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mmu_circXpo1_756
Basic information of circular RNA
PanCircBase ID:
mmu_circXpo1_756
mm39_Chr. Position ID:
chr11|23239757|23244692|+
Gene name:
Xpo1
Transcript:
ENSMUST00000020538.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
21,22,23,24,25
Exon/intron offsets:
0,1705,4014,4231,4838
Genomic length:
4935
Exon/intron sizes in nt:
195,169,135,160,97
Flanking exon/introns:
chr11:23237451-23239757|chr11:23244692-23245960
Splice length:
756
Other database IDs:
circAtlas: mmu-Xpo1_0014
circBase: hsa_circ_0120648, circAtlas: hsa-XPO1_0016, CIRCpedia: HSA_CIRCpedia_114105
Human Ortholog IDs:
Mature spliced Sequence:
GTAGCTGAAAACTTTGTTCCTCCTTTGTTGGATGCAGTTCTTATTGATTACCAGAGAAATGTACCAGCTGCTAGAGAACCAGAAGTGCTTAGTACTATGGCCATTATTGTCAACAAATTAGGTGGACATATAACAGCTGAAATACCTCAAATATTCGATGCAGTTTTTGAGTGCACATTGAATATGATAAATAAGGATTTTGAAGAGTATCCAGAACACAGAACAAACTTTTTCTTATTACTTCAAGCTGTCAATTCTCACTGTTTCCCAGCATTCCTAGCTATTCCACCTGCACAGTTCAAGCTGGTTTTGGATTCTATTATTTGGGCTTTTAAACATACTATGAGGAATGTTGCAGATACAGGCTTACAGATACTTTTTACACTTTTACAAAATGTTGCACAAGAGGAAGCTGCCGCACAGAGTTTTTATCAAACTTATTTTTGTGATATTCTTCAGCATATTTTCTCTGTTGTAACAGACACTTCACATACTGCAGGTCTAACAATGCATGCATCAATTCTTGCATATATGTTTAATTTGGTTGAAGAAGGAAAAATAAGTACACCACTAAATCCTGGAAATCCAGTTAACAACCAAATGTTTATTCAAGACTATGTGGCTAATCTCCTTAAATCTGCATTCCCTCATCTACAAGATGCTCAAGTAAAGCTCTTTGTAACAGGACTTTTCAGCTTAAATCAGGATATTCCTGCTTTCAAAGAACACCTAAGGGATTTCTTAGTTCAAATAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTCAAGTAAAGCTCTTTGT
55.73
CTGGTTCTCTAGCAGCTGGT
59.1
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTTTGTAACAGGACTTTTCAGCT
58.56
CTGGTTCTCTAGCAGCTGGT
59.1
165
PCR template sequence:
AGATGCTCAAGTAAAGCTCTTTGTAACAGGACTTTTCAGCTTAAATCAGGATATTCCTGCTTTCAAAGAACACCTAAGGGATTTCTTAGTTCAAATAAAGGTAGCTGAAAACTTTGTTCCTCCTTTGTTGGATGCAGTTCTTATTGATTACCAGAGAAATGTACCAGCTGCTAGAGAACCAGAAGTGCTTAGTACTATGG
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-217-5p(2), mmu-miR-9-5p(1), mmu-miR-33-5p(1), mmu-miR-301a-3p(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGTTCAAATAAAGGTAGCTGAAAACT
siRNA sets
TTCAGCTACCTTTATTTGA, TTTCAGCTACCTTTATTTG, TTTTCAGCTACCTTTATTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCXPO1_756_ORF_1
0.9669
-0.171717668
0.997614354
1416
ORF sequence:
ATGGCCATTATTGTCAACAAATTAGGTGGACATATAACAGCTGAAATACCTCAAATATTCGATGCAGTTTTTGAGTGCACATTGAATATGATAAATAAGGATTTTGAAGAGTATCCAGAACACAGAACAAACTTTTTCTTATTACTTCAAGCTGTCAATTCTCACTGTTTCCCAGCATTCCTAGCTATTCCACCTGCACAGTTCAAGCTGGTTTTGGATTCTATTATTTGGGCTTTTAAACATACTATGAGGAATGTTGCAGATACAGGCTTACAGATACTTTTTACACTTTTACAAAATGTTGCACAAGAGGAAGCTGCCGCACAGAGTTTTTATCAAACTTATTTTTGTGATATTCTTCAGCATATTTTCTCTGTTGTAACAGACACTTCACATACTGCAGGTCTAACAATGCATGCATCAATTCTTGCATATATGTTTAATTTGGTTGAAGAAGGAAAAATAAGTACACCACTAAATCCTGGAAATCCAGTTAACAACCAAATGTTTATTCAAGACTATGTGGCTAATCTCCTTAAATCTGCATTCCCTCATCTACAAGATGCTCAAGTAAAGCTCTTTGTAACAGGACTTTTCAGCTTAAATCAGGATATTCCTGCTTTCAAAGAACACCTAAGGGATTTCTTAGTTCAAATAAAGGTAGCTGAAAACTTTGTTCCTCCTTTGTTGGATGCAGTTCTTATTGATTACCAGAGAAATGTACCAGCTGCTAGAGAACCAGAAGTGCTTAGTACTATGGCCATTATTGTCAACAAATTAGGTGGACATATAACAGCTGAAATACCTCAAATATTCGATGCAGTTTTTGAGTGCACATTGAATATGATAAATAAGGATTTTGAAGAGTATCCAGAACACAGAACAAACTTTTTCTTATTACTTCAAGCTGTCAATTCTCACTGTTTCCCAGCATTCCTAGCTATTCCACCTGCACAGTTCAAGCTGGTTTTGGATTCTATTATTTGGGCTTTTAAACATACTATGAGGAATGTTGCAGATACAGGCTTACAGATACTTTTTACACTTTTACAAAATGTTGCACAAGAGGAAGCTGCCGCACAGAGTTTTTATCAAACTTATTTTTGTGATATTCTTCAGCATATTTTCTCTGTTGTAACAGACACTTCACATACTGCAGGTCTAACAATGCATGCATCAATTCTTGCATATATGTTTAATTTGGTTGAAGAAGGAAAAATAAGTACACCACTAAATCCTGGAAATCCAGTTAACAACCAAATGTTTATTCAAGACTATGTGGCTAATCTCCTTAAATCTGCATTCCCTCATCTACAAGATGCTCAAGTAAAGCTCTTTGTAACAGGACTTTTCAGCTTAAATCAGGATATTCCTGCTTTCAAAGAACACCTAAGGGATTTCTTAGTTCAAATAAAG
Peptide sequence:
MAIIVNKLGGHITAEIPQIFDAVFECTLNMINKDFEEYPEHRTNFFLLLQAVNSHCFPAFLAIPPAQFKLVLDSIIWAFKHTMRNVADTGLQILFTLLQNVAQEEAAAQSFYQTYFCDILQHIFSVVTDTSHTAGLTMHASILAYMFNLVEEGKISTPLNPGNPVNNQMFIQDYVANLLKSAFPHLQDAQVKLFVTGLFSLNQDIPAFKEHLRDFLVQIKVAENFVPPLLDAVLIDYQRNVPAAREPEVLSTMAIIVNKLGGHITAEIPQIFDAVFECTLNMINKDFEEYPEHRTNFFLLLQAVNSHCFPAFLAIPPAQFKLVLDSIIWAFKHTMRNVADTGLQILFTLLQNVAQEEAAAQSFYQTYFCDILQHIFSVVTDTSHTAGLTMHASILAYMFNLVEEGKISTPLNPGNPVNNQMFIQDYVANLLKSAFPHLQDAQVKLFVTGLFSLNQDIPAFKEHLRDFLVQIK
IRESfinder result
IRESfinder score
0.885370694
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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