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mmu_circGm28539_902
Basic information of circular RNA
PanCircBase ID:
mmu_circGm28539_902
mm39_Chr. Position ID:
chr16|18716447|18741709|+
Gene name:
Gm28539
Transcript:
ENSMUST00000190050.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
5,6,7,8,9,10,11,12
Exon/intron offsets:
0,1665,12950,14348,18742,21278,24619,25156
Genomic length:
25262
Exon/intron sizes in nt:
9,19,59,61,61,16,81,14,00,000
Flanking exon/introns:
chr16:18715314-18716447|chr16:18741709-18744397
Splice length:
902
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CATGTGTGAACTGTGTGCGGTGGTCAAACAGTGGGATGTATTTAGCTTCTGGGGGAGATGACAAACTGATTATGGTGTGGAAGCGGGCTACGTACATTGGGCCCAGCACTGTGTTTGGTTCCAGTGGTAAGCTTGCCAATGTGGAGCAATGGCGGTGTGTCTCCATCCTCCGGAGTCACTCAGGCGATGTGATGGATGTAGCATGGTCTCCCCACGACGCCTGGCTGGCCTCATGCAGCGTGGATAACACTGTTGTCATTTGGAATGCCGTGAAGTTCCCAGAAATTCTTGCAACTCTGAGAGGTCATTCTGGCTTAGTAAAAGGTTTGACTTGGGATCCCGTTGGTAAATATATTGCCTCTCAAGCTGATGATCGAAGTTTGAAGGTATGGAGGACGCTGGACTGGCAGCTAGAGACTAGCATCACCAAGCCTTTTGATGAGTGTGGAGGAACGACGCATGTTCTCCGGCTTAGTTGGTCACCTGATGGCCATTACCTGGTATCTGCCCATGCCATGAATAATTCTGGCCCCACTGCTCAGATCATCGAAAGAGAGGGCTGGAAGACCAACATGGACTTTGTGGGTCACCGGAAAGCTGTGACTGTTGTGAAATTCAACCCAAAAATCTTCAAGAAGAAGCAGAAGAATGGGAGCTCTACAAAGCCCAGCTGCCCATACTGCTGCTGTGCTGTTGGCAGCAAGGACCGCTCACTCTCTGTCTGGCTCACATGTTTGAAACGGCCTCTGGTTGTCATCCATGAACTGTTTGACAAGTCCATCATGGATATTTCCTGGACTCTGAATGGGTTGGGTATCCTGGTGTGCTCCATGGACGGCTCTGTGGCGTTCCTTGATTTCTCTCAGGATGAACTCGGAGACCCCCTGAGTGAGGAGGAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGGTTGGGTATCCTGGTGTG
60.03
TGTCATCTCCCCCAGAAGCT
60.25
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTTGGGTATCCTGGTGTGCT
59.67
TGTCATCTCCCCCAGAAGCT
60.25
157
PCR template sequence:
GAATGGGTTGGGTATCCTGGTGTGCTCCATGGACGGCTCTGTGGCGTTCCTTGATTTCTCTCAGGATGAACTCGGAGACCCCCTGAGTGAGGAGGAAAAGCATGTGTGAACTGTGTGCGGTGGTCAAACAGTGGGATGTATTTAGCTTCTGGGGGAGATGACAAACTGATTATGGTGTGGAAGCGGGCTACGTACATTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-223-3p(1), mmu-miR-222-3p(1), mmu-miR-132-3p(1), mmu-miR-23a-3p(1), mmu-miR-433-3p(1), mmu-miR-22-3p(1), mmu-miR-182-5p(1), mmu-miR-673-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
TGAGGAGGAAAAGCATGTGTGAACTG
siRNA sets
TCACACATGCTTTTCCTCC, TTCACACATGCTTTTCCTC, ACACATGCTTTTCCTCCTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGM28539_902_ORF_1
0.9087
0.205947113
0.972564685
876
ORF sequence:
ATGTATTTAGCTTCTGGGGGAGATGACAAACTGATTATGGTGTGGAAGCGGGCTACGTACATTGGGCCCAGCACTGTGTTTGGTTCCAGTGGTAAGCTTGCCAATGTGGAGCAATGGCGGTGTGTCTCCATCCTCCGGAGTCACTCAGGCGATGTGATGGATGTAGCATGGTCTCCCCACGACGCCTGGCTGGCCTCATGCAGCGTGGATAACACTGTTGTCATTTGGAATGCCGTGAAGTTCCCAGAAATTCTTGCAACTCTGAGAGGTCATTCTGGCTTAGTAAAAGGTTTGACTTGGGATCCCGTTGGTAAATATATTGCCTCTCAAGCTGATGATCGAAGTTTGAAGGTATGGAGGACGCTGGACTGGCAGCTAGAGACTAGCATCACCAAGCCTTTTGATGAGTGTGGAGGAACGACGCATGTTCTCCGGCTTAGTTGGTCACCTGATGGCCATTACCTGGTATCTGCCCATGCCATGAATAATTCTGGCCCCACTGCTCAGATCATCGAAAGAGAGGGCTGGAAGACCAACATGGACTTTGTGGGTCACCGGAAAGCTGTGACTGTTGTGAAATTCAACCCAAAAATCTTCAAGAAGAAGCAGAAGAATGGGAGCTCTACAAAGCCCAGCTGCCCATACTGCTGCTGTGCTGTTGGCAGCAAGGACCGCTCACTCTCTGTCTGGCTCACATGTTTGAAACGGCCTCTGGTTGTCATCCATGAACTGTTTGACAAGTCCATCATGGATATTTCCTGGACTCTGAATGGGTTGGGTATCCTGGTGTGCTCCATGGACGGCTCTGTGGCGTTCCTTGATTTCTCTCAGGATGAACTCGGAGACCCCCTGAGTGAGGAGGAAAAGCATGTGTGA
Peptide sequence:
MYLASGGDDKLIMVWKRATYIGPSTVFGSSGKLANVEQWRCVSILRSHSGDVMDVAWSPHDAWLASCSVDNTVVIWNAVKFPEILATLRGHSGLVKGLTWDPVGKYIASQADDRSLKVWRTLDWQLETSITKPFDECGGTTHVLRLSWSPDGHYLVSAHAMNNSGPTAQIIEREGWKTNMDFVGHRKAVTVVKFNPKIFKKKQKNGSSTKPSCPYCCCAVGSKDRSLSVWLTCLKRPLVVIHELFDKSIMDISWTLNGLGILVCSMDGSVAFLDFSQDELGDPLSEEEKHV
IRESfinder result
IRESfinder score
0.415103663
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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