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mmu_circNae1_860
Basic information of circular RNA
PanCircBase ID:
mmu_circNae1_860
mm39_Chr. Position ID:
chr8|105244538|105254849|-
Gene name:
Nae1
Transcript:
ENSMUST00000162466.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
14,13,12,11,10,9,8,7,6,5,4
Exon/intron offsets:
0,281,1638,1857,4740,5255,5669,6428,8373,9176,10280
Genomic length:
10311
Exon/intron sizes in nt:
40,76,134,60,92,64,63,110,110,80,31
Flanking exon/introns:
chr8:105243366-105244538|chr8:105254849-105256687
Splice length:
860
Other database IDs:
circBase: hsa_circ_0039755
Human Ortholog IDs:
Mature spliced Sequence:
CTTTTTCCTTCAAAAAAGCAGTATTGGCAAGAGTCCAGAAAACCTTCTAGACAATGATCCTTCATTTTTCTGTAGGTTTACTATTGTGGTTGCAACTCAGCTTCTTGAAAGTACATTGCTGCGTTTAGCAGATGTTCTCTGGAATTCCCAGATCCCTCTTTTGATCTGTAGGACATATGGACTAGTTGGTTATATGAGGATTATTATAAAAGAACACCCAGTAATAGAATCTCATCCAGATAATGCATTGGAGGATCTACGACTAGATAAGCCATTTCCTGAACTGAGAGAACATCTTCAGTCTTATGACTTGGACCATATGGAAAAAAAGGACCATAGCCATACTCCATGGATTGTGATCATAGCTAAATATTTAGCACAGTGGTATAATGAAACAAATGGACGGATTCCTAAAAGTTATAAAGAAAAAGAGGACTTCAGAGATTTGATAAGACAAGGGATTTTAAAGAATGAAAATGGAGCTCCAGAAGACGAAGAGAATTTTGAAGAAGCCATCAAAAATGTGAACACAGCACTAAATACAACTCAGATCCCAAGCAGTATTGAAGATATATTTAATGATGATCGATGCATAAATATCACCAAACAGACACCAACTTTTTGGATTCTAGCTCGTGCCTTAAAGGAATTTGTGGCCAAGGAGGGTCAAGGAAATTTACCTGTCCGAGGCACAATTCCTGATATGATTGCAGATTCAAACAAATACATAAAACTGCAGAATGTTTACCGAGAGAAAGCAAAGAAAGATGCTGCTGCTGTAGGCAATCACGTTGCCAAATTGCTTCAGTCTGTTGGCCAGGCACCAGAGTCCATTTCAGAGAAAGAATTAAAATTGCTTT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGATGCTGCTGCTGTAGGC
60.75
AGGTTTTCTGGACTCTTGCCA
59.51
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGATGCTGCTGCTGTAGGC
60.15
AGGTTTTCTGGACTCTTGCCA
59.51
140
PCR template sequence:
AAGAAAGATGCTGCTGCTGTAGGCAATCACGTTGCCAAATTGCTTCAGTCTGTTGGCCAGGCACCAGAGTCCATTTCAGAGAAAGAATTAAAATTGCTTTCTTTTTCCTTCAAAAAAGCAGTATTGGCAAGAGTCCAGAAAACCTTCTAGACAATGATCCTTCATTTTTCTGTAGGTTTACTATTGTGGTTGCAACTCAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
22
Interacting miRNAs (#binding sites)
mmu-miR-200b-3p(2), mmu-miR-135a-5p(2), mmu-miR-136-5p(2), mmu-miR-124-3p(1), mmu-miR-15a-5p(1), mmu-miR-429-3p(1), mmu-miR-103-3p(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-107-3p(1), mmu-miR-499-5p(1), mmu-miR-410-3p(1), mmu-miR-344d-3p(1), mmu-miR-5101(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTAAAATTGCTTTCTTTTTCCTTCAA
siRNA sets
TTGAAGGAAAAAGAAAGCA, AAAAAGAAAGCAATTTTAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNAE1_860_ORF_1
1.0294
0.061869645
0.886761443
717
ORF sequence:
ATGAGGATTATTATAAAAGAACACCCAGTAATAGAATCTCATCCAGATAATGCATTGGAGGATCTACGACTAGATAAGCCATTTCCTGAACTGAGAGAACATCTTCAGTCTTATGACTTGGACCATATGGAAAAAAAGGACCATAGCCATACTCCATGGATTGTGATCATAGCTAAATATTTAGCACAGTGGTATAATGAAACAAATGGACGGATTCCTAAAAGTTATAAAGAAAAAGAGGACTTCAGAGATTTGATAAGACAAGGGATTTTAAAGAATGAAAATGGAGCTCCAGAAGACGAAGAGAATTTTGAAGAAGCCATCAAAAATGTGAACACAGCACTAAATACAACTCAGATCCCAAGCAGTATTGAAGATATATTTAATGATGATCGATGCATAAATATCACCAAACAGACACCAACTTTTTGGATTCTAGCTCGTGCCTTAAAGGAATTTGTGGCCAAGGAGGGTCAAGGAAATTTACCTGTCCGAGGCACAATTCCTGATATGATTGCAGATTCAAACAAATACATAAAACTGCAGAATGTTTACCGAGAGAAAGCAAAGAAAGATGCTGCTGCTGTAGGCAATCACGTTGCCAAATTGCTTCAGTCTGTTGGCCAGGCACCAGAGTCCATTTCAGAGAAAGAATTAAAATTGCTTTCTTTTTCCTTCAAAAAAGCAGTATTGGCAAGAGTCCAGAAAACCTTCTAG
Peptide sequence:
MRIIIKEHPVIESHPDNALEDLRLDKPFPELREHLQSYDLDHMEKKDHSHTPWIVIIAKYLAQWYNETNGRIPKSYKEKEDFRDLIRQGILKNENGAPEDEENFEEAIKNVNTALNTTQIPSSIEDIFNDDRCINITKQTPTFWILARALKEFVAKEGQGNLPVRGTIPDMIADSNKYIKLQNVYREKAKKDAAAVGNHVAKLLQSVGQAPESISEKELKLLSFSFKKAVLARVQKTF
IRESfinder result
IRESfinder score
0.759927542
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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