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mmu_circFgd4_1161
Basic information of circular RNA
PanCircBase ID:
mmu_circFgd4_1161
mm39_Chr. Position ID:
chr16|16253804|16295377|-
Gene name:
Fgd4
Transcript:
ENSMUST00000161861.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
14,13,12,11,10,9,8,7,6,5
Exon/intron offsets:
0,592,1069,18051,25653,26060,33763,38286,39075,41483
Genomic length:
41573
Exon/intron sizes in nt:
126,93,31,173,147,59,139,157,146,90
Flanking exon/introns:
chr16:16243771-16253804|chr16:16295377-16301953
Splice length:
1161
Other database IDs:
circBase: hsa_circ_0098417, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_8323
Human Ortholog IDs:
Mature spliced Sequence:
GAGACTAATGAACAGAAACTTCACAAAATAGCCACTGAACTTTTACTTACAGAAAGAGCTTATGTCAGCCGGCTCGACCTCCTAGATCAGGTATTTTATTGCAAACTATTAGAAGAAGCAAACCGAGGCTCATTTCCTGCAGAGATGGTGAATAAAATCTTTTCTAACATTTCATCAATAAATGCCTTCCATAGTAAATTCCTATTACCTGAGCTGGAGAAACGAATGCAAGAATGGGAAACTACACCCAGAATTGGAGATATCCTGCAAAAGTTGGCGCCATTCCTTAAGATGTATGGAGAATACGTGAAGGGATTTGATAATGCAGTGGAACTGGTTAAAACCATGACAGAGCGTGTTCCCCAGTTTAAATCAGTGACTGAAGAGATTCAGAAACAGAAGATCTGTGGAAGCTTAACGCTGCAGCATCACATGCTGGAGCCTATTCAGCGCATTCCTCGCTATGAGATGCTCCTGAAGGACTACCTGAAGAAGTTGTCTCCTGACTCCCCAGACTGGAATGATGCAAAAAAGTCACTTGAAATTATATCTACAGCAGCAAGCCATTCTAATAGTGCAATAAGAAAAATGGAGAACCTGAAGAAACTTTTAGAAATTTATGAGATGTTGGGAGAAGAAGAGGATATTGTAAATCCCTCAAATGAACTAATAAAAGAAGGACAAATCCTCAAACTAGCAGCTCGGAACACATCAGCACAAGAGCGCTACCTCTTCTTATTCAACAACATGTTGCTATATTGTGTGCCCAGATTCAGCTTGGTTGGCTCAAAATTCACAGTTCGAACCAGAGTTGGCATTGATGGAATGAAAATTGTGGAGACTCACAATGAAGAATATCCACACACTTTCCAGATATCTGGGAAAGAAAGAACCCTGGAGCTGCAGGCCAGTTCTGAACAAGACAAGGAAGAATGGATCAAGGCCCTTCAAGAAAGTATTGATGCTTTTCATCAAAGGCATGAAACTTTCAGAAATGCAATCGCAAAGGAAAATGACATTCCCCTAGAAGTTTCTACTGCTGAGCTGGGAAAACGAGCTCCAAGATGGATACGTGATAATGAAGTGACCATGTGTATGAAGTGCAAAGAGTCCTTCAATGCACTGACCAGAAGGCGGCATCACTGCCGGGCATGTGGACAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTCCTTCAATGCACTGACCA
59.58
TGATCTAGGAGGTCGAGCCG
60.54
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTTCAATGCACTGACCAGA
59.3
TGATCTAGGAGGTCGAGCCG
60.54
140
PCR template sequence:
AAGATGGATACGTGATAATGAAGTGACCATGTGTATGAAGTGCAAAGAGTCCTTCAATGCACTGACCAGAAGGCGGCATCACTGCCGGGCATGTGGACATGAGACTAATGAACAGAAACTTCACAAAATAGCCACTGAACTTTTACTTACAGAAAGAGCTTATGTCAGCCGGCTCGACCTCCTAGATCAGGTATTTTATT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-miR-32-5p(1), mmu-let-7b-5p(1), mmu-miR-150-5p(1), mmu-miR-33-5p(1), mmu-miR-152-3p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-217-5p(1), mmu-miR-203-3p(1), mmu-miR-136-5p(1), mmu-miR-98-5p(1), mmu-miR-1198-5p(1), mmu-miR-207(1), mmu-miR-335-3p(1), mmu-miR-532-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGCATGTGGACATGAGACTAATGAAC
siRNA sets
GTTCATTAGTCTCATGTCC, TTCATTAGTCTCATGTCCA, TCATTAGTCTCATGTCCAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFGD4_1161_ORF_1
0.8533
0.152600396
0.999996729
2178
ORF sequence:
ATGGTGAATAAAATCTTTTCTAACATTTCATCAATAAATGCCTTCCATAGTAAATTCCTATTACCTGAGCTGGAGAAACGAATGCAAGAATGGGAAACTACACCCAGAATTGGAGATATCCTGCAAAAGTTGGCGCCATTCCTTAAGATGTATGGAGAATACGTGAAGGGATTTGATAATGCAGTGGAACTGGTTAAAACCATGACAGAGCGTGTTCCCCAGTTTAAATCAGTGACTGAAGAGATTCAGAAACAGAAGATCTGTGGAAGCTTAACGCTGCAGCATCACATGCTGGAGCCTATTCAGCGCATTCCTCGCTATGAGATGCTCCTGAAGGACTACCTGAAGAAGTTGTCTCCTGACTCCCCAGACTGGAATGATGCAAAAAAGTCACTTGAAATTATATCTACAGCAGCAAGCCATTCTAATAGTGCAATAAGAAAAATGGAGAACCTGAAGAAACTTTTAGAAATTTATGAGATGTTGGGAGAAGAAGAGGATATTGTAAATCCCTCAAATGAACTAATAAAAGAAGGACAAATCCTCAAACTAGCAGCTCGGAACACATCAGCACAAGAGCGCTACCTCTTCTTATTCAACAACATGTTGCTATATTGTGTGCCCAGATTCAGCTTGGTTGGCTCAAAATTCACAGTTCGAACCAGAGTTGGCATTGATGGAATGAAAATTGTGGAGACTCACAATGAAGAATATCCACACACTTTCCAGATATCTGGGAAAGAAAGAACCCTGGAGCTGCAGGCCAGTTCTGAACAAGACAAGGAAGAATGGATCAAGGCCCTTCAAGAAAGTATTGATGCTTTTCATCAAAGGCATGAAACTTTCAGAAATGCAATCGCAAAGGAAAATGACATTCCCCTAGAAGTTTCTACTGCTGAGCTGGGAAAACGAGCTCCAAGATGGATACGTGATAATGAAGTGACCATGTGTATGAAGTGCAAAGAGTCCTTCAATGCACTGACCAGAAGGCGGCATCACTGCCGGGCATGTGGACATGAGACTAATGAACAGAAACTTCACAAAATAGCCACTGAACTTTTACTTACAGAAAGAGCTTATGTCAGCCGGCTCGACCTCCTAGATCAGGTATTTTATTGCAAACTATTAGAAGAAGCAAACCGAGGCTCATTTCCTGCAGAGATGGTGAATAAAATCTTTTCTAACATTTCATCAATAAATGCCTTCCATAGTAAATTCCTATTACCTGAGCTGGAGAAACGAATGCAAGAATGGGAAACTACACCCAGAATTGGAGATATCCTGCAAAAGTTGGCGCCATTCCTTAAGATGTATGGAGAATACGTGAAGGGATTTGATAATGCAGTGGAACTGGTTAAAACCATGACAGAGCGTGTTCCCCAGTTTAAATCAGTGACTGAAGAGATTCAGAAACAGAAGATCTGTGGAAGCTTAACGCTGCAGCATCACATGCTGGAGCCTATTCAGCGCATTCCTCGCTATGAGATGCTCCTGAAGGACTACCTGAAGAAGTTGTCTCCTGACTCCCCAGACTGGAATGATGCAAAAAAGTCACTTGAAATTATATCTACAGCAGCAAGCCATTCTAATAGTGCAATAAGAAAAATGGAGAACCTGAAGAAACTTTTAGAAATTTATGAGATGTTGGGAGAAGAAGAGGATATTGTAAATCCCTCAAATGAACTAATAAAAGAAGGACAAATCCTCAAACTAGCAGCTCGGAACACATCAGCACAAGAGCGCTACCTCTTCTTATTCAACAACATGTTGCTATATTGTGTGCCCAGATTCAGCTTGGTTGGCTCAAAATTCACAGTTCGAACCAGAGTTGGCATTGATGGAATGAAAATTGTGGAGACTCACAATGAAGAATATCCACACACTTTCCAGATATCTGGGAAAGAAAGAACCCTGGAGCTGCAGGCCAGTTCTGAACAAGACAAGGAAGAATGGATCAAGGCCCTTCAAGAAAGTATTGATGCTTTTCATCAAAGGCATGAAACTTTCAGAAATGCAATCGCAAAGGAAAATGACATTCCCCTAGAAGTTTCTACTGCTGAGCTGGGAAAACGAGCTCCAAGATGGATACGTGATAATGAAGTGACCATGTGTATGAAGTGCAAAGAGTCCTTCAATGCACTGACCAGAAGGCGGCATCACTGCCGGGCATGTGGACAT
Peptide sequence:
MVNKIFSNISSINAFHSKFLLPELEKRMQEWETTPRIGDILQKLAPFLKMYGEYVKGFDNAVELVKTMTERVPQFKSVTEEIQKQKICGSLTLQHHMLEPIQRIPRYEMLLKDYLKKLSPDSPDWNDAKKSLEIISTAASHSNSAIRKMENLKKLLEIYEMLGEEEDIVNPSNELIKEGQILKLAARNTSAQERYLFLFNNMLLYCVPRFSLVGSKFTVRTRVGIDGMKIVETHNEEYPHTFQISGKERTLELQASSEQDKEEWIKALQESIDAFHQRHETFRNAIAKENDIPLEVSTAELGKRAPRWIRDNEVTMCMKCKESFNALTRRRHHCRACGHETNEQKLHKIATELLLTERAYVSRLDLLDQVFYCKLLEEANRGSFPAEMVNKIFSNISSINAFHSKFLLPELEKRMQEWETTPRIGDILQKLAPFLKMYGEYVKGFDNAVELVKTMTERVPQFKSVTEEIQKQKICGSLTLQHHMLEPIQRIPRYEMLLKDYLKKLSPDSPDWNDAKKSLEIISTAASHSNSAIRKMENLKKLLEIYEMLGEEEDIVNPSNELIKEGQILKLAARNTSAQERYLFLFNNMLLYCVPRFSLVGSKFTVRTRVGIDGMKIVETHNEEYPHTFQISGKERTLELQASSEQDKEEWIKALQESIDAFHQRHETFRNAIAKENDIPLEVSTAELGKRAPRWIRDNEVTMCMKCKESFNALTRRRHHCRACGH
IRESfinder result
IRESfinder score
0.550733597
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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