top of page
mmu_circPsme4_837
Basic information of circular RNA
PanCircBase ID:
mmu_circPsme4_837
mm39_Chr. Position ID:
chr11|30787281|30795897|+
Gene name:
Psme4
Transcript:
ENSMUST00000041231.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
28,29,30,31,32,33,34
Exon/intron offsets:
0,1603,4287,4709,6225,7898,8546
Genomic length:
8616
Exon/intron sizes in nt:
210,137,54,130,82,154,70
Flanking exon/introns:
chr11:30785467-30787281|chr11:30795897-30797397
Splice length:
837
Other database IDs:
circAtlas: mmu-Psme4_0010
circBase: hsa_circ_0005779, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_41640
Human Ortholog IDs:
Mature spliced Sequence:
GGCGCCTTATATTGTCTACTTGGAAATCACAGTGGTGTGTGCCTGGCAAACCTTCATGATTGGGACTGTATTGTGCAGACCTGGCCAGCACTTGTTTCTTCAGGGCTTAGCCAAGCAATGTCACTGGAAAAGCCATCAATAGTGAGACTATTTGATGACCTTGCTGAAAAGATTCATAGACAATATGAAACAATTGGCTTGGATTTTACAATTCCAAAGTCATGTGCTGCAATAGCAGAATTACTTCAACAATCAAAGAATCCTTCCATTAGCCAGACACTACTTAGCCCAGAAAAGATTAAAGAAGGACAGAAGCGTCAACAAGATAAGAATGCTGATGCCCTAAGGAACTATGAATGTTTGGTAAATACTTTACTAGATGGTGTGGAGCAAAGAAATCTGCCTTGGAAATTTGAGCATATAGGAATCGGGCTTCTGTCTCTACTCCTAAGGGATGACAGAGTGTTGCCTCTTCGTGCCATACGTTTTTTTGTTGAAAATCTCAACCATGATGCAATTGTTGTTCGAAAGATGGCTATCTCAGCTGTTGCTGGTATTCTCAAGCAGCTAAAGAGAACTCACAAAAAGCTGACTATCAACCCTTATGAAATCAGTGGATGTCCTAAACCTACCAAAATTCTTGCTGGTGATAGACCTGATAACCATTGGTTGCATTATGATAGTAAAAATATACCAAGAACAAAAAAAGAATGGGAGTCAAGTTGCTTTGTTGAAAAAACTCACTGGGGATACTACAACTGGCCAAAGAATATGGTTGTTTATGCTGGTGTGGAAGAACAGCCTAAACTTGGCAGAAGCAGGGAGGATATGATAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGTGTGGAAGAACAGCCT
59.89
CTGGCCAGGTCTGCACAATA
60.04
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGTGTGGAAGAACAGCCT
59.89
TGGCCAGGTCTGCACAATAC
60.32
140
PCR template sequence:
AACTCACTGGGGATACTACAACTGGCCAAAGAATATGGTTGTTTATGCTGGTGTGGAAGAACAGCCTAAACTTGGCAGAAGCAGGGAGGATATGATAGAGGGCGCCTTATATTGTCTACTTGGAAATCACAGTGGTGTGTGCCTGGCAAACCTTCATGATTGGGACTGTATTGTGCAGACCTGGCCAGCACTTGTTTCTT
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-181b-5p(2), mmu-miR-3065-5p(2), mmu-miR-135a-5p(1), mmu-miR-29b-1-5p(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
GGATATGATAGAGGGCGCCTTATATT
siRNA sets
AATATAAGGCGCCCTCTAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPSME4_837_ORF_1
0.8635
-0.031901199
0.999406547
1557
ORF sequence:
ATGTCACTGGAAAAGCCATCAATAGTGAGACTATTTGATGACCTTGCTGAAAAGATTCATAGACAATATGAAACAATTGGCTTGGATTTTACAATTCCAAAGTCATGTGCTGCAATAGCAGAATTACTTCAACAATCAAAGAATCCTTCCATTAGCCAGACACTACTTAGCCCAGAAAAGATTAAAGAAGGACAGAAGCGTCAACAAGATAAGAATGCTGATGCCCTAAGGAACTATGAATGTTTGGTAAATACTTTACTAGATGGTGTGGAGCAAAGAAATCTGCCTTGGAAATTTGAGCATATAGGAATCGGGCTTCTGTCTCTACTCCTAAGGGATGACAGAGTGTTGCCTCTTCGTGCCATACGTTTTTTTGTTGAAAATCTCAACCATGATGCAATTGTTGTTCGAAAGATGGCTATCTCAGCTGTTGCTGGTATTCTCAAGCAGCTAAAGAGAACTCACAAAAAGCTGACTATCAACCCTTATGAAATCAGTGGATGTCCTAAACCTACCAAAATTCTTGCTGGTGATAGACCTGATAACCATTGGTTGCATTATGATAGTAAAAATATACCAAGAACAAAAAAAGAATGGGAGTCAAGTTGCTTTGTTGAAAAAACTCACTGGGGATACTACAACTGGCCAAAGAATATGGTTGTTTATGCTGGTGTGGAAGAACAGCCTAAACTTGGCAGAAGCAGGGAGGATATGATAGAGGGCGCCTTATATTGTCTACTTGGAAATCACAGTGGTGTGTGCCTGGCAAACCTTCATGATTGGGACTGTATTGTGCAGACCTGGCCAGCACTTGTTTCTTCAGGGCTTAGCCAAGCAATGTCACTGGAAAAGCCATCAATAGTGAGACTATTTGATGACCTTGCTGAAAAGATTCATAGACAATATGAAACAATTGGCTTGGATTTTACAATTCCAAAGTCATGTGCTGCAATAGCAGAATTACTTCAACAATCAAAGAATCCTTCCATTAGCCAGACACTACTTAGCCCAGAAAAGATTAAAGAAGGACAGAAGCGTCAACAAGATAAGAATGCTGATGCCCTAAGGAACTATGAATGTTTGGTAAATACTTTACTAGATGGTGTGGAGCAAAGAAATCTGCCTTGGAAATTTGAGCATATAGGAATCGGGCTTCTGTCTCTACTCCTAAGGGATGACAGAGTGTTGCCTCTTCGTGCCATACGTTTTTTTGTTGAAAATCTCAACCATGATGCAATTGTTGTTCGAAAGATGGCTATCTCAGCTGTTGCTGGTATTCTCAAGCAGCTAAAGAGAACTCACAAAAAGCTGACTATCAACCCTTATGAAATCAGTGGATGTCCTAAACCTACCAAAATTCTTGCTGGTGATAGACCTGATAACCATTGGTTGCATTATGATAGTAAAAATATACCAAGAACAAAAAAAGAATGGGAGTCAAGTTGCTTTGTTGAAAAAACTCACTGGGGATACTACAACTGGCCAAAGAATATGGTTGTTTATGCTGGTGTGGAAGAACAGCCTAAACTTGGCAGAAGCAGGGAGGATATGATAGAG
Peptide sequence:
MSLEKPSIVRLFDDLAEKIHRQYETIGLDFTIPKSCAAIAELLQQSKNPSISQTLLSPEKIKEGQKRQQDKNADALRNYECLVNTLLDGVEQRNLPWKFEHIGIGLLSLLLRDDRVLPLRAIRFFVENLNHDAIVVRKMAISAVAGILKQLKRTHKKLTINPYEISGCPKPTKILAGDRPDNHWLHYDSKNIPRTKKEWESSCFVEKTHWGYYNWPKNMVVYAGVEEQPKLGRSREDMIEGALYCLLGNHSGVCLANLHDWDCIVQTWPALVSSGLSQAMSLEKPSIVRLFDDLAEKIHRQYETIGLDFTIPKSCAAIAELLQQSKNPSISQTLLSPEKIKEGQKRQQDKNADALRNYECLVNTLLDGVEQRNLPWKFEHIGIGLLSLLLRDDRVLPLRAIRFFVENLNHDAIVVRKMAISAVAGILKQLKRTHKKLTINPYEISGCPKPTKILAGDRPDNHWLHYDSKNIPRTKKEWESSCFVEKTHWGYYNWPKNMVVYAGVEEQPKLGRSREDMIE
IRESfinder result
IRESfinder score
0.578801917
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page