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mmu_circNek7_391
Basic information of circular RNA
PanCircBase ID:
mmu_circNek7_391
mm39_Chr. Position ID:
chr1|138443362|138462164|-
Gene name:
Nek7
Transcript:
ENSMUST00000186017.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
7,6,5,4
Exon/intron offsets:
0,903,17112,18739
Genomic length:
18802
Exon/intron sizes in nt:
108,109,111,63
Flanking exon/introns:
chr1:138430403-138443362|chr1:138462164-138471940
Splice length:
391
Other database IDs:
circAtlas: mmu-Nek7_0003
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_110226
Human Ortholog IDs:
Mature spliced Sequence:
ATATTTGATTTAATGGATGCCAAAGCACGTGCTGATTGTATCAAAGAAATAGACCTCCTTAAGCAACTCAACCATCCAAATGTAATTAAATACTATGCATCATTCATTGAGGATAATGAGCTGAACATAGTTTTGGAGTTAGCAGATGCTGGTGACCTCTCCAGAATGATAAAGCACTTTAAGAAACAAAAGAGGCTAATCCCTGAGAGAACCGTTTGGAAATACTTCGTTCAGCTCTGCAGTGCACTGGACCACATGCATTCTCGAAGAGTCATGCACAGAGATATAAAACCAGCTAATGTGTTCATTACAGCCACTGGGGTAGTAAAACTCGGAGACCTTGGGCTTGGTCGGTTTTTCAGCTCCAAAACCACAGCTGCACATTCTTTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAAACTCGGAGACCTTGGGC
60.25
TGGATGGTTGAGTTGCTTAAGGA
59.93
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAAACTCGGAGACCTTGGGC
60.25
ATGGTTGAGTTGCTTAAGGAGGT
59.93
140
PCR template sequence:
CCAGCTAATGTGTTCATTACAGCCACTGGGGTAGTAAAACTCGGAGACCTTGGGCTTGGTCGGTTTTTCAGCTCCAAAACCACAGCTGCACATTCTTTAGATATTTGATTTAATGGATGCCAAAGCACGTGCTGATTGTATCAAAGAAATAGACCTCCTTAAGCAACTCAACCATCCAAATGTAATTAAATACTATGCAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-152-3p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-680(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCACATTCTTTAGATATTTGATTTAA
siRNA sets
TAAATCAAATATCTAAAGA, TTAAATCAAATATCTAAAG, AAATCAAATATCTAAAGAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNEK7_391_ORF_1
0.9557
0.022767943
0.354727273
387
ORF sequence:
ATGGATGCCAAAGCACGTGCTGATTGTATCAAAGAAATAGACCTCCTTAAGCAACTCAACCATCCAAATGTAATTAAATACTATGCATCATTCATTGAGGATAATGAGCTGAACATAGTTTTGGAGTTAGCAGATGCTGGTGACCTCTCCAGAATGATAAAGCACTTTAAGAAACAAAAGAGGCTAATCCCTGAGAGAACCGTTTGGAAATACTTCGTTCAGCTCTGCAGTGCACTGGACCACATGCATTCTCGAAGAGTCATGCACAGAGATATAAAACCAGCTAATGTGTTCATTACAGCCACTGGGGTAGTAAAACTCGGAGACCTTGGGCTTGGTCGGTTTTTCAGCTCCAAAACCACAGCTGCACATTCTTTAGATATTTGA
Peptide sequence:
MDAKARADCIKEIDLLKQLNHPNVIKYYASFIEDNELNIVLELADAGDLSRMIKHFKKQKRLIPERTVWKYFVQLCSALDHMHSRRVMHRDIKPANVFITATGVVKLGDLGLGRFFSSKTTAAHSLDI
IRESfinder result
IRESfinder score
0.760463923
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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