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mmu_circSusd1_867
Basic information of circular RNA
PanCircBase ID:
mmu_circSusd1_867
mm39_Chr. Position ID:
chr4|59349825|59380958|-
Gene name:
Susd1
Transcript:
ENSMUST00000040166.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
12,11,10,9,8,7
Exon/intron offsets:
0,1812,15896,19705,29773,31035
Genomic length:
31133
Exon/intron sizes in nt:
187,92,193,110,187,98
Flanking exon/introns:
chr4:59333033-59349825|chr4:59380958-59390572
Splice length:
867
Other database IDs:
circAtlas: mmu-Susd1_0005
circBase: hsa_circ_0088038, circAtlas: hsa-SUSD1_0011, CIRCpedia: HSA_CIRCpedia_111794
Human Ortholog IDs:
Mature spliced Sequence:
AAATAATGATAGAAATTCATGATGTGTTGGTGTTTAATGACACCTGTGTGAGATGGCAAATAAGTCCAGAGAGAGTGAACGCCAGGATCGTGTACTTGATACGCGTTGAAAGACAGCAGCCGGATGCTGCGGAATCAGTTTATGAGGAGACAGTCAATGTGACCACAGACAGCAGAACCCCAGAAGTGTGCCTGCACCTCCAACAAGGAACCAATTACACCATAAGCATTTCTGCAGCCCCTCCCAGGCGCTCTGTGCCCGCCATCCTTGGCTTCCAGACCCCTGAAGATGATCTCTTAGAAGATGACGGACTTTTCAATATCTCAGTATTTAATGAAACTTGTTTGACGTTGAGCAGGCACTCTAGGCAAGTTGGATCAGAACAAATGTACCAAGTGGAGGTTCTGGGTCAGAGGTGGTATCTAGAGAGCTCCTACCATGCTGCTCTCTTTAACTTCACAACAAGAGACCGAGCTCCAGAAGTGTGTTTAGATCTGTACCCCGCTACTGATTACACGATAAACATCACCCTTCTGAGACCCACTGAGCCGCGCTCCGCACAAATAACCATAACAACCTCAGTGACAGCAAAACAGACCATCGCTAATATTTCGGTATATAATGATACCTGCCTGAGATGGAGCAGCCTCAAGACAGCTGATGTACTAGAGATGTATTTATTCCACATTTGGGGCCAGAGATGGTATCAGAAGGCATTTGTCCAGGAAATGGTCTTCAATACAACCAGCAGCAGCCAGGACCCTGAGATATGCCTGGACCTGCATCAAGGCACCAGCTACAACGTTAGCCTTCAGGCTCTGTCTTCGGCACTTCCCGTGGTCATCTACCTGACAACCCAGATCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTTCAGGCTCTGTCTTCGG
60.11
CAAGTACACGATCCTGGCGT
60.11
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTTCAGGCTCTGTCTTCGG
60.11
CTGGCGTTCACTCTCTCTGG
60.11
144
PCR template sequence:
ATATGCCTGGACCTGCATCAAGGCACCAGCTACAACGTTAGCCTTCAGGCTCTGTCTTCGGCACTTCCCGTGGTCATCTACCTGACAACCCAGATCACAGAAATAATGATAGAAATTCATGATGTGTTGGTGTTTAATGACACCTGTGTGAGATGGCAAATAAGTCCAGAGAGAGTGAACGCCAGGATCGTGTACTTGAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-200b-3p(1), mmu-miR-103-3p(1), mmu-miR-200c-3p(1), mmu-miR-138-5p(1), mmu-miR-24-3p(1), mmu-miR-107-3p(1), mmu-miR-666-5p(1), mmu-miR-342-3p(1), mmu-miR-532-5p(1), mmu-miR-1904(1), mmu-miR-339-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACCCAGATCACAGAAATAATGATAGA
siRNA sets
TTATTTCTGTGATCTGGGT, ATTATTTCTGTGATCTGGG, CATTATTTCTGTGATCTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSUSD1_867_ORF_1
0.9637
0.129801596
0.999925826
1728
ORF sequence:
ATGATAGAAATTCATGATGTGTTGGTGTTTAATGACACCTGTGTGAGATGGCAAATAAGTCCAGAGAGAGTGAACGCCAGGATCGTGTACTTGATACGCGTTGAAAGACAGCAGCCGGATGCTGCGGAATCAGTTTATGAGGAGACAGTCAATGTGACCACAGACAGCAGAACCCCAGAAGTGTGCCTGCACCTCCAACAAGGAACCAATTACACCATAAGCATTTCTGCAGCCCCTCCCAGGCGCTCTGTGCCCGCCATCCTTGGCTTCCAGACCCCTGAAGATGATCTCTTAGAAGATGACGGACTTTTCAATATCTCAGTATTTAATGAAACTTGTTTGACGTTGAGCAGGCACTCTAGGCAAGTTGGATCAGAACAAATGTACCAAGTGGAGGTTCTGGGTCAGAGGTGGTATCTAGAGAGCTCCTACCATGCTGCTCTCTTTAACTTCACAACAAGAGACCGAGCTCCAGAAGTGTGTTTAGATCTGTACCCCGCTACTGATTACACGATAAACATCACCCTTCTGAGACCCACTGAGCCGCGCTCCGCACAAATAACCATAACAACCTCAGTGACAGCAAAACAGACCATCGCTAATATTTCGGTATATAATGATACCTGCCTGAGATGGAGCAGCCTCAAGACAGCTGATGTACTAGAGATGTATTTATTCCACATTTGGGGCCAGAGATGGTATCAGAAGGCATTTGTCCAGGAAATGGTCTTCAATACAACCAGCAGCAGCCAGGACCCTGAGATATGCCTGGACCTGCATCAAGGCACCAGCTACAACGTTAGCCTTCAGGCTCTGTCTTCGGCACTTCCCGTGGTCATCTACCTGACAACCCAGATCACAGAAATAATGATAGAAATTCATGATGTGTTGGTGTTTAATGACACCTGTGTGAGATGGCAAATAAGTCCAGAGAGAGTGAACGCCAGGATCGTGTACTTGATACGCGTTGAAAGACAGCAGCCGGATGCTGCGGAATCAGTTTATGAGGAGACAGTCAATGTGACCACAGACAGCAGAACCCCAGAAGTGTGCCTGCACCTCCAACAAGGAACCAATTACACCATAAGCATTTCTGCAGCCCCTCCCAGGCGCTCTGTGCCCGCCATCCTTGGCTTCCAGACCCCTGAAGATGATCTCTTAGAAGATGACGGACTTTTCAATATCTCAGTATTTAATGAAACTTGTTTGACGTTGAGCAGGCACTCTAGGCAAGTTGGATCAGAACAAATGTACCAAGTGGAGGTTCTGGGTCAGAGGTGGTATCTAGAGAGCTCCTACCATGCTGCTCTCTTTAACTTCACAACAAGAGACCGAGCTCCAGAAGTGTGTTTAGATCTGTACCCCGCTACTGATTACACGATAAACATCACCCTTCTGAGACCCACTGAGCCGCGCTCCGCACAAATAACCATAACAACCTCAGTGACAGCAAAACAGACCATCGCTAATATTTCGGTATATAATGATACCTGCCTGAGATGGAGCAGCCTCAAGACAGCTGATGTACTAGAGATGTATTTATTCCACATTTGGGGCCAGAGATGGTATCAGAAGGCATTTGTCCAGGAAATGGTCTTCAATACAACCAGCAGCAGCCAGGACCCTGAGATATGCCTGGACCTGCATCAAGGCACCAGCTACAACGTTAGCCTTCAGGCTCTGTCTTCGGCACTTCCCGTGGTCATCTACCTGACAACCCAGATCACA
Peptide sequence:
MIEIHDVLVFNDTCVRWQISPERVNARIVYLIRVERQQPDAAESVYEETVNVTTDSRTPEVCLHLQQGTNYTISISAAPPRRSVPAILGFQTPEDDLLEDDGLFNISVFNETCLTLSRHSRQVGSEQMYQVEVLGQRWYLESSYHAALFNFTTRDRAPEVCLDLYPATDYTINITLLRPTEPRSAQITITTSVTAKQTIANISVYNDTCLRWSSLKTADVLEMYLFHIWGQRWYQKAFVQEMVFNTTSSSQDPEICLDLHQGTSYNVSLQALSSALPVVIYLTTQITEIMIEIHDVLVFNDTCVRWQISPERVNARIVYLIRVERQQPDAAESVYEETVNVTTDSRTPEVCLHLQQGTNYTISISAAPPRRSVPAILGFQTPEDDLLEDDGLFNISVFNETCLTLSRHSRQVGSEQMYQVEVLGQRWYLESSYHAALFNFTTRDRAPEVCLDLYPATDYTINITLLRPTEPRSAQITITTSVTAKQTIANISVYNDTCLRWSSLKTADVLEMYLFHIWGQRWYQKAFVQEMVFNTTSSSQDPEICLDLHQGTSYNVSLQALSSALPVVIYLTTQIT
IRESfinder result
IRESfinder score
0.569890147
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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