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mmu_circUbxn4_759
Basic information of circular RNA
PanCircBase ID:
mmu_circUbxn4_759
mm39_Chr. Position ID:
chr1|128183169|128194151|+
Gene name:
Ubxn4
Transcript:
ENSMUST00000027592.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
3,4,5,6,7,8,9
Exon/intron offsets:
0,686,3399,4011,5401,7360,10857
Genomic length:
10982
Exon/intron sizes in nt:
29,119,172,94,55,165,125
Flanking exon/introns:
chr1:128180042-128183169|chr1:128194151-128197605
Splice length:
759
Other database IDs:
circAtlas: mmu-Ubxn4_0017
circAtlas: hsa-UBXN4_0017, CIRCpedia: HSA_CIRCpedia_374837
Human Ortholog IDs:
Mature spliced Sequence:
TGAAGCCTGTCTGCAGTTTTCACAAATTTATCCTGTAGTATGTGTTCCATCCAGTTTCTTTATAGGAGACAGTGGAATCCCTTTGGAAGTAATAGCGGGGAGTGTTTCTGCAGATGAGCTTGTTACAAGAATTCATAAAGTCCAACAGATGCACTCGTCAAAAGGTGAAGCATCAGTGACAAATGACAACCAGTCAGAAAGTTCAGTATCTACCCCATCTGCCTCATTTGAACCTGATGTATGTGAAAATCCCGAGTCCAAAAATACAGAGCTTTGTGAGACACCAGCTACCTCTGACACAAAGTCAGATACTGCAACAGGAGGAGAATGCACAGGTCATGACAGCCACTCTCAGGAGCCTCATGGATGTTCAAACCAGAGACCAGCCGAGGACCTCACCGTCAGAGTAGAAAGACTAACAAAAAAACTTGAAGAAAGGAGAGAAGAGAAGCGGAAGGAAGAAGCACAGAGAGAGATTAAGAAGGAAATTGAAAGGAGAAAAACTGGAAAGGAAATGTTGGATTATAAAAGAAAACAAGAAGAAGAATTAACAAAAAGAATGTTAGAAGAAAGAAGCAGAGAGAAGGCAGAAGATAGAGCGGCTCGAGAGCGCATCAAGCAGCAGATTGCCCTGGATCGTGCAGAAAGAGCTGCTCGTTTTGCAAAGACAAAGGAAGCAGAAGCTGCCAAAGCTGCTGCCTTGCTGACCAAACAGGCAGGAACGGAAGTCAAGAGAGAGTCTACAGCACGAGACAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTTGCTGACCAAACAGGCAG
59.69
CCCGCTATTACTTCCAAAGGGA
59.83
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGCCTTGCTGACCAAACAG
59.69
CCCGCTATTACTTCCAAAGGGA
59.83
163
PCR template sequence:
TTGCAAAGACAAAGGAAGCAGAAGCTGCCAAAGCTGCTGCCTTGCTGACCAAACAGGCAGGAACGGAAGTCAAGAGAGAGTCTACAGCACGAGACAGAAGTGAAGCCTGTCTGCAGTTTTCACAAATTTATCCTGTAGTATGTGTTCCATCCAGTTTCTTTATAGGAGACAGTGGAATCCCTTTGGAAGTAATAGCGGGG
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-let-7a-5p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-709(1), mmu-miR-138-5p(1), mmu-let-7d-5p(1), mmu-miR-541-5p(1), mmu-miR-340-5p(1), mmu-miR-98-5p(1), mmu-miR-350-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
CACGAGACAGAAGTGAAGCCTGTCTG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUBXN4_759_ORF_1
1.0913
0.156053839
0.999297962
1368
ORF sequence:
ATGCACTCGTCAAAAGGTGAAGCATCAGTGACAAATGACAACCAGTCAGAAAGTTCAGTATCTACCCCATCTGCCTCATTTGAACCTGATGTATGTGAAAATCCCGAGTCCAAAAATACAGAGCTTTGTGAGACACCAGCTACCTCTGACACAAAGTCAGATACTGCAACAGGAGGAGAATGCACAGGTCATGACAGCCACTCTCAGGAGCCTCATGGATGTTCAAACCAGAGACCAGCCGAGGACCTCACCGTCAGAGTAGAAAGACTAACAAAAAAACTTGAAGAAAGGAGAGAAGAGAAGCGGAAGGAAGAAGCACAGAGAGAGATTAAGAAGGAAATTGAAAGGAGAAAAACTGGAAAGGAAATGTTGGATTATAAAAGAAAACAAGAAGAAGAATTAACAAAAAGAATGTTAGAAGAAAGAAGCAGAGAGAAGGCAGAAGATAGAGCGGCTCGAGAGCGCATCAAGCAGCAGATTGCCCTGGATCGTGCAGAAAGAGCTGCTCGTTTTGCAAAGACAAAGGAAGCAGAAGCTGCCAAAGCTGCTGCCTTGCTGACCAAACAGGCAGGAACGGAAGTCAAGAGAGAGTCTACAGCACGAGACAGAAGTGAAGCCTGTCTGCAGTTTTCACAAATTTATCCTGTAGTATGTGTTCCATCCAGTTTCTTTATAGGAGACAGTGGAATCCCTTTGGAAGTAATAGCGGGGAGTGTTTCTGCAGATGAGCTTGTTACAAGAATTCATAAAGTCCAACAGATGCACTCGTCAAAAGGTGAAGCATCAGTGACAAATGACAACCAGTCAGAAAGTTCAGTATCTACCCCATCTGCCTCATTTGAACCTGATGTATGTGAAAATCCCGAGTCCAAAAATACAGAGCTTTGTGAGACACCAGCTACCTCTGACACAAAGTCAGATACTGCAACAGGAGGAGAATGCACAGGTCATGACAGCCACTCTCAGGAGCCTCATGGATGTTCAAACCAGAGACCAGCCGAGGACCTCACCGTCAGAGTAGAAAGACTAACAAAAAAACTTGAAGAAAGGAGAGAAGAGAAGCGGAAGGAAGAAGCACAGAGAGAGATTAAGAAGGAAATTGAAAGGAGAAAAACTGGAAAGGAAATGTTGGATTATAAAAGAAAACAAGAAGAAGAATTAACAAAAAGAATGTTAGAAGAAAGAAGCAGAGAGAAGGCAGAAGATAGAGCGGCTCGAGAGCGCATCAAGCAGCAGATTGCCCTGGATCGTGCAGAAAGAGCTGCTCGTTTTGCAAAGACAAAGGAAGCAGAAGCTGCCAAAGCTGCTGCCTTGCTGACCAAACAGGCAGGAACGGAAGTCAAGAGAGAGTCTACAGCACGAGACAGA
Peptide sequence:
MHSSKGEASVTNDNQSESSVSTPSASFEPDVCENPESKNTELCETPATSDTKSDTATGGECTGHDSHSQEPHGCSNQRPAEDLTVRVERLTKKLEERREEKRKEEAQREIKKEIERRKTGKEMLDYKRKQEEELTKRMLEERSREKAEDRAARERIKQQIALDRAERAARFAKTKEAEAAKAAALLTKQAGTEVKRESTARDRSEACLQFSQIYPVVCVPSSFFIGDSGIPLEVIAGSVSADELVTRIHKVQQMHSSKGEASVTNDNQSESSVSTPSASFEPDVCENPESKNTELCETPATSDTKSDTATGGECTGHDSHSQEPHGCSNQRPAEDLTVRVERLTKKLEERREEKRKEEAQREIKKEIERRKTGKEMLDYKRKQEEELTKRMLEERSREKAEDRAARERIKQQIALDRAERAARFAKTKEAEAAKAAALLTKQAGTEVKRESTARDR
IRESfinder result
IRESfinder score
0.518252522
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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