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mmu_circSpidr_904_1
Basic information of circular RNA
PanCircBase ID:
mmu_circSpidr_904_1
mm39_Chr. Position ID:
chr16|15713006|15733251|-
Gene name:
Spidr
Transcript:
ENSMUST00000040248.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
19,18,17,16,15,14,13,12
Exon/intron offsets:
0,383,2081,7766,8914,17376,17526,20157
Genomic length:
20245
Exon/intron sizes in nt:
54,115,94,147,205,60,141,88
Flanking exon/introns:
chr16:15707649-15713006|chr16:15733251-15754416
Splice length:
904
Other database IDs:
circAtlas: mmu-Spidr_0016
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GACACCAGGGCTCTTCAGTTTAATTGACAGTTTGTGGCCCCCAGTGATATCTCTGACTGAGCCTTCCTGTGGCCAGCCCAGTGGAGAGACAAAGACTTATCTGCCTCCTCCTATCTTCTGTTATATCTTCTCTGCACATCCAACACTGGGACAAATTGATGCAATTGAAGACCACATTTCCAAGCTTTACCAGCCTCCAGTTGTCCGCTGCTTAAAAGAAATCCTCCAGACTAATGAGTGCAGTACACGTTGCAGCTTCTATGCCAGAGTGATTTATCAAAAACCACAGCTAAAGAATCTTTTGGCGCAAAAGGAAATCTGGCTGCTGGTGACTGACATCACTCTGCAAACACAGGATGAAAGGGACCACTCTCTTCCCAAAACCCTGCCTGTCTATATAGCCCCCTCGTGTGTGCTGGGCCCAGAGGTTGTAGAAGAACTTGCCTTGCTGGTGTCTTATAACTTACTCTTCAGGGACGCTTTTAAGGACAACGGTCAGATTGTTTGTATTGAACGGACAGTCATCCTACCCCAGAAACCTCTCTTGTGTGTACCTTCTGCTTCCTGTGACTTGCCCAGCCCAGTGACACTGGATGAACTGAGTGCCCTCACACCTGTCAACTCCATTTGCAGTGTGCAAGGTACTGTGGTTGATGTAGATGAGAGCACTGCTTTCTCGTGGCCTGTGTGTGACCGGTGTGGCAATGGGAGACTGGAACAGAAGCCAGAAGATGGAGGCACCTTCTCCTGTGGGGACTGTTCCCAACTGGTCCTGTCACCTCTTCAAGAGAGGCACCTGCATGTCTTTCTGGACTGTCCCACGAGACCTGAGAGTACTGTGAAGGTCAAGCTATTGGAGAGCAGTATTTCTTTACTTCTGATGTCTGCTGCCTCTGAGGATGGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTGGACTGTCCCACGAGA
60.18
CCACAGGAAGGCTCAGTCAG
60.04
170
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTGGACTGTCCCACGAGA
60.18
TATCACTGGGGGCCACAAAC
59.96
147
PCR template sequence:
CTTTCTGGACTGTCCCACGAGACCTGAGAGTACTGTGAAGGTCAAGCTATTGGAGAGCAGTATTTCTTTACTTCTGATGTCTGCTGCCTCTGAGGATGGGGACACCAGGGCTCTTCAGTTTAATTGACAGTTTGTGGCCCCCAGTGATATCTCTGACTGAGCCTTCCTGTGGCCAGCCCAGTGGAGAGACAAAGACTTAT
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-101a-3p(2), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-200c-3p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-18a-5p(1), mmu-miR-132-3p(1), mmu-miR-709(1), mmu-miR-326-3p(1), mmu-miR-24-3p(1), mmu-miR-503-5p(1), mmu-miR-676-3p(1), mmu-miR-212-3p(1), mmu-miR-377-3p(1), mmu-miR-410-3p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTCTGAGGATGGGGACACCAGGGCTC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSPIDR_904_1_ORF_1
0.8406
0.113928747
0.96454134
909
ORF sequence:
ATGGGGACACCAGGGCTCTTCAGTTTAATTGACAGTTTGTGGCCCCCAGTGATATCTCTGACTGAGCCTTCCTGTGGCCAGCCCAGTGGAGAGACAAAGACTTATCTGCCTCCTCCTATCTTCTGTTATATCTTCTCTGCACATCCAACACTGGGACAAATTGATGCAATTGAAGACCACATTTCCAAGCTTTACCAGCCTCCAGTTGTCCGCTGCTTAAAAGAAATCCTCCAGACTAATGAGTGCAGTACACGTTGCAGCTTCTATGCCAGAGTGATTTATCAAAAACCACAGCTAAAGAATCTTTTGGCGCAAAAGGAAATCTGGCTGCTGGTGACTGACATCACTCTGCAAACACAGGATGAAAGGGACCACTCTCTTCCCAAAACCCTGCCTGTCTATATAGCCCCCTCGTGTGTGCTGGGCCCAGAGGTTGTAGAAGAACTTGCCTTGCTGGTGTCTTATAACTTACTCTTCAGGGACGCTTTTAAGGACAACGGTCAGATTGTTTGTATTGAACGGACAGTCATCCTACCCCAGAAACCTCTCTTGTGTGTACCTTCTGCTTCCTGTGACTTGCCCAGCCCAGTGACACTGGATGAACTGAGTGCCCTCACACCTGTCAACTCCATTTGCAGTGTGCAAGGTACTGTGGTTGATGTAGATGAGAGCACTGCTTTCTCGTGGCCTGTGTGTGACCGGTGTGGCAATGGGAGACTGGAACAGAAGCCAGAAGATGGAGGCACCTTCTCCTGTGGGGACTGTTCCCAACTGGTCCTGTCACCTCTTCAAGAGAGGCACCTGCATGTCTTTCTGGACTGTCCCACGAGACCTGAGAGTACTGTGAAGGTCAAGCTATTGGAGAGCAGTATTTCTTTACTTCTGATGTCTGCTGCCTCTGAGGATGGG
Peptide sequence:
MGTPGLFSLIDSLWPPVISLTEPSCGQPSGETKTYLPPPIFCYIFSAHPTLGQIDAIEDHISKLYQPPVVRCLKEILQTNECSTRCSFYARVIYQKPQLKNLLAQKEIWLLVTDITLQTQDERDHSLPKTLPVYIAPSCVLGPEVVEELALLVSYNLLFRDAFKDNGQIVCIERTVILPQKPLLCVPSASCDLPSPVTLDELSALTPVNSICSVQGTVVDVDESTAFSWPVCDRCGNGRLEQKPEDGGTFSCGDCSQLVLSPLQERHLHVFLDCPTRPESTVKVKLLESSISLLLMSAASEDG
IRESfinder result
IRESfinder score
0.761368708
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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