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mmu_circNae1_709
Basic information of circular RNA
PanCircBase ID:
mmu_circNae1_709
mm39_Chr. Position ID:
chr8|105242760|105250270|-
Gene name:
Nae1
Transcript:
ENSMUST00000162466.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
16,15,14,13,12,11,10,9,8
Exon/intron offsets:
0,519,1778,2059,3416,3635,6518,7033,7447
Genomic length:
7510
Exon/intron sizes in nt:
93,87,40,76,134,60,92,64,63
Flanking exon/introns:
chr8:105240087-105242760|chr8:105250270-105250966
Splice length:
709
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GACCATAGCCATACTCCATGGATTGTGATCATAGCTAAATATTTAGCACAGTGGTATAATGAAACAAATGGACGGATTCCTAAAAGTTATAAAGAAAAAGAGGACTTCAGAGATTTGATAAGACAAGGGATTTTAAAGAATGAAAATGGAGCTCCAGAAGACGAAGAGAATTTTGAAGAAGCCATCAAAAATGTGAACACAGCACTAAATACAACTCAGATCCCAAGCAGTATTGAAGATATATTTAATGATGATCGATGCATAAATATCACCAAACAGACACCAACTTTTTGGATTCTAGCTCGTGCCTTAAAGGAATTTGTGGCCAAGGAGGGTCAAGGAAATTTACCTGTCCGAGGCACAATTCCTGATATGATTGCAGATTCAAACAAATACATAAAACTGCAGAATGTTTACCGAGAGAAAGCAAAGAAAGATGCTGCTGCTGTAGGCAATCACGTTGCCAAATTGCTTCAGTCTGTTGGCCAGGCACCAGAGTCCATTTCAGAGAAAGAATTAAAATTGCTTTGCAGCAATTCTGCATTTCTTCGAGTGGTAAGATGTCGATCTTTAGCTGAAGAGTATGGCTTGGATACAGTCAACAAAGATGAAATTATTTCTAGCATGGACAATCCGGATAATGAGATAGTCCTGTACCTGATGTTGCGGGCTGTTGATCGATTTCATAAACAGCATGGCAGATACCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTGTACCTGATGTTGCGG
59.75
GGAATCCGTCCATTTGTTTCA
56.79
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTGTACCTGATGTTGCGG
59.75
GGAATCCGTCCATTTGTTTCAT
57.28
140
PCR template sequence:
GAAATTATTTCTAGCATGGACAATCCGGATAATGAGATAGTCCTGTACCTGATGTTGCGGGCTGTTGATCGATTTCATAAACAGCATGGCAGATACCCAGGACCATAGCCATACTCCATGGATTGTGATCATAGCTAAATATTTAGCACAGTGGTATAATGAAACAAATGGACGGATTCCTAAAAGTTATAAAGAAAAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
19
Interacting miRNAs (#binding sites)
mmu-miR-103-3p(2), mmu-miR-136-5p(2), mmu-miR-107-3p(2), mmu-miR-124-3p(1), mmu-miR-15a-5p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-135a-5p(1), mmu-miR-30e-5p(1), mmu-miR-200c-3p(1), mmu-miR-122-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-30a-5p(1), mmu-miR-30c-5p(1), mmu-miR-30b-5p(1), mmu-miR-182-5p(1), mmu-miR-5101(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGCAGATACCCAGGACCATAGCCATA
siRNA sets
ATGGTCCTGGGTATCTGCC, TATGGTCCTGGGTATCTGC, TATGGCTATGGTCCTGGGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNAE1_709_ORF_1
0.969
0.138318215
0.909592234
723
ORF sequence:
ATGGCAGATACCCAGGACCATAGCCATACTCCATGGATTGTGATCATAGCTAAATATTTAGCACAGTGGTATAATGAAACAAATGGACGGATTCCTAAAAGTTATAAAGAAAAAGAGGACTTCAGAGATTTGATAAGACAAGGGATTTTAAAGAATGAAAATGGAGCTCCAGAAGACGAAGAGAATTTTGAAGAAGCCATCAAAAATGTGAACACAGCACTAAATACAACTCAGATCCCAAGCAGTATTGAAGATATATTTAATGATGATCGATGCATAAATATCACCAAACAGACACCAACTTTTTGGATTCTAGCTCGTGCCTTAAAGGAATTTGTGGCCAAGGAGGGTCAAGGAAATTTACCTGTCCGAGGCACAATTCCTGATATGATTGCAGATTCAAACAAATACATAAAACTGCAGAATGTTTACCGAGAGAAAGCAAAGAAAGATGCTGCTGCTGTAGGCAATCACGTTGCCAAATTGCTTCAGTCTGTTGGCCAGGCACCAGAGTCCATTTCAGAGAAAGAATTAAAATTGCTTTGCAGCAATTCTGCATTTCTTCGAGTGGTAAGATGTCGATCTTTAGCTGAAGAGTATGGCTTGGATACAGTCAACAAAGATGAAATTATTTCTAGCATGGACAATCCGGATAATGAGATAGTCCTGTACCTGATGTTGCGGGCTGTTGATCGATTTCATAAACAGCATGGCAGATACCCA
Peptide sequence:
MADTQDHSHTPWIVIIAKYLAQWYNETNGRIPKSYKEKEDFRDLIRQGILKNENGAPEDEENFEEAIKNVNTALNTTQIPSSIEDIFNDDRCINITKQTPTFWILARALKEFVAKEGQGNLPVRGTIPDMIADSNKYIKLQNVYREKAKKDAAAVGNHVAKLLQSVGQAPESISEKELKLLCSNSAFLRVVRCRSLAEEYGLDTVNKDEIISSMDNPDNEIVLYLMLRAVDRFHKQHGRYP
IRESfinder result
IRESfinder score
0.622886454
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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