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mmu_circUsp54_1948
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp54_1948
mm39_Chr. Position ID:
chr14|20620315|20641681|-
Gene name:
Usp54
Transcript:
ENSMUST00000035340.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
15,14,13,12,11,10,9,8,7,6,5,4
Exon/intron offsets:
0,3520,6225,6687,7207,13074,15752,17827,18085,18936,19126,21231
Genomic length:
21366
Exon/intron sizes in nt:
16,81,34,23,23,78,13,20,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr14:20616130-20620315|chr14:20641681-20654119
Splice length:
1948
Other database IDs:
CIRCpedia: MMU_CIRCpedia_216089, circAtlas: mmu-Usp54_0016
Human Ortholog IDs:
Mature spliced Sequence:
GGCATCTTTAACCAGTTTCAGTGTAGTAGTGAAAAAGTGCTTCCTTCCGACACTCTCCGCAGTGCTCTGGCAAAGACTTTCCAAGATGAACAACGCTTCCAGCTGGGGATTATGGATGATGCTGCAGAATGCTTTGAAAACCTCCTGATGAGAATTCACTTCCATATTGCTGATGAAACCAAAGAGGATATATGTACTGCTCAACACTGCATATCCCACCAGAAATTTGCAATGACATTGTTTGAGCAGTGTGTGTGCAGCAGCTGTGGCGCCACGTCCGACCCGCTGCCCTTTATCCAGATGGTGCACTACATCTCCACCACTGCCCTCTGTAACCAGGCTATTTGTATGCTGGAAAAGCGAGAGAAACCCTCACCAAGTATGTTTGGTGAGCTGCTTCAGAATGCCAGCACCATGGGGGACCTGCGGAACTGTCCGAGCAACTGTGGGGAGAGAATCCGGATCCGCCGTGTCTTGATGAATGCACCACAGATTATCACGATTGGTCTGGTTTGGGACTCAGAGCATTCAGACTTGGCAGAGGACGTCATCCACAGCCTGGGCACCTGCCTTAAGCTGGGTGATCTGTTTTTCAGAGTGACAGATGACCGGGCCAAGCAGTCTGAACTATACTTAGTAGGAATGATCTGTTACTATGGCAAGCATTATTCTACATTCTTTTTTCAAACAAAGATCCGCAAATGGATGTATTTTGATGATGCTCATGTCAAGGAGATTGGTCCGAAGTGGAAGGATGTGGTCACCAAATGCATTAAAGGGCACTATCAACCCTTGCTGCTGCTCTATGCAGACCCCCAGGGTACTCCAGTGTCTGCCCAGGACCTGCCTCCCCACGCTCAGTTCCTGCCATACACCAAGACATGCTACGATAGTGAAGACTCAGGACACCTGACTGATAGTGAATGTAATCAGAAACACACATCGAAGAAAGGGTCCCTGGTGGAGCGCAGGAGGAGCAGTGGCCGTGTTCGGAGAAAAGGCGATGAGCCACAGGCCTCAGGGTACCACAGCGAAGGAGAAACACTGAAAGAGAAGCAGGCTCCTAGGAATGCCTCTAAATCCAGCAGCAGCAGCAGGCTAAAGGATTTCAAAGAGACAGTCAGCAACATGATCCACAGCAGGCCTTCCCTGGCTTCTCAGACCAGTGCAGGATCTCCCTGTGTAGGTAGGGCAGGAGACCAGCTAGACAAGATACCACCAAGGAACTTCCCTTTACAGGCTCGGGGCTGGGAAACGGAGAGTACCAGTAGTGAGGCAAAATCCAGTTCTTCCAGCAAGTACCGCCCAACATGGAGACCTAAACGAGAATCTCTAAATATTGACAGCATTTTTAGTAAGGACAGAAGGAAGCATTGTGGCTACACCCAGCTTAGGACCTTTCCTGAAGATGCAGCTAAAGAATTTACACCGGATGAAGTAAGCAAGCCAACTGCTAATGACATTAAAGATGGCGGATCAAGGTCACAGCATAAACTCTGGGGAACAGCTCGGCCAGGCTCTCATCTTTTAGAGCAGCATCCTCGCCTAATCCAGCGGATGGAATCTGGCTATGAGAGCAGTGAGAGGAACAGCAGCAGCCCTGTCAGTTTGGATGCTGCCCCGCCTGACAGCGTGAATGTCTACAGGGATCAAAGCACAAAGAGGCCTGTTGGGTTTGTCCCTTCTTGGCGTCATATTCCAAAGTCTCACAGCAGTAGCATCCTGGAGGTAGACTGTACAGCACCCATGACCAGCTGGACAAAGACTCAACCTCTCTCAGATGGGGAGGTCACCTCTAGAAGTGAATTGGATGAACTACAGGAAGAAGTGGTCAGGCGAGCCCAGGAACAGGAGCTGCGGAAGAAACGGGAGAAGGAATTAGAGGCTGCTAAAGGCTTTAACCCTCATCCCAGCCGCTACATGGATTTGGATGAACTGCAGAATCAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCGGAAGAAACGGGAGAAG
60.32
GGAGAGTGTCGGAAGGAAGC
60.11
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGCGGAAGAAACGGGAGAA
60.32
GGAGAGTGTCGGAAGGAAGC
60.11
152
PCR template sequence:
CAGGAGCTGCGGAAGAAACGGGAGAAGGAATTAGAGGCTGCTAAAGGCTTTAACCCTCATCCCAGCCGCTACATGGATTTGGATGAACTGCAGAATCAGGGGCATCTTTAACCAGTTTCAGTGTAGTAGTGAAAAAGTGCTTCCTTCCGACACTCTCCGCAGTGCTCTGGCAAAGACTTTCCAAGATGAACAACGCTTCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
26
Interacting miRNAs (#binding sites)
mmu-miR-181a-5p(2), mmu-miR-103-3p(2), mmu-miR-181b-5p(2), mmu-miR-107-3p(2), mmu-miR-207(2), mmu-miR-181d-5p(2), mmu-miR-9-5p(1), mmu-miR-155-5p(1), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-141-3p(1), mmu-miR-15b-5p(1), mmu-miR-132-3p(1), mmu-miR-125b-5p(1), mmu-miR-351-5p(1), mmu-miR-218-5p(1), mmu-miR-370-3p(1), mmu-miR-541-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-335-3p(1), mmu-miR-3470b(1), mmu-miR-1199-5p(1), mmu-miR-697(1), mmu-miR-296-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGCAGAATCAGGGGCATCTTTAACC
siRNA sets
TTAAAGATGCCCCTGATTC, TAAAGATGCCCCTGATTCT, GATGCCCCTGATTCTGCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP54_1948_ORF_1
0.8594
0.239366352
0.999989057
1965
ORF sequence:
ATGAACTGCAGAATCAGGGGCATCTTTAACCAGTTTCAGTGTAGTAGTGAAAAAGTGCTTCCTTCCGACACTCTCCGCAGTGCTCTGGCAAAGACTTTCCAAGATGAACAACGCTTCCAGCTGGGGATTATGGATGATGCTGCAGAATGCTTTGAAAACCTCCTGATGAGAATTCACTTCCATATTGCTGATGAAACCAAAGAGGATATATGTACTGCTCAACACTGCATATCCCACCAGAAATTTGCAATGACATTGTTTGAGCAGTGTGTGTGCAGCAGCTGTGGCGCCACGTCCGACCCGCTGCCCTTTATCCAGATGGTGCACTACATCTCCACCACTGCCCTCTGTAACCAGGCTATTTGTATGCTGGAAAAGCGAGAGAAACCCTCACCAAGTATGTTTGGTGAGCTGCTTCAGAATGCCAGCACCATGGGGGACCTGCGGAACTGTCCGAGCAACTGTGGGGAGAGAATCCGGATCCGCCGTGTCTTGATGAATGCACCACAGATTATCACGATTGGTCTGGTTTGGGACTCAGAGCATTCAGACTTGGCAGAGGACGTCATCCACAGCCTGGGCACCTGCCTTAAGCTGGGTGATCTGTTTTTCAGAGTGACAGATGACCGGGCCAAGCAGTCTGAACTATACTTAGTAGGAATGATCTGTTACTATGGCAAGCATTATTCTACATTCTTTTTTCAAACAAAGATCCGCAAATGGATGTATTTTGATGATGCTCATGTCAAGGAGATTGGTCCGAAGTGGAAGGATGTGGTCACCAAATGCATTAAAGGGCACTATCAACCCTTGCTGCTGCTCTATGCAGACCCCCAGGGTACTCCAGTGTCTGCCCAGGACCTGCCTCCCCACGCTCAGTTCCTGCCATACACCAAGACATGCTACGATAGTGAAGACTCAGGACACCTGACTGATAGTGAATGTAATCAGAAACACACATCGAAGAAAGGGTCCCTGGTGGAGCGCAGGAGGAGCAGTGGCCGTGTTCGGAGAAAAGGCGATGAGCCACAGGCCTCAGGGTACCACAGCGAAGGAGAAACACTGAAAGAGAAGCAGGCTCCTAGGAATGCCTCTAAATCCAGCAGCAGCAGCAGGCTAAAGGATTTCAAAGAGACAGTCAGCAACATGATCCACAGCAGGCCTTCCCTGGCTTCTCAGACCAGTGCAGGATCTCCCTGTGTAGGTAGGGCAGGAGACCAGCTAGACAAGATACCACCAAGGAACTTCCCTTTACAGGCTCGGGGCTGGGAAACGGAGAGTACCAGTAGTGAGGCAAAATCCAGTTCTTCCAGCAAGTACCGCCCAACATGGAGACCTAAACGAGAATCTCTAAATATTGACAGCATTTTTAGTAAGGACAGAAGGAAGCATTGTGGCTACACCCAGCTTAGGACCTTTCCTGAAGATGCAGCTAAAGAATTTACACCGGATGAAGTAAGCAAGCCAACTGCTAATGACATTAAAGATGGCGGATCAAGGTCACAGCATAAACTCTGGGGAACAGCTCGGCCAGGCTCTCATCTTTTAGAGCAGCATCCTCGCCTAATCCAGCGGATGGAATCTGGCTATGAGAGCAGTGAGAGGAACAGCAGCAGCCCTGTCAGTTTGGATGCTGCCCCGCCTGACAGCGTGAATGTCTACAGGGATCAAAGCACAAAGAGGCCTGTTGGGTTTGTCCCTTCTTGGCGTCATATTCCAAAGTCTCACAGCAGTAGCATCCTGGAGGTAGACTGTACAGCACCCATGACCAGCTGGACAAAGACTCAACCTCTCTCAGATGGGGAGGTCACCTCTAGAAGTGAATTGGATGAACTACAGGAAGAAGTGGTCAGGCGAGCCCAGGAACAGGAGCTGCGGAAGAAACGGGAGAAGGAATTAGAGGCTGCTAAAGGCTTTAACCCTCATCCCAGCCGCTACATGGATTTGGATGAACTGCAGAATCAG
Peptide sequence:
MNCRIRGIFNQFQCSSEKVLPSDTLRSALAKTFQDEQRFQLGIMDDAAECFENLLMRIHFHIADETKEDICTAQHCISHQKFAMTLFEQCVCSSCGATSDPLPFIQMVHYISTTALCNQAICMLEKREKPSPSMFGELLQNASTMGDLRNCPSNCGERIRIRRVLMNAPQIITIGLVWDSEHSDLAEDVIHSLGTCLKLGDLFFRVTDDRAKQSELYLVGMICYYGKHYSTFFFQTKIRKWMYFDDAHVKEIGPKWKDVVTKCIKGHYQPLLLLYADPQGTPVSAQDLPPHAQFLPYTKTCYDSEDSGHLTDSECNQKHTSKKGSLVERRRSSGRVRRKGDEPQASGYHSEGETLKEKQAPRNASKSSSSSRLKDFKETVSNMIHSRPSLASQTSAGSPCVGRAGDQLDKIPPRNFPLQARGWETESTSSEAKSSSSSKYRPTWRPKRESLNIDSIFSKDRRKHCGYTQLRTFPEDAAKEFTPDEVSKPTANDIKDGGSRSQHKLWGTARPGSHLLEQHPRLIQRMESGYESSERNSSSPVSLDAAPPDSVNVYRDQSTKRPVGFVPSWRHIPKSHSSSILEVDCTAPMTSWTKTQPLSDGEVTSRSELDELQEEVVRRAQEQELRKKREKELEAAKGFNPHPSRYMDLDELQNQ
IRESfinder result
IRESfinder score
0.450502337
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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