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mmu_circZswim5_837
Basic information of circular RNA
PanCircBase ID:
mmu_circZswim5_837
mm39_Chr. Position ID:
chr4|116808021|116822972|+
Gene name:
Zswim5
Transcript:
ENSMUST00000044823.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
2,3,4,5
Exon/intron offsets:
0,7853,11685,14771
Genomic length:
14951
Exon/intron sizes in nt:
3,57,14,91,51,180
Flanking exon/introns:
chr4:116735260-116808021|chr4:116822972-116830067
Splice length:
837
Other database IDs:
CIRCpedia: MMU_CIRCpedia_223817, circAtlas: mmu-Zswim5_0007
circBase: hsa_circ_0113443, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_32072
Human Ortholog IDs:
Mature spliced Sequence:
GCTTCCATCTGAGTGGCACAGTCACGGAACCAGCCATGGCTTCTGAGCCAGCAGTGACTTACAAGGTTGCCATCAGCTTTGATCGATGCAAAATCACGTCTGTGAGCTGCGGCTGTGGGAATAAGGACATATTCTACTGTGCTCACGTGGTAGCACTCTCTCTCTACCGGATCCGGAAACCAGACCAGGTCAAACTTCGTCTTCCTATCTCAGAAACCCTTTTCCAGATGAACAGGGACCAGCTACAGAAGTTTATTCAGTATTTAATCACAGCACACCACACTGAAGTTCTTCCTACTGCACAAAAGCTGGCAGATGAGATTCTGTCCTCCAACTCAGAAATCAACCAAGTGAATGGCGCCCCTGACCCCACAGCTGGGGCCAGCATCGATGATGAGAACTGTTGGCACTTGGATGAAGAACAAGTGAAAGAACAAGTGAAGCTCTTTCTCTCCCAGGGGGGTTACTATGGCTCTGGGAAGCAGCTCAACTCAATGTTTGCCAAGGTTCGAGAGATGCTTCGAATGAGAGATTCTAATGGAGCCAGGATGCTGACACTTATCACTGAGCAATTTATGGCTGATCCACGCCTCACACTCTGGAGGCAGCAAGGAACAAGCATGACAGACAAGTGCAGGCAGCTCTGGGATGAGCTAGGGGCTTTATGGGTGTGCATAATTTTAAATCCACACTGCAAACTAGAAGAAAAATCTTGTTGGCTCCAGCAACTGCAGAAGTGGAGCGACCTGGATATCTGTCCCCTGGAGGATGGAAACTATGGGCATGAGCTGCCCAACATTACCAATGCGCTCTCCCAGAGTGCCAGCCACAGCCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCCCCTGGAGGATGGAAA
60.18
AGTCACTGCTGGCTCAGAAG
59.68
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTCCCCTGGAGGATGGAAAC
59.74
AGTCACTGCTGGCTCAGAAG
59.68
140
PCR template sequence:
TGGAGCGACCTGGATATCTGTCCCCTGGAGGATGGAAACTATGGGCATGAGCTGCCCAACATTACCAATGCGCTCTCCCAGAGTGCCAGCCACAGCCCAGGCTTCCATCTGAGTGGCACAGTCACGGAACCAGCCATGGCTTCTGAGCCAGCAGTGACTTACAAGGTTGCCATCAGCTTTGATCGATGCAAAATCACGTC
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-134-5p(1), mmu-miR-106a-5p(1), mmu-miR-7b-5p(1), mmu-miR-216a-5p(1), mmu-miR-7a-5p(1), mmu-miR-185-5p(1), mmu-miR-149-5p(1), mmu-miR-127-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-224-5p(1), mmu-miR-335-3p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGCCACAGCCCAGGCTTCCATCTGAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCZSWIM5_837_ORF_1
1.0448
0.250188524
0.999925451
1638
ORF sequence:
ATGGCTTCTGAGCCAGCAGTGACTTACAAGGTTGCCATCAGCTTTGATCGATGCAAAATCACGTCTGTGAGCTGCGGCTGTGGGAATAAGGACATATTCTACTGTGCTCACGTGGTAGCACTCTCTCTCTACCGGATCCGGAAACCAGACCAGGTCAAACTTCGTCTTCCTATCTCAGAAACCCTTTTCCAGATGAACAGGGACCAGCTACAGAAGTTTATTCAGTATTTAATCACAGCACACCACACTGAAGTTCTTCCTACTGCACAAAAGCTGGCAGATGAGATTCTGTCCTCCAACTCAGAAATCAACCAAGTGAATGGCGCCCCTGACCCCACAGCTGGGGCCAGCATCGATGATGAGAACTGTTGGCACTTGGATGAAGAACAAGTGAAAGAACAAGTGAAGCTCTTTCTCTCCCAGGGGGGTTACTATGGCTCTGGGAAGCAGCTCAACTCAATGTTTGCCAAGGTTCGAGAGATGCTTCGAATGAGAGATTCTAATGGAGCCAGGATGCTGACACTTATCACTGAGCAATTTATGGCTGATCCACGCCTCACACTCTGGAGGCAGCAAGGAACAAGCATGACAGACAAGTGCAGGCAGCTCTGGGATGAGCTAGGGGCTTTATGGGTGTGCATAATTTTAAATCCACACTGCAAACTAGAAGAAAAATCTTGTTGGCTCCAGCAACTGCAGAAGTGGAGCGACCTGGATATCTGTCCCCTGGAGGATGGAAACTATGGGCATGAGCTGCCCAACATTACCAATGCGCTCTCCCAGAGTGCCAGCCACAGCCCAGGCTTCCATCTGAGTGGCACAGTCACGGAACCAGCCATGGCTTCTGAGCCAGCAGTGACTTACAAGGTTGCCATCAGCTTTGATCGATGCAAAATCACGTCTGTGAGCTGCGGCTGTGGGAATAAGGACATATTCTACTGTGCTCACGTGGTAGCACTCTCTCTCTACCGGATCCGGAAACCAGACCAGGTCAAACTTCGTCTTCCTATCTCAGAAACCCTTTTCCAGATGAACAGGGACCAGCTACAGAAGTTTATTCAGTATTTAATCACAGCACACCACACTGAAGTTCTTCCTACTGCACAAAAGCTGGCAGATGAGATTCTGTCCTCCAACTCAGAAATCAACCAAGTGAATGGCGCCCCTGACCCCACAGCTGGGGCCAGCATCGATGATGAGAACTGTTGGCACTTGGATGAAGAACAAGTGAAAGAACAAGTGAAGCTCTTTCTCTCCCAGGGGGGTTACTATGGCTCTGGGAAGCAGCTCAACTCAATGTTTGCCAAGGTTCGAGAGATGCTTCGAATGAGAGATTCTAATGGAGCCAGGATGCTGACACTTATCACTGAGCAATTTATGGCTGATCCACGCCTCACACTCTGGAGGCAGCAAGGAACAAGCATGACAGACAAGTGCAGGCAGCTCTGGGATGAGCTAGGGGCTTTATGGGTGTGCATAATTTTAAATCCACACTGCAAACTAGAAGAAAAATCTTGTTGGCTCCAGCAACTGCAGAAGTGGAGCGACCTGGATATCTGTCCCCTGGAGGATGGAAACTATGGGCATGAGCTGCCCAACATTACCAATGCGCTCTCCCAGAGTGCCAGCCACAGCCCA
Peptide sequence:
MASEPAVTYKVAISFDRCKITSVSCGCGNKDIFYCAHVVALSLYRIRKPDQVKLRLPISETLFQMNRDQLQKFIQYLITAHHTEVLPTAQKLADEILSSNSEINQVNGAPDPTAGASIDDENCWHLDEEQVKEQVKLFLSQGGYYGSGKQLNSMFAKVREMLRMRDSNGARMLTLITEQFMADPRLTLWRQQGTSMTDKCRQLWDELGALWVCIILNPHCKLEEKSCWLQQLQKWSDLDICPLEDGNYGHELPNITNALSQSASHSPGFHLSGTVTEPAMASEPAVTYKVAISFDRCKITSVSCGCGNKDIFYCAHVVALSLYRIRKPDQVKLRLPISETLFQMNRDQLQKFIQYLITAHHTEVLPTAQKLADEILSSNSEINQVNGAPDPTAGASIDDENCWHLDEEQVKEQVKLFLSQGGYYGSGKQLNSMFAKVREMLRMRDSNGARMLTLITEQFMADPRLTLWRQQGTSMTDKCRQLWDELGALWVCIILNPHCKLEEKSCWLQQLQKWSDLDICPLEDGNYGHELPNITNALSQSASHSP
IRESfinder result
IRESfinder score
0.502408705
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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