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mmu_circPsme4_700
Basic information of circular RNA
PanCircBase ID:
mmu_circPsme4_700
mm39_Chr. Position ID:
chr11|30795179|30801234|+
Gene name:
Psme4
Transcript:
ENSMUST00000041231.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
33,34,35,36,37,38
Exon/intron offsets:
0,648,2218,2867,5423,5963
Genomic length:
6055
Exon/intron sizes in nt:
154,70,126,153,105,92
Flanking exon/introns:
chr11:30793588-30795179|chr11:30801234-30802672
Splice length:
700
Other database IDs:
CIRCpedia: MMU_CIRCpedia_215376, circAtlas: mmu-Psme4_0041
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_163654
Human Ortholog IDs:
Mature spliced Sequence:
GTGGATGTCCTAAACCTACCAAAATTCTTGCTGGTGATAGACCTGATAACCATTGGTTGCATTATGATAGTAAAAATATACCAAGAACAAAAAAAGAATGGGAGTCAAGTTGCTTTGTTGAAAAAACTCACTGGGGATACTACAACTGGCCAAAGAATATGGTTGTTTATGCTGGTGTGGAAGAACAGCCTAAACTTGGCAGAAGCAGGGAGGATATGATAGAGGCAGAACAGATTATATATGATCGTTTTTCTGATCCTAAGTTTGTTGAGCAGTTAATCACATTTCTATCTTTAGAAGACAGAAAAGGAAGAGATAAGTTTAGTCCCCGGCGTTTCTGCCTCTTTAAGGGTATATTTAGAAATTTTGATGATGCTTTTCTGCCTGTTCTGAAGCCCCATTTAGAACGTTTGGTTGCAGATTCTCATGAAAGTACCCAGAGATGTGTTGCAGAAATTATAGCTGGTTTAATCAGAGGTTCTAAGCATTGGACGTTTGAGAAGGTGGAGAAGCTTTGGGAGCTCCTGTGCCCGCTGCTGAGAACGGCACTGTCCAACATGACAGTGGAGACATACAATGACTGGGGGACCTGTATAGCCACTTCCTGTGAAAGCAGAGATCCCCGGAAGCTTCACTGGCTTTTTGAGCTGCTCTTGGAGTCACCATTGAGTGGTGAAGGGGGGTCCTTTGTAGATGCATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGAGATCCCCGGAAGCTTC
59.89
TGCAACCAATGGTTATCAGGTC
58.91
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGATCCCCGGAAGCTTCAC
60.18
TGCAACCAATGGTTATCAGGTC
58.91
146
PCR template sequence:
CTTCCTGTGAAAGCAGAGATCCCCGGAAGCTTCACTGGCTTTTTGAGCTGCTCTTGGAGTCACCATTGAGTGGTGAAGGGGGGTCCTTTGTAGATGCATGGTGGATGTCCTAAACCTACCAAAATTCTTGCTGGTGATAGACCTGATAACCATTGGTTGCATTATGATAGTAAAAATATACCAAGAACAAAAAAAGAATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-296-5p(1), mmu-miR-150-5p(1), mmu-miR-335-5p(1), mmu-miR-709(1), mmu-miR-326-3p(1), mmu-miR-503-5p(1), mmu-miR-127-5p(1), mmu-miR-297a-5p(1), mmu-miR-666-5p(1), mmu-miR-383-5p(1), mmu-miR-3065-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTGTAGATGCATGGTGGATGTCCTAA
siRNA sets
TTAGGACATCCACCATGCA, ACATCCACCATGCATCTAC, TAGGACATCCACCATGCAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPSME4_700_ORF_1
0.7822
-0.052123636
0.74138341
705
ORF sequence:
ATGCATGGTGGATGTCCTAAACCTACCAAAATTCTTGCTGGTGATAGACCTGATAACCATTGGTTGCATTATGATAGTAAAAATATACCAAGAACAAAAAAAGAATGGGAGTCAAGTTGCTTTGTTGAAAAAACTCACTGGGGATACTACAACTGGCCAAAGAATATGGTTGTTTATGCTGGTGTGGAAGAACAGCCTAAACTTGGCAGAAGCAGGGAGGATATGATAGAGGCAGAACAGATTATATATGATCGTTTTTCTGATCCTAAGTTTGTTGAGCAGTTAATCACATTTCTATCTTTAGAAGACAGAAAAGGAAGAGATAAGTTTAGTCCCCGGCGTTTCTGCCTCTTTAAGGGTATATTTAGAAATTTTGATGATGCTTTTCTGCCTGTTCTGAAGCCCCATTTAGAACGTTTGGTTGCAGATTCTCATGAAAGTACCCAGAGATGTGTTGCAGAAATTATAGCTGGTTTAATCAGAGGTTCTAAGCATTGGACGTTTGAGAAGGTGGAGAAGCTTTGGGAGCTCCTGTGCCCGCTGCTGAGAACGGCACTGTCCAACATGACAGTGGAGACATACAATGACTGGGGGACCTGTATAGCCACTTCCTGTGAAAGCAGAGATCCCCGGAAGCTTCACTGGCTTTTTGAGCTGCTCTTGGAGTCACCATTGAGTGGTGAAGGGGGGTCCTTTGTAGATGCA
Peptide sequence:
MHGGCPKPTKILAGDRPDNHWLHYDSKNIPRTKKEWESSCFVEKTHWGYYNWPKNMVVYAGVEEQPKLGRSREDMIEAEQIIYDRFSDPKFVEQLITFLSLEDRKGRDKFSPRRFCLFKGIFRNFDDAFLPVLKPHLERLVADSHESTQRCVAEIIAGLIRGSKHWTFEKVEKLWELLCPLLRTALSNMTVETYNDWGTCIATSCESRDPRKLHWLFELLLESPLSGEGGSFVDA
IRESfinder result
IRESfinder score
0.672685747
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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