDTNFVLGNAQIVDWPIVYSNDGFCKLSGYHRAEVMQKSSACSFMYGELTDKDTVEKVRQTFENYEMNSFEILMYKKNRTPVWFFVKIAPIRNEQDKVVLFLCTFSDITAFKQPIEDDSCK
IRESfinder result
IRESfinder score
0.411305833
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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