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mmu_circFgd4_502
Basic information of circular RNA
PanCircBase ID:
mmu_circFgd4_502
mm39_Chr. Position ID:
chr16|16279457|16292247|-
Gene name:
Fgd4
Transcript:
ENSMUST00000161861.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
10,9,8,7
Exon/intron offsets:
0,407,8110,12633
Genomic length:
12790
Exon/intron sizes in nt:
14,75,91,39,157
Flanking exon/introns:
chr16:16272028-16279457|chr16:16292247-16292879
Splice length:
502
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_149862
Human Ortholog IDs:
Mature spliced Sequence:
GGAAACTACACCCAGAATTGGAGATATCCTGCAAAAGTTGGCGCCATTCCTTAAGATGTATGGAGAATACGTGAAGGGATTTGATAATGCAGTGGAACTGGTTAAAACCATGACAGAGCGTGTTCCCCAGTTTAAATCAGTGACTGAAGAGATTCAGAAACAGAAGATCTGTGGAAGCTTAACGCTGCAGCATCACATGCTGGAGCCTATTCAGCGCATTCCTCGCTATGAGATGCTCCTGAAGGACTACCTGAAGAAGTTGTCTCCTGACTCCCCAGACTGGAATGATGCAAAAAAGTCACTTGAAATTATATCTACAGCAGCAAGCCATTCTAATAGTGCAATAAGAAAAATGGAGAACCTGAAGAAACTTTTAGAAATTTATGAGATGTTGGGAGAAGAAGAGGATATTGTAAATCCCTCAAATGAACTAATAAAAGAAGGACAAATCCTCAAACTAGCAGCTCGGAACACATCAGCACAAGAGCGCTACCTCTTCTTA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTCAAACTAGCAGCTCGGA
59.47
TGCATTATCAAATCCCTTCACGT
58.73
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTCAAACTAGCAGCTCGG
59.47
TGCATTATCAAATCCCTTCACGT
58.73
144
PCR template sequence:
AGAGGATATTGTAAATCCCTCAAATGAACTAATAAAAGAAGGACAAATCCTCAAACTAGCAGCTCGGAACACATCAGCACAAGAGCGCTACCTCTTCTTAGGAAACTACACCCAGAATTGGAGATATCCTGCAAAAGTTGGCGCCATTCCTTAAGATGTATGGAGAATACGTGAAGGGATTTGATAATGCAGTGGAACTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-32-5p(1), mmu-let-7b-5p(1), mmu-miR-150-5p(1), mmu-miR-217-5p(1), mmu-miR-136-5p(1), mmu-miR-98-5p(1), mmu-miR-1198-5p(1), mmu-miR-207(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTACCTCTTCTTAGGAAACTACACCC
siRNA sets
TAGTTTCCTAAGAAGAGGT, GTAGTTTCCTAAGAAGAGG, TGTAGTTTCCTAAGAAGAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFGD4_502_ORF_1
0.9046
0.199863235
0.700184036
501
ORF sequence:
ATGTATGGAGAATACGTGAAGGGATTTGATAATGCAGTGGAACTGGTTAAAACCATGACAGAGCGTGTTCCCCAGTTTAAATCAGTGACTGAAGAGATTCAGAAACAGAAGATCTGTGGAAGCTTAACGCTGCAGCATCACATGCTGGAGCCTATTCAGCGCATTCCTCGCTATGAGATGCTCCTGAAGGACTACCTGAAGAAGTTGTCTCCTGACTCCCCAGACTGGAATGATGCAAAAAAGTCACTTGAAATTATATCTACAGCAGCAAGCCATTCTAATAGTGCAATAAGAAAAATGGAGAACCTGAAGAAACTTTTAGAAATTTATGAGATGTTGGGAGAAGAAGAGGATATTGTAAATCCCTCAAATGAACTAATAAAAGAAGGACAAATCCTCAAACTAGCAGCTCGGAACACATCAGCACAAGAGCGCTACCTCTTCTTAGGAAACTACACCCAGAATTGGAGATATCCTGCAAAAGTTGGCGCCATTCCTTAA
Peptide sequence:
MYGEYVKGFDNAVELVKTMTERVPQFKSVTEEIQKQKICGSLTLQHHMLEPIQRIPRYEMLLKDYLKKLSPDSPDWNDAKKSLEIISTAASHSNSAIRKMENLKKLLEIYEMLGEEEDIVNPSNELIKEGQILKLAARNTSAQERYLFLGNYTQNWRYPAKVGAIP
IRESfinder result
IRESfinder score
0.529060815
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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