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mmu_circGm28539_922
Basic information of circular RNA
PanCircBase ID:
mmu_circGm28539_922
mm39_Chr. Position ID:
chr16|18730795|18746273|+
Gene name:
Gm28539
Transcript:
ENSMUST00000190050.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
8,9,10,11,12,13,14
Exon/intron offsets:
0,4394,6930,10271,10808,13602,15392
Genomic length:
15478
Exon/intron sizes in nt:
161,168,114,71,106,216,86
Flanking exon/introns:
chr16:18729493-18730795|chr16:18746273-18751617
Splice length:
922
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
AAATTCTTGCAACTCTGAGAGGTCATTCTGGCTTAGTAAAAGGTTTGACTTGGGATCCCGTTGGTAAATATATTGCCTCTCAAGCTGATGATCGAAGTTTGAAGGTATGGAGGACGCTGGACTGGCAGCTAGAGACTAGCATCACCAAGCCTTTTGATGAGTGTGGAGGAACGACGCATGTTCTCCGGCTTAGTTGGTCACCTGATGGCCATTACCTGGTATCTGCCCATGCCATGAATAATTCTGGCCCCACTGCTCAGATCATCGAAAGAGAGGGCTGGAAGACCAACATGGACTTTGTGGGTCACCGGAAAGCTGTGACTGTTGTGAAATTCAACCCAAAAATCTTCAAGAAGAAGCAGAAGAATGGGAGCTCTACAAAGCCCAGCTGCCCATACTGCTGCTGTGCTGTTGGCAGCAAGGACCGCTCACTCTCTGTCTGGCTCACATGTTTGAAACGGCCTCTGGTTGTCATCCATGAACTGTTTGACAAGTCCATCATGGATATTTCCTGGACTCTGAATGGGTTGGGTATCCTGGTGTGCTCCATGGACGGCTCTGTGGCGTTCCTTGATTTCTCTCAGGATGAACTCGGAGACCCCCTGAGTGAGGAGGAAAAGAGCCGAATTCACCAGTCTACCTATGGCAAGAGCCTGGCAATAATGACTGAGGCCCAGCTTTCCACAGCTGTTATTGAGAACCCTGAGATGCTCAAGTACCAGCGGAGACAGCAACAGCAGCAGCTGGATCAGAAGAATGCCACTACTAGGGAGACAAGCTCAGCATCCTCAGTCACGGGTGTGGTCAATGGGGAAAGTCTAGAAGATATCAGAAAGAATCTTTTGAAGAAACAAGTGGAAACTCGGACAGCAGATGGTCGGAGGAGAATCACGCCTCTTTGCATAGCACAGCTGGACACTGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGGAAACTCGGACAGCAGA
59.97
TCGATCATCAGCTTGAGAGGC
59.93
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTGGAAACTCGGACAGCAG
59.97
TCGATCATCAGCTTGAGAGGC
59.93
164
PCR template sequence:
AAGATATCAGAAAGAATCTTTTGAAGAAACAAGTGGAAACTCGGACAGCAGATGGTCGGAGGAGAATCACGCCTCTTTGCATAGCACAGCTGGACACTGGAAATTCTTGCAACTCTGAGAGGTCATTCTGGCTTAGTAAAAGGTTTGACTTGGGATCCCGTTGGTAAATATATTGCCTCTCAAGCTGATGATCGAAGTTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-199a-5p(1), mmu-miR-132-3p(1), mmu-miR-320-3p(1), mmu-miR-433-3p(1), mmu-miR-22-3p(1), mmu-miR-673-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
AGCTGGACACTGGAAATTCTTGCAAC
siRNA sets
AAGAATTTCCAGTGTCCAG, AGAATTTCCAGTGTCCAGC, GAATTTCCAGTGTCCAGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGM28539_922_ORF_1
0.9439
0.256818496
0.951416226
756
ORF sequence:
ATGAATAATTCTGGCCCCACTGCTCAGATCATCGAAAGAGAGGGCTGGAAGACCAACATGGACTTTGTGGGTCACCGGAAAGCTGTGACTGTTGTGAAATTCAACCCAAAAATCTTCAAGAAGAAGCAGAAGAATGGGAGCTCTACAAAGCCCAGCTGCCCATACTGCTGCTGTGCTGTTGGCAGCAAGGACCGCTCACTCTCTGTCTGGCTCACATGTTTGAAACGGCCTCTGGTTGTCATCCATGAACTGTTTGACAAGTCCATCATGGATATTTCCTGGACTCTGAATGGGTTGGGTATCCTGGTGTGCTCCATGGACGGCTCTGTGGCGTTCCTTGATTTCTCTCAGGATGAACTCGGAGACCCCCTGAGTGAGGAGGAAAAGAGCCGAATTCACCAGTCTACCTATGGCAAGAGCCTGGCAATAATGACTGAGGCCCAGCTTTCCACAGCTGTTATTGAGAACCCTGAGATGCTCAAGTACCAGCGGAGACAGCAACAGCAGCAGCTGGATCAGAAGAATGCCACTACTAGGGAGACAAGCTCAGCATCCTCAGTCACGGGTGTGGTCAATGGGGAAAGTCTAGAAGATATCAGAAAGAATCTTTTGAAGAAACAAGTGGAAACTCGGACAGCAGATGGTCGGAGGAGAATCACGCCTCTTTGCATAGCACAGCTGGACACTGGAAATTCTTGCAACTCTGAGAGGTCATTCTGGCTTAGTAAAAGGTTTGACTTGGGATCCCGTTGGTAA
Peptide sequence:
MNNSGPTAQIIEREGWKTNMDFVGHRKAVTVVKFNPKIFKKKQKNGSSTKPSCPYCCCAVGSKDRSLSVWLTCLKRPLVVIHELFDKSIMDISWTLNGLGILVCSMDGSVAFLDFSQDELGDPLSEEEKSRIHQSTYGKSLAIMTEAQLSTAVIENPEMLKYQRRQQQQQLDQKNATTRETSSASSVTGVVNGESLEDIRKNLLKKQVETRTADGRRRITPLCIAQLDTGNSCNSERSFWLSKRFDLGSRW
IRESfinder result
IRESfinder score
0.475220536
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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