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mmu_circPsme4_1654
Basic information of circular RNA
PanCircBase ID:
mmu_circPsme4_1654
mm39_Chr. Position ID:
chr11|30787281|30803385|+
Gene name:
Psme4
Transcript:
ENSMUST00000041231.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
13
Exon/intron indexes:
28,29,30,31,32,33,34,35,36,37,38,39,40
Exon/intron offsets:
0,1603,4287,4709,6225,7898,8546,10116,10765,13321,13861,15391,15895
Genomic length:
16104
Exon/intron sizes in nt:
21,01,37,54,13,08,21,50,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr11:30785467-30787281|chr11:30803385-30806029
Splice length:
1654
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GGCGCCTTATATTGTCTACTTGGAAATCACAGTGGTGTGTGCCTGGCAAACCTTCATGATTGGGACTGTATTGTGCAGACCTGGCCAGCACTTGTTTCTTCAGGGCTTAGCCAAGCAATGTCACTGGAAAAGCCATCAATAGTGAGACTATTTGATGACCTTGCTGAAAAGATTCATAGACAATATGAAACAATTGGCTTGGATTTTACAATTCCAAAGTCATGTGCTGCAATAGCAGAATTACTTCAACAATCAAAGAATCCTTCCATTAGCCAGACACTACTTAGCCCAGAAAAGATTAAAGAAGGACAGAAGCGTCAACAAGATAAGAATGCTGATGCCCTAAGGAACTATGAATGTTTGGTAAATACTTTACTAGATGGTGTGGAGCAAAGAAATCTGCCTTGGAAATTTGAGCATATAGGAATCGGGCTTCTGTCTCTACTCCTAAGGGATGACAGAGTGTTGCCTCTTCGTGCCATACGTTTTTTTGTTGAAAATCTCAACCATGATGCAATTGTTGTTCGAAAGATGGCTATCTCAGCTGTTGCTGGTATTCTCAAGCAGCTAAAGAGAACTCACAAAAAGCTGACTATCAACCCTTATGAAATCAGTGGATGTCCTAAACCTACCAAAATTCTTGCTGGTGATAGACCTGATAACCATTGGTTGCATTATGATAGTAAAAATATACCAAGAACAAAAAAAGAATGGGAGTCAAGTTGCTTTGTTGAAAAAACTCACTGGGGATACTACAACTGGCCAAAGAATATGGTTGTTTATGCTGGTGTGGAAGAACAGCCTAAACTTGGCAGAAGCAGGGAGGATATGATAGAGGCAGAACAGATTATATATGATCGTTTTTCTGATCCTAAGTTTGTTGAGCAGTTAATCACATTTCTATCTTTAGAAGACAGAAAAGGAAGAGATAAGTTTAGTCCCCGGCGTTTCTGCCTCTTTAAGGGTATATTTAGAAATTTTGATGATGCTTTTCTGCCTGTTCTGAAGCCCCATTTAGAACGTTTGGTTGCAGATTCTCATGAAAGTACCCAGAGATGTGTTGCAGAAATTATAGCTGGTTTAATCAGAGGTTCTAAGCATTGGACGTTTGAGAAGGTGGAGAAGCTTTGGGAGCTCCTGTGCCCGCTGCTGAGAACGGCACTGTCCAACATGACAGTGGAGACATACAATGACTGGGGGACCTGTATAGCCACTTCCTGTGAAAGCAGAGATCCCCGGAAGCTTCACTGGCTTTTTGAGCTGCTCTTGGAGTCACCATTGAGTGGTGAAGGGGGGTCCTTTGTAGATGCATGCCGACTCTATGTGCTACAAGGTGGCCTTGCCCAGCAAGAGTGGAGAGTCCCTGAACTATTGCACAGACTTCTGAAGTACTTGGAACCAAAACTCACCCAGGTTTACAAAAATGTCAGAGAAAGAATAGGAAGTGTGCTGACCTACATATTTATGATAGATGTTTCTTTGCCAAATACTGCTCCAACAACATCTCCTTGTATCCCTGAGTTTACTGCTCGCGTCCTAGAAAAACTGAAACCACTCACAGATGTGGATGAAGAAATTCAGAACCATGTTATGGAAGAAAATGGCATTGGTGAAGAAGATGAACGAACTCAGGGCATTAAACTCTTAAAAACTA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAAGATGAACGAACTCAGGGC
59
AAGAAACAAGTGCTGGCCAG
58.96
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGAAGATGAACGAACTCAGGGC
60.35
AGAAACAAGTGCTGGCCAGG
60.83
140
PCR template sequence:
CTCACAGATGTGGATGAAGAAATTCAGAACCATGTTATGGAAGAAAATGGCATTGGTGAAGAAGATGAACGAACTCAGGGCATTAAACTCTTAAAAACTAGGCGCCTTATATTGTCTACTTGGAAATCACAGTGGTGTGTGCCTGGCAAACCTTCATGATTGGGACTGTATTGTGCAGACCTGGCCAGCACTTGTTTCTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
24
Interacting miRNAs (#binding sites)
mmu-miR-181b-5p(2), mmu-miR-3065-5p(2), mmu-miR-140-5p(1), mmu-miR-296-5p(1), mmu-miR-150-5p(1), mmu-miR-135a-5p(1), mmu-miR-335-5p(1), mmu-miR-709(1), mmu-miR-326-3p(1), mmu-miR-381-3p(1), mmu-miR-503-5p(1), mmu-miR-26b-5p(1), mmu-miR-125a-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-127-5p(1), mmu-miR-182-5p(1), mmu-miR-297a-5p(1), mmu-miR-666-5p(1), mmu-miR-383-5p(1), mmu-miR-3470b(1), mmu-miR-296-3p(1), mmu-miR-338-3p(1), mmu-miR-181d-5p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTCTTAAAAACTAGGCGCCTTATATT
siRNA sets
AATATAAGGCGCCTAGTTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPSME4_1654_ORF_1
0.9064
-0.012910109
0.999602392
1596
ORF sequence:
ATGTCACTGGAAAAGCCATCAATAGTGAGACTATTTGATGACCTTGCTGAAAAGATTCATAGACAATATGAAACAATTGGCTTGGATTTTACAATTCCAAAGTCATGTGCTGCAATAGCAGAATTACTTCAACAATCAAAGAATCCTTCCATTAGCCAGACACTACTTAGCCCAGAAAAGATTAAAGAAGGACAGAAGCGTCAACAAGATAAGAATGCTGATGCCCTAAGGAACTATGAATGTTTGGTAAATACTTTACTAGATGGTGTGGAGCAAAGAAATCTGCCTTGGAAATTTGAGCATATAGGAATCGGGCTTCTGTCTCTACTCCTAAGGGATGACAGAGTGTTGCCTCTTCGTGCCATACGTTTTTTTGTTGAAAATCTCAACCATGATGCAATTGTTGTTCGAAAGATGGCTATCTCAGCTGTTGCTGGTATTCTCAAGCAGCTAAAGAGAACTCACAAAAAGCTGACTATCAACCCTTATGAAATCAGTGGATGTCCTAAACCTACCAAAATTCTTGCTGGTGATAGACCTGATAACCATTGGTTGCATTATGATAGTAAAAATATACCAAGAACAAAAAAAGAATGGGAGTCAAGTTGCTTTGTTGAAAAAACTCACTGGGGATACTACAACTGGCCAAAGAATATGGTTGTTTATGCTGGTGTGGAAGAACAGCCTAAACTTGGCAGAAGCAGGGAGGATATGATAGAGGCAGAACAGATTATATATGATCGTTTTTCTGATCCTAAGTTTGTTGAGCAGTTAATCACATTTCTATCTTTAGAAGACAGAAAAGGAAGAGATAAGTTTAGTCCCCGGCGTTTCTGCCTCTTTAAGGGTATATTTAGAAATTTTGATGATGCTTTTCTGCCTGTTCTGAAGCCCCATTTAGAACGTTTGGTTGCAGATTCTCATGAAAGTACCCAGAGATGTGTTGCAGAAATTATAGCTGGTTTAATCAGAGGTTCTAAGCATTGGACGTTTGAGAAGGTGGAGAAGCTTTGGGAGCTCCTGTGCCCGCTGCTGAGAACGGCACTGTCCAACATGACAGTGGAGACATACAATGACTGGGGGACCTGTATAGCCACTTCCTGTGAAAGCAGAGATCCCCGGAAGCTTCACTGGCTTTTTGAGCTGCTCTTGGAGTCACCATTGAGTGGTGAAGGGGGGTCCTTTGTAGATGCATGCCGACTCTATGTGCTACAAGGTGGCCTTGCCCAGCAAGAGTGGAGAGTCCCTGAACTATTGCACAGACTTCTGAAGTACTTGGAACCAAAACTCACCCAGGTTTACAAAAATGTCAGAGAAAGAATAGGAAGTGTGCTGACCTACATATTTATGATAGATGTTTCTTTGCCAAATACTGCTCCAACAACATCTCCTTGTATCCCTGAGTTTACTGCTCGCGTCCTAGAAAAACTGAAACCACTCACAGATGTGGATGAAGAAATTCAGAACCATGTTATGGAAGAAAATGGCATTGGTGAAGAAGATGAACGAACTCAGGGCATTAAACTCTTAAAAACTAGGCGCCTTATATTGTCTACTTGGAAATCACAGTGGTGTGTGCCTGGCAAACCTTCATGA
Peptide sequence:
MSLEKPSIVRLFDDLAEKIHRQYETIGLDFTIPKSCAAIAELLQQSKNPSISQTLLSPEKIKEGQKRQQDKNADALRNYECLVNTLLDGVEQRNLPWKFEHIGIGLLSLLLRDDRVLPLRAIRFFVENLNHDAIVVRKMAISAVAGILKQLKRTHKKLTINPYEISGCPKPTKILAGDRPDNHWLHYDSKNIPRTKKEWESSCFVEKTHWGYYNWPKNMVVYAGVEEQPKLGRSREDMIEAEQIIYDRFSDPKFVEQLITFLSLEDRKGRDKFSPRRFCLFKGIFRNFDDAFLPVLKPHLERLVADSHESTQRCVAEIIAGLIRGSKHWTFEKVEKLWELLCPLLRTALSNMTVETYNDWGTCIATSCESRDPRKLHWLFELLLESPLSGEGGSFVDACRLYVLQGGLAQQEWRVPELLHRLLKYLEPKLTQVYKNVRERIGSVLTYIFMIDVSLPNTAPTTSPCIPEFTARVLEKLKPLTDVDEEIQNHVMEENGIGEEDERTQGIKLLKTRRLILSTWKSQWCVPGKPS
IRESfinder result
IRESfinder score
0.626064304
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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