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mmu_circSmg7_919
Basic information of circular RNA
PanCircBase ID:
mmu_circSmg7_919
mm39_Chr. Position ID:
chr1|152730060|152737603|-
Gene name:
Smg7
Transcript:
ENSMUST00000073441.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
11,10,9,8,7,6,5
Exon/intron offsets:
0,1539,2139,4569,5042,6140,7371
Genomic length:
7543
Exon/intron sizes in nt:
71,15,41,63,13,61,51,70,000
Flanking exon/introns:
chr1:152728409-152730060|chr1:152737603-152742331
Splice length:
919
Other database IDs:
circAtlas: mmu-Smg7_0029
Human Ortholog IDs:
Mature spliced Sequence:
TTATTACAGGAACTGTGTACGGTGTTTAATGTAGATTTGCCATGCCGTGTGAAGTCTTCCCAGTTGGGAATTATTAGCAATAAACAGACGCACAGCAGCACCATAGTGAAGCCACAGTCTAGCTCCTGCTCCTACATTTGCCAACACTGCCTCGTCCACCTTGGAGACATTGCTCGATACAGAAATCAGACTAGCCAGGCAGAGTCCTACTATAGGCATGCAGCTCAGCTTGTCCCCTCCAATGGTCAGCCTTACAATCAGTTGGCTATCTTAGCTTCTTCCAAAGGAGACCACCTGACCACAATTTTCTACTACTGCAGAAGCATTGCTGTGAAATTCCCTTTCCCAGCTGCCTCCACTAATCTACAAAAAGCACTTTCTAAAGCACTGGAAAGCCGGGATGAGTTGAAAACCAAGTGGGGTGTTTCTGACTTCATCAAGGCCTTTATTAAATTCCACGGTCATGTATACCTGAGTAAGAGTTTGGAAAAGCTGAGCCCTCTTCGAGAGAAGTTGGAAGAACAGTTTAAGAGACTGCTGTTCCAAAAGGCTTTCAACTCTCAACAGTTAGTTCATGTCACTGTCATTAACCTGTTTCAACTTCATCATCTTCGTGACTTTAGCAATGAAACAGAGCAACACAGTTACAGCCAAGATGAACAGCTGTGTTGGACACAGTTGCTGGCCCTCTTTATGTCTTTTCTCGGCATCCTGTGCAAATGTCCTCTCCAGAATGATTCTCAGGAGTCCAACAATGCCTACCCCCTTCCTGCAGTCAAGGTCTCCATGGACTGGCTAAGACTCCGACCTAGAGTCTTTCAAGAAGCAGTGGTGGATGAAAGACAGTACATTTGGCCCTGGCTAATTTCTCTTCTAAATAGTTTCCATCCCCGTGAAGATGATCTCTCAAATACTAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGTACATTTGGCCCTGGCT
60.32
ACTGGGAAGACTTCACACGG
59.61
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGTACATTTGGCCCTGGCT
60.32
TGCTGCTGTGCGTCTGTTTA
60.53
176
PCR template sequence:
CAAGAAGCAGTGGTGGATGAAAGACAGTACATTTGGCCCTGGCTAATTTCTCTTCTAAATAGTTTCCATCCCCGTGAAGATGATCTCTCAAATACTAATGTTATTACAGGAACTGTGTACGGTGTTTAATGTAGATTTGCCATGCCGTGTGAAGTCTTCCCAGTTGGGAATTATTAGCAATAAACAGACGCACAGCAGCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-34b-5p(2), mmu-miR-137-3p(1), mmu-miR-20b-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-7b-5p(1), mmu-miR-34c-5p(1), mmu-miR-199b-3p(1), mmu-miR-182-5p(1), mmu-miR-199a-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-673-5p(1), mmu-miR-539-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCAAATACTAATGTTATTACAGGAAC
siRNA sets
TTCCTGTAATAACATTAGT, GTTCCTGTAATAACATTAG, TAATAACATTAGTATTTGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMG7_919_ORF_1
0.7321
0.087465367
0.961175193
939
ORF sequence:
ATGATCTCTCAAATACTAATGTTATTACAGGAACTGTGTACGGTGTTTAATGTAGATTTGCCATGCCGTGTGAAGTCTTCCCAGTTGGGAATTATTAGCAATAAACAGACGCACAGCAGCACCATAGTGAAGCCACAGTCTAGCTCCTGCTCCTACATTTGCCAACACTGCCTCGTCCACCTTGGAGACATTGCTCGATACAGAAATCAGACTAGCCAGGCAGAGTCCTACTATAGGCATGCAGCTCAGCTTGTCCCCTCCAATGGTCAGCCTTACAATCAGTTGGCTATCTTAGCTTCTTCCAAAGGAGACCACCTGACCACAATTTTCTACTACTGCAGAAGCATTGCTGTGAAATTCCCTTTCCCAGCTGCCTCCACTAATCTACAAAAAGCACTTTCTAAAGCACTGGAAAGCCGGGATGAGTTGAAAACCAAGTGGGGTGTTTCTGACTTCATCAAGGCCTTTATTAAATTCCACGGTCATGTATACCTGAGTAAGAGTTTGGAAAAGCTGAGCCCTCTTCGAGAGAAGTTGGAAGAACAGTTTAAGAGACTGCTGTTCCAAAAGGCTTTCAACTCTCAACAGTTAGTTCATGTCACTGTCATTAACCTGTTTCAACTTCATCATCTTCGTGACTTTAGCAATGAAACAGAGCAACACAGTTACAGCCAAGATGAACAGCTGTGTTGGACACAGTTGCTGGCCCTCTTTATGTCTTTTCTCGGCATCCTGTGCAAATGTCCTCTCCAGAATGATTCTCAGGAGTCCAACAATGCCTACCCCCTTCCTGCAGTCAAGGTCTCCATGGACTGGCTAAGACTCCGACCTAGAGTCTTTCAAGAAGCAGTGGTGGATGAAAGACAGTACATTTGGCCCTGGCTAATTTCTCTTCTAAATAGTTTCCATCCCCGTGAAGATGATCTCTCAAATACTAAT
Peptide sequence:
MISQILMLLQELCTVFNVDLPCRVKSSQLGIISNKQTHSSTIVKPQSSSCSYICQHCLVHLGDIARYRNQTSQAESYYRHAAQLVPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVKFPFPAASTNLQKALSKALESRDELKTKWGVSDFIKAFIKFHGHVYLSKSLEKLSPLREKLEEQFKRLLFQKAFNSQQLVHVTVINLFQLHHLRDFSNETEQHSYSQDEQLCWTQLLALFMSFLGILCKCPLQNDSQESNNAYPLPAVKVSMDWLRLRPRVFQEAVVDERQYIWPWLISLLNSFHPREDDLSNTN
IRESfinder result
IRESfinder score
0.683969847
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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