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mmu_circNcbp3_613
Basic information of circular RNA
PanCircBase ID:
mmu_circNcbp3_613
mm39_Chr. Position ID:
chr11|72940684|72958637|+
Gene name:
Ncbp3
Transcript:
ENSMUST00000021135.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
2,3,4,5,6,7
Exon/intron offsets:
0,3564,15129,15712,16824,17844
Genomic length:
17953
Exon/intron sizes in nt:
6,61,06,12,61,29,77,100
Flanking exon/introns:
chr11:72938908-72940684|chr11:72958637-72960539
Splice length:
613
Other database IDs:
circAtlas: mmu-1200014J11Rik_0011
Human Ortholog IDs:
Mature spliced Sequence:
GACACAAGCAGAAGATATGAAAACAAGGCTGGCAGCTTCATCACTGGGATCGATGTCACCTCCAAGGAAGCAATTGAAAAGAAAGAACAGCGAGCCAAGCGCTTCCACTTTCGAGCAGAAGTAAATCTTGCCCAGAGAAATGTAGCCTTGGACCGAGACATGATGAAGAAAGCAATTCCCAAGGTGAGACTGGAGACAATCTACATTTGTGGAGTGGATGAAATGAGCACCCAGGATATCTTCTCCTATTTTAAGGAATATCCTCCAGCTCACATTGAGTGGTTGGATGACACCTCCTGCAATGTGGTTTGGCTGGACGAGATGACGGCCACACGAGCTCTCATCAATATGAGTTCTCTGCCAGCCCAGGATAAGATGAGAAGCAGAGATGCCAGTGAAGACAAGTCGTCGGAGAAGAACAAGAAAGACAAGCAGGAAGACAGTTCAGATGACGACGAGACTGAAGAAGGAGAAGTGGAAGATGAGAATTCAAGTGATGTAGAGTTGGACACGTTGTCTCAGGTAGAAGAAGAGTCTCTGTTACGAAATGATCTTCGTCCAGCTAACAAACTTGCTAAAGGAAATAGACTATTCATGAGATTTGCTACAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCGTCCAGCTAACAAACTTGC
59.13
GCTTGGCTCGCTGTTCTTTC
60.11
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGTCCAGCTAACAAACTTGCT
59.13
GCTTGGCTCGCTGTTCTTTC
60.11
158
PCR template sequence:
TTGTCTCAGGTAGAAGAAGAGTCTCTGTTACGAAATGATCTTCGTCCAGCTAACAAACTTGCTAAAGGAAATAGACTATTCATGAGATTTGCTACAAAAGGACACAAGCAGAAGATATGAAAACAAGGCTGGCAGCTTCATCACTGGGATCGATGTCACCTCCAAGGAAGCAATTGAAAAGAAAGAACAGCGAGCCAAGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-452-3p(2), mmu-miR-221-3p(1), mmu-miR-146a-5p(1), mmu-miR-222-3p(1), mmu-miR-22-3p(1), mmu-miR-194-5p(1), mmu-miR-207(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTGCTACAAAAGGACACAAGCAGAA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNCBP3_613_ORF_1
0.9749
0.34819242
0.799845825
474
ORF sequence:
ATGATGAAGAAAGCAATTCCCAAGGTGAGACTGGAGACAATCTACATTTGTGGAGTGGATGAAATGAGCACCCAGGATATCTTCTCCTATTTTAAGGAATATCCTCCAGCTCACATTGAGTGGTTGGATGACACCTCCTGCAATGTGGTTTGGCTGGACGAGATGACGGCCACACGAGCTCTCATCAATATGAGTTCTCTGCCAGCCCAGGATAAGATGAGAAGCAGAGATGCCAGTGAAGACAAGTCGTCGGAGAAGAACAAGAAAGACAAGCAGGAAGACAGTTCAGATGACGACGAGACTGAAGAAGGAGAAGTGGAAGATGAGAATTCAAGTGATGTAGAGTTGGACACGTTGTCTCAGGTAGAAGAAGAGTCTCTGTTACGAAATGATCTTCGTCCAGCTAACAAACTTGCTAAAGGAAATAGACTATTCATGAGATTTGCTACAAAAGGACACAAGCAGAAGATATGA
Peptide sequence:
MMKKAIPKVRLETIYICGVDEMSTQDIFSYFKEYPPAHIEWLDDTSCNVVWLDEMTATRALINMSSLPAQDKMRSRDASEDKSSEKNKKDKQEDSSDDDETEEGEVEDENSSDVELDTLSQVEEESLLRNDLRPANKLAKGNRLFMRFATKGHKQKI
IRESfinder result
IRESfinder score
0.288508796
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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