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mmu_circCse1l_1335
Basic information of circular RNA
PanCircBase ID:
mmu_circCse1l_1335
mm39_Chr. Position ID:
chr2|166761532|166772586|+
Gene name:
Cse1l
Transcript:
ENSMUST00000002790.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
3,4,5,6,7,8,9,10,11,12,13
Exon/intron offsets:
0,2357,2542,3141,6738,7631,7830,8100,9345,10172,10969
Genomic length:
11054
Exon/intron sizes in nt:
143,102,146,91,108,93,168,130,66,203,85
Flanking exon/introns:
chr2:166757184-166761532|chr2:166772586-166774052
Splice length:
1335
Other database IDs:
CIRCpedia: MMU_CIRCpedia_11631, circAtlas: mmu-Cse1l_0031
Human Ortholog IDs:
Mature spliced Sequence:
CTGAGAAGTTTCTCGAATCCGTAGAAGGAAATCAGAATTACCCACTGTTGCTTTTAACATTATTGGAAAAGTCACAGGATAATGTCATTAAAGTATGTGCTTCAGTAACCTTCAAGAACTATATTAAAAGGAATTGGAGAATTGTTGAAGATGAACCAAACAAAATTTGCGAAGCTGATCGAGTAGCTATTAAAGCCAACATAGTGCATCTGATGCTGAGCAGTCCAGAGCAGATTCAGAAGCAGCTGAGTGATGCTATTAGCATCATTGGCAGAGAAGATTTCCCTCAGAAATGGCCTGACTTGTTGACAGAAATGGTGAATCGCTTTCAGAGTGGAGATTTTCACGTCATTAATGGAGTCCTTCGTACAGCGCACTCACTATTTAAGAGATACCGGCATGAGTTCAAGTCAAATGAGCTGTGGACTGAAATTAAACTTGTCTTGGATGCCTTTGCTTTGCCTTTGACTAATCTATTCAAGGCCACCATTGAACTGTGCAGTACCCATGCAAATGACGCCTCTGCCCTGAGGATTCTTTTTTCTTCCTTGATTTTGATCTCAAAATTGTTCTATAGTTTGAACTTTCAGGATCTCCCTGAATTCTTTGAAGATAATATGGAAACTTGGATGAACAATTTTCATACCCTCCTGACACTGGATAATAAGCTCTTGCAGACTGATGATGAAGAGGAAGCAGGCTTACTGGAGCTTTTAAAGTCTCAGATCTGTGATAATGCCGCTCTCTATGCACAGAAATATGACGAAGAGTTTCAGCGGTACCTCCCTCGCTTTGTCACAGCTATCTGGAACTTACTCGTTACAACAGGGCGAGAAGTTAAATATGACTTGTTGGTTAGCAATGCAATTCAGTTTCTGGCTTCAGTTTGTGAAAGGCCACATTATAAGAATCTGTTTGAGGACCAGAACACGCTGACAAGTATCTGTGAAAAAGTTATTGTGCCTAACATGGAATTTAGAGCTGCTGATGAAGAAGCTTTTGAAGATAATTCTGAGGAGTACATACGGAGGGATTTGGAAGGCTCTGATATTGATACTAGACGCAGGGCTGCTTGTGATCTTGTACGAGGATTATGCAAATTTTTTGAAGGTCCTGTGACAGGAATCTTCTCTGGTTATGTTAATTCCATGCTCCAGGAGTATGCAAAAAACCCGTCTGTCAACTGGAAACACAAAGATGCAGCTATTTACCTTGTCACATCTTTGGCATCAAAAGCCCAGACACAGAAGCATGGAATCACGCAAGCCAATGAACTTGTAAACCTAACTGAATTTTTCGTGAATCACATACTTCCTGATTTAAAATCAAATAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCATGGAATCACGCAAGC
59.83
AGCAACAGTGGGTAATTCTGA
57.21
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCCAGACACAGAAGCATGGA
59.67
AGCAACAGTGGGTAATTCTGA
57.21
151
PCR template sequence:
GCCCAGACACAGAAGCATGGAATCACGCAAGCCAATGAACTTGTAAACCTAACTGAATTTTTCGTGAATCACATACTTCCTGATTTAAAATCAAATAATGCTGAGAAGTTTCTCGAATCCGTAGAAGGAAATCAGAATTACCCACTGTTGCTTTTAACATTATTGGAAAAGTCACAGGATAATGTCATTAAAGTATGTGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-210-3p(1), mmu-miR-136-5p(1), mmu-miR-5101(1), mmu-miR-338-3p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AAATCAAATAATGCTGAGAAGTTTCT
siRNA sets
AACTTCTCAGCATTATTTG, ACTTCTCAGCATTATTTGA, AAACTTCTCAGCATTATTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCSE1L_1335_ORF_1
0.9129
0.115729117
0.999999542
2457
ORF sequence:
ATGCTGAGCAGTCCAGAGCAGATTCAGAAGCAGCTGAGTGATGCTATTAGCATCATTGGCAGAGAAGATTTCCCTCAGAAATGGCCTGACTTGTTGACAGAAATGGTGAATCGCTTTCAGAGTGGAGATTTTCACGTCATTAATGGAGTCCTTCGTACAGCGCACTCACTATTTAAGAGATACCGGCATGAGTTCAAGTCAAATGAGCTGTGGACTGAAATTAAACTTGTCTTGGATGCCTTTGCTTTGCCTTTGACTAATCTATTCAAGGCCACCATTGAACTGTGCAGTACCCATGCAAATGACGCCTCTGCCCTGAGGATTCTTTTTTCTTCCTTGATTTTGATCTCAAAATTGTTCTATAGTTTGAACTTTCAGGATCTCCCTGAATTCTTTGAAGATAATATGGAAACTTGGATGAACAATTTTCATACCCTCCTGACACTGGATAATAAGCTCTTGCAGACTGATGATGAAGAGGAAGCAGGCTTACTGGAGCTTTTAAAGTCTCAGATCTGTGATAATGCCGCTCTCTATGCACAGAAATATGACGAAGAGTTTCAGCGGTACCTCCCTCGCTTTGTCACAGCTATCTGGAACTTACTCGTTACAACAGGGCGAGAAGTTAAATATGACTTGTTGGTTAGCAATGCAATTCAGTTTCTGGCTTCAGTTTGTGAAAGGCCACATTATAAGAATCTGTTTGAGGACCAGAACACGCTGACAAGTATCTGTGAAAAAGTTATTGTGCCTAACATGGAATTTAGAGCTGCTGATGAAGAAGCTTTTGAAGATAATTCTGAGGAGTACATACGGAGGGATTTGGAAGGCTCTGATATTGATACTAGACGCAGGGCTGCTTGTGATCTTGTACGAGGATTATGCAAATTTTTTGAAGGTCCTGTGACAGGAATCTTCTCTGGTTATGTTAATTCCATGCTCCAGGAGTATGCAAAAAACCCGTCTGTCAACTGGAAACACAAAGATGCAGCTATTTACCTTGTCACATCTTTGGCATCAAAAGCCCAGACACAGAAGCATGGAATCACGCAAGCCAATGAACTTGTAAACCTAACTGAATTTTTCGTGAATCACATACTTCCTGATTTAAAATCAAATAATGCTGAGAAGTTTCTCGAATCCGTAGAAGGAAATCAGAATTACCCACTGTTGCTTTTAACATTATTGGAAAAGTCACAGGATAATGTCATTAAAGTATGTGCTTCAGTAACCTTCAAGAACTATATTAAAAGGAATTGGAGAATTGTTGAAGATGAACCAAACAAAATTTGCGAAGCTGATCGAGTAGCTATTAAAGCCAACATAGTGCATCTGATGCTGAGCAGTCCAGAGCAGATTCAGAAGCAGCTGAGTGATGCTATTAGCATCATTGGCAGAGAAGATTTCCCTCAGAAATGGCCTGACTTGTTGACAGAAATGGTGAATCGCTTTCAGAGTGGAGATTTTCACGTCATTAATGGAGTCCTTCGTACAGCGCACTCACTATTTAAGAGATACCGGCATGAGTTCAAGTCAAATGAGCTGTGGACTGAAATTAAACTTGTCTTGGATGCCTTTGCTTTGCCTTTGACTAATCTATTCAAGGCCACCATTGAACTGTGCAGTACCCATGCAAATGACGCCTCTGCCCTGAGGATTCTTTTTTCTTCCTTGATTTTGATCTCAAAATTGTTCTATAGTTTGAACTTTCAGGATCTCCCTGAATTCTTTGAAGATAATATGGAAACTTGGATGAACAATTTTCATACCCTCCTGACACTGGATAATAAGCTCTTGCAGACTGATGATGAAGAGGAAGCAGGCTTACTGGAGCTTTTAAAGTCTCAGATCTGTGATAATGCCGCTCTCTATGCACAGAAATATGACGAAGAGTTTCAGCGGTACCTCCCTCGCTTTGTCACAGCTATCTGGAACTTACTCGTTACAACAGGGCGAGAAGTTAAATATGACTTGTTGGTTAGCAATGCAATTCAGTTTCTGGCTTCAGTTTGTGAAAGGCCACATTATAAGAATCTGTTTGAGGACCAGAACACGCTGACAAGTATCTGTGAAAAAGTTATTGTGCCTAACATGGAATTTAGAGCTGCTGATGAAGAAGCTTTTGAAGATAATTCTGAGGAGTACATACGGAGGGATTTGGAAGGCTCTGATATTGATACTAGACGCAGGGCTGCTTGTGATCTTGTACGAGGATTATGCAAATTTTTTGAAGGTCCTGTGACAGGAATCTTCTCTGGTTATGTTAATTCCATGCTCCAGGAGTATGCAAAAAACCCGTCTGTCAACTGGAAACACAAAGATGCAGCTATTTACCTTGTCACATCTTTGGCATCAAAAGCCCAGACACAGAAGCATGGAATCACGCAAGCCAATGAACTTGTAAACCTAACTGAATTTTTCGTGAATCACATACTTCCTGATTTAAAATCAAATAAT
Peptide sequence:
MLSSPEQIQKQLSDAISIIGREDFPQKWPDLLTEMVNRFQSGDFHVINGVLRTAHSLFKRYRHEFKSNELWTEIKLVLDAFALPLTNLFKATIELCSTHANDASALRILFSSLILISKLFYSLNFQDLPEFFEDNMETWMNNFHTLLTLDNKLLQTDDEEEAGLLELLKSQICDNAALYAQKYDEEFQRYLPRFVTAIWNLLVTTGREVKYDLLVSNAIQFLASVCERPHYKNLFEDQNTLTSICEKVIVPNMEFRAADEEAFEDNSEEYIRRDLEGSDIDTRRRAACDLVRGLCKFFEGPVTGIFSGYVNSMLQEYAKNPSVNWKHKDAAIYLVTSLASKAQTQKHGITQANELVNLTEFFVNHILPDLKSNNAEKFLESVEGNQNYPLLLLTLLEKSQDNVIKVCASVTFKNYIKRNWRIVEDEPNKICEADRVAIKANIVHLMLSSPEQIQKQLSDAISIIGREDFPQKWPDLLTEMVNRFQSGDFHVINGVLRTAHSLFKRYRHEFKSNELWTEIKLVLDAFALPLTNLFKATIELCSTHANDASALRILFSSLILISKLFYSLNFQDLPEFFEDNMETWMNNFHTLLTLDNKLLQTDDEEEAGLLELLKSQICDNAALYAQKYDEEFQRYLPRFVTAIWNLLVTTGREVKYDLLVSNAIQFLASVCERPHYKNLFEDQNTLTSICEKVIVPNMEFRAADEEAFEDNSEEYIRRDLEGSDIDTRRRAACDLVRGLCKFFEGPVTGIFSGYVNSMLQEYAKNPSVNWKHKDAAIYLVTSLASKAQTQKHGITQANELVNLTEFFVNHILPDLKSNN
IRESfinder result
IRESfinder score
0.74534332
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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