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mmu_circFgd4_1723
Basic information of circular RNA
PanCircBase ID:
mmu_circFgd4_1723
mm39_Chr. Position ID:
chr16|16271855|16322080|-
Gene name:
Fgd4
Transcript:
ENSMUST00000161861.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
11,10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,7602,8009,15712,20235,21024,23432,30098,36431,50105
Genomic length:
50225
Exon/intron sizes in nt:
173,147,59,139,157,146,90,508,184,120
Flanking exon/introns:
chr16:16254904-16271855|chr16:16322080-16377900
Splice length:
1723
Other database IDs:
CIRCpedia: MMU_CIRCpedia_36711, circAtlas: mmu-Fgd4_0015
CIRCpedia: HSA_CIRCpedia_353366
Human Ortholog IDs:
Mature spliced Sequence:
GCATCAATACTTGTGCAAAGGTTACTCCACCTTGTACGACAAGCAACACAACCACAGAAGCTCAGGGAATAAATGGGAGGACACCAGCAAAACGCTCCACTGCAAGTGCAAAGCCACAAGTGCCTCCAAAACCATTATATCTGCAGAATTCACCTTCATCCCATATTCCCCAAGTCCCCAGGCATAAAGCTTTACCTAGTGCAAAGCCAAGGATGGAGGAGTCTAATCCGGCCCCTACTTCTTGTACCTCAAAAGGGAAGCATAGTAAGGTATCGGATCTCATCAGCCACTTTGAAGGAGGCAGTGTTTTGTCAAGTTACATTGATTTGCAGAAAGATTCTACTATGAACCTCAATATTCCTCAAACTCTAGGACAGCCTGGGTTAACCTCCTCACCTCCACGAAAATTTCTGCCCCAGCACTCTCCACAGAAGCAGGAAAACGACCCAGATCAGACTCAGGGGCAACATGGTTGTTTGGCCAATGGTGTAGTGGCTGCACAAAACCAGATGGAATGTGAAGATGAGAAGGAGACTACTCTTAGCCCAGAGATGGCTATTCAGACTGCTGCCGCCTCTCCTGATACACATGTGCTGAATGGAGAAAGAAATGAAACCATCACAGATTCTGCATCATCCATAGCCAATAGTCATGATGAAAATGCTTCTGACAGCAGCTGCAGGACTCCAGGGACGGACTTAGGGCTTCCCTCAAAAGAAGGGGAGCCAGGGATGGACGCTGAGCTCCAAGAGAGGGAAAATGGGGTGAACACCATGGGATTGGATACGTTGGACCAGCACCATGAAGTGAAGGAGACTAATGAACAGAAACTTCACAAAATAGCCACTGAACTTTTACTTACAGAAAGAGCTTATGTCAGCCGGCTCGACCTCCTAGATCAGGTATTTTATTGCAAACTATTAGAAGAAGCAAACCGAGGCTCATTTCCTGCAGAGATGGTGAATAAAATCTTTTCTAACATTTCATCAATAAATGCCTTCCATAGTAAATTCCTATTACCTGAGCTGGAGAAACGAATGCAAGAATGGGAAACTACACCCAGAATTGGAGATATCCTGCAAAAGTTGGCGCCATTCCTTAAGATGTATGGAGAATACGTGAAGGGATTTGATAATGCAGTGGAACTGGTTAAAACCATGACAGAGCGTGTTCCCCAGTTTAAATCAGTGACTGAAGAGATTCAGAAACAGAAGATCTGTGGAAGCTTAACGCTGCAGCATCACATGCTGGAGCCTATTCAGCGCATTCCTCGCTATGAGATGCTCCTGAAGGACTACCTGAAGAAGTTGTCTCCTGACTCCCCAGACTGGAATGATGCAAAAAAGTCACTTGAAATTATATCTACAGCAGCAAGCCATTCTAATAGTGCAATAAGAAAAATGGAGAACCTGAAGAAACTTTTAGAAATTTATGAGATGTTGGGAGAAGAAGAGGATATTGTAAATCCCTCAAATGAACTAATAAAAGAAGGACAAATCCTCAAACTAGCAGCTCGGAACACATCAGCACAAGAGCGCTACCTCTTCTTATTCAACAACATGTTGCTATATTGTGTGCCCAGATTCAGCTTGGTTGGCTCAAAATTCACAGTTCGAACCAGAGTTGGCATTGATGGAATGAAAATTGTGGAGACTCACAATGAAGAATATCCACACACTTTCCAGATATCTGGGAAAGAAAGAACCCTGGAGCTGCAGGCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGGAGACTCACAATGAAGA
56.6
CCCTGAGCTTCTGTGGTTGT
59.89
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGGAGACTCACAATGAAGAA
57.31
CCCTGAGCTTCTGTGGTTGT
59.89
145
PCR template sequence:
TTGGCATTGATGGAATGAAAATTGTGGAGACTCACAATGAAGAATATCCACACACTTTCCAGATATCTGGGAAAGAAAGAACCCTGGAGCTGCAGGCCAGGCATCAATACTTGTGCAAAGGTTACTCCACCTTGTACGACAAGCAACACAACCACAGAAGCTCAGGGAATAAATGGGAGGACACCAGCAAAACGCTCCAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
19
Interacting miRNAs (#binding sites)
mmu-miR-335-3p(2), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-32-5p(1), mmu-let-7b-5p(1), mmu-miR-150-5p(1), mmu-miR-217-5p(1), mmu-miR-203-3p(1), mmu-miR-23a-3p(1), mmu-miR-149-5p(1), mmu-miR-136-5p(1), mmu-miR-125b-1-3p(1), mmu-miR-511-3p(1), mmu-miR-98-5p(1), mmu-miR-1198-5p(1), mmu-miR-207(1), mmu-miR-670-5p(1), mmu-miR-1904(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGCTGCAGGCCAGGCATCAATACTTG
siRNA sets
AAGTATTGATGCCTGGCCT, GTATTGATGCCTGGCCTGC, ATTGATGCCTGGCCTGCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFGD4_1723_ORF_1
0.8633
0.131410757
0.999938733
1785
ORF sequence:
ATGAAGAATATCCACACACTTTCCAGATATCTGGGAAAGAAAGAACCCTGGAGCTGCAGGCCAGGCATCAATACTTGTGCAAAGGTTACTCCACCTTGTACGACAAGCAACACAACCACAGAAGCTCAGGGAATAAATGGGAGGACACCAGCAAAACGCTCCACTGCAAGTGCAAAGCCACAAGTGCCTCCAAAACCATTATATCTGCAGAATTCACCTTCATCCCATATTCCCCAAGTCCCCAGGCATAAAGCTTTACCTAGTGCAAAGCCAAGGATGGAGGAGTCTAATCCGGCCCCTACTTCTTGTACCTCAAAAGGGAAGCATAGTAAGGTATCGGATCTCATCAGCCACTTTGAAGGAGGCAGTGTTTTGTCAAGTTACATTGATTTGCAGAAAGATTCTACTATGAACCTCAATATTCCTCAAACTCTAGGACAGCCTGGGTTAACCTCCTCACCTCCACGAAAATTTCTGCCCCAGCACTCTCCACAGAAGCAGGAAAACGACCCAGATCAGACTCAGGGGCAACATGGTTGTTTGGCCAATGGTGTAGTGGCTGCACAAAACCAGATGGAATGTGAAGATGAGAAGGAGACTACTCTTAGCCCAGAGATGGCTATTCAGACTGCTGCCGCCTCTCCTGATACACATGTGCTGAATGGAGAAAGAAATGAAACCATCACAGATTCTGCATCATCCATAGCCAATAGTCATGATGAAAATGCTTCTGACAGCAGCTGCAGGACTCCAGGGACGGACTTAGGGCTTCCCTCAAAAGAAGGGGAGCCAGGGATGGACGCTGAGCTCCAAGAGAGGGAAAATGGGGTGAACACCATGGGATTGGATACGTTGGACCAGCACCATGAAGTGAAGGAGACTAATGAACAGAAACTTCACAAAATAGCCACTGAACTTTTACTTACAGAAAGAGCTTATGTCAGCCGGCTCGACCTCCTAGATCAGGTATTTTATTGCAAACTATTAGAAGAAGCAAACCGAGGCTCATTTCCTGCAGAGATGGTGAATAAAATCTTTTCTAACATTTCATCAATAAATGCCTTCCATAGTAAATTCCTATTACCTGAGCTGGAGAAACGAATGCAAGAATGGGAAACTACACCCAGAATTGGAGATATCCTGCAAAAGTTGGCGCCATTCCTTAAGATGTATGGAGAATACGTGAAGGGATTTGATAATGCAGTGGAACTGGTTAAAACCATGACAGAGCGTGTTCCCCAGTTTAAATCAGTGACTGAAGAGATTCAGAAACAGAAGATCTGTGGAAGCTTAACGCTGCAGCATCACATGCTGGAGCCTATTCAGCGCATTCCTCGCTATGAGATGCTCCTGAAGGACTACCTGAAGAAGTTGTCTCCTGACTCCCCAGACTGGAATGATGCAAAAAAGTCACTTGAAATTATATCTACAGCAGCAAGCCATTCTAATAGTGCAATAAGAAAAATGGAGAACCTGAAGAAACTTTTAGAAATTTATGAGATGTTGGGAGAAGAAGAGGATATTGTAAATCCCTCAAATGAACTAATAAAAGAAGGACAAATCCTCAAACTAGCAGCTCGGAACACATCAGCACAAGAGCGCTACCTCTTCTTATTCAACAACATGTTGCTATATTGTGTGCCCAGATTCAGCTTGGTTGGCTCAAAATTCACAGTTCGAACCAGAGTTGGCATTGATGGAATGAAAATTGTGGAGACTCACAATGAAGAATATCCACACACTTTCCAGATATCTGGGAAAGAAAGAACCCTGGAGCTGCAGGCC
Peptide sequence:
MKNIHTLSRYLGKKEPWSCRPGINTCAKVTPPCTTSNTTTEAQGINGRTPAKRSTASAKPQVPPKPLYLQNSPSSHIPQVPRHKALPSAKPRMEESNPAPTSCTSKGKHSKVSDLISHFEGGSVLSSYIDLQKDSTMNLNIPQTLGQPGLTSSPPRKFLPQHSPQKQENDPDQTQGQHGCLANGVVAAQNQMECEDEKETTLSPEMAIQTAAASPDTHVLNGERNETITDSASSIANSHDENASDSSCRTPGTDLGLPSKEGEPGMDAELQERENGVNTMGLDTLDQHHEVKETNEQKLHKIATELLLTERAYVSRLDLLDQVFYCKLLEEANRGSFPAEMVNKIFSNISSINAFHSKFLLPELEKRMQEWETTPRIGDILQKLAPFLKMYGEYVKGFDNAVELVKTMTERVPQFKSVTEEIQKQKICGSLTLQHHMLEPIQRIPRYEMLLKDYLKKLSPDSPDWNDAKKSLEIISTAASHSNSAIRKMENLKKLLEIYEMLGEEEDIVNPSNELIKEGQILKLAARNTSAQERYLFLFNNMLLYCVPRFSLVGSKFTVRTRVGIDGMKIVETHNEEYPHTFQISGKERTLELQA
IRESfinder result
IRESfinder score
0.534266873
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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