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mmu_circFgd4_1430
Basic information of circular RNA
PanCircBase ID:
mmu_circFgd4_1430
mm39_Chr. Position ID:
chr16|16279457|16308470|-
Gene name:
Fgd4
Transcript:
ENSMUST00000161861.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
10,9,8,7,6,5,4,3
Exon/intron offsets:
0,407,8110,12633,13422,15830,22496,28829
Genomic length:
29013
Exon/intron sizes in nt:
1,47,59,13,91,57,14,69,00,00,000
Flanking exon/introns:
chr16:16272028-16279457|chr16:16308470-16321960
Splice length:
1430
Other database IDs:
CIRCpedia: MMU_CIRCpedia_11472, circAtlas: mmu-Fgd4_0004
circBase: hsa_circ_0025842, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_8315
Human Ortholog IDs:
Mature spliced Sequence:
TGCCTCCAAAACCATTATATCTGCAGAATTCACCTTCATCCCATATTCCCCAAGTCCCCAGGCATAAAGCTTTACCTAGTGCAAAGCCAAGGATGGAGGAGTCTAATCCGGCCCCTACTTCTTGTACCTCAAAAGGGAAGCATAGTAAGGTATCGGATCTCATCAGCCACTTTGAAGGAGGCAGTGTTTTGTCAAGTTACATTGATTTGCAGAAAGATTCTACTATGAACCTCAATATTCCTCAAACTCTAGGACAGCCTGGGTTAACCTCCTCACCTCCACGAAAATTTCTGCCCCAGCACTCTCCACAGAAGCAGGAAAACGACCCAGATCAGACTCAGGGGCAACATGGTTGTTTGGCCAATGGTGTAGTGGCTGCACAAAACCAGATGGAATGTGAAGATGAGAAGGAGACTACTCTTAGCCCAGAGATGGCTATTCAGACTGCTGCCGCCTCTCCTGATACACATGTGCTGAATGGAGAAAGAAATGAAACCATCACAGATTCTGCATCATCCATAGCCAATAGTCATGATGAAAATGCTTCTGACAGCAGCTGCAGGACTCCAGGGACGGACTTAGGGCTTCCCTCAAAAGAAGGGGAGCCAGGGATGGACGCTGAGCTCCAAGAGAGGGAAAATGGGGTGAACACCATGGGATTGGATACGTTGGACCAGCACCATGAAGTGAAGGAGACTAATGAACAGAAACTTCACAAAATAGCCACTGAACTTTTACTTACAGAAAGAGCTTATGTCAGCCGGCTCGACCTCCTAGATCAGGTATTTTATTGCAAACTATTAGAAGAAGCAAACCGAGGCTCATTTCCTGCAGAGATGGTGAATAAAATCTTTTCTAACATTTCATCAATAAATGCCTTCCATAGTAAATTCCTATTACCTGAGCTGGAGAAACGAATGCAAGAATGGGAAACTACACCCAGAATTGGAGATATCCTGCAAAAGTTGGCGCCATTCCTTAAGATGTATGGAGAATACGTGAAGGGATTTGATAATGCAGTGGAACTGGTTAAAACCATGACAGAGCGTGTTCCCCAGTTTAAATCAGTGACTGAAGAGATTCAGAAACAGAAGATCTGTGGAAGCTTAACGCTGCAGCATCACATGCTGGAGCCTATTCAGCGCATTCCTCGCTATGAGATGCTCCTGAAGGACTACCTGAAGAAGTTGTCTCCTGACTCCCCAGACTGGAATGATGCAAAAAAGTCACTTGAAATTATATCTACAGCAGCAAGCCATTCTAATAGTGCAATAAGAAAAATGGAGAACCTGAAGAAACTTTTAGAAATTTATGAGATGTTGGGAGAAGAAGAGGATATTGTAAATCCCTCAAATGAACTAATAAAAGAAGGACAAATCCTCAAACTAGCAGCTCGGAACACATCAGCACAAGAGCGCTACCTCTTCTTA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCAGCTCGGAACACATCAG
60.39
TCCATCCTTGGCTTTGCACT
59.89
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTCAAACTAGCAGCTCGGA
59.47
TCCATCCTTGGCTTTGCACT
59.89
149
PCR template sequence:
AGAGGATATTGTAAATCCCTCAAATGAACTAATAAAAGAAGGACAAATCCTCAAACTAGCAGCTCGGAACACATCAGCACAAGAGCGCTACCTCTTCTTATGCCTCCAAAACCATTATATCTGCAGAATTCACCTTCATCCCATATTCCCCAAGTCCCCAGGCATAAAGCTTTACCTAGTGCAAAGCCAAGGATGGAGGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
18
Interacting miRNAs (#binding sites)
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-335-3p(1), mmu-miR-1904(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTACCTCTTCTTATGCCTCCAAAACC
siRNA sets
TTTTGGAGGCATAAGAAGA, TTGGAGGCATAAGAAGAGG, GTTTTGGAGGCATAAGAAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFGD4_1430_ORF_1
0.917
0.112194266
0.999712738
1566
ORF sequence:
ATGGAGGAGTCTAATCCGGCCCCTACTTCTTGTACCTCAAAAGGGAAGCATAGTAAGGTATCGGATCTCATCAGCCACTTTGAAGGAGGCAGTGTTTTGTCAAGTTACATTGATTTGCAGAAAGATTCTACTATGAACCTCAATATTCCTCAAACTCTAGGACAGCCTGGGTTAACCTCCTCACCTCCACGAAAATTTCTGCCCCAGCACTCTCCACAGAAGCAGGAAAACGACCCAGATCAGACTCAGGGGCAACATGGTTGTTTGGCCAATGGTGTAGTGGCTGCACAAAACCAGATGGAATGTGAAGATGAGAAGGAGACTACTCTTAGCCCAGAGATGGCTATTCAGACTGCTGCCGCCTCTCCTGATACACATGTGCTGAATGGAGAAAGAAATGAAACCATCACAGATTCTGCATCATCCATAGCCAATAGTCATGATGAAAATGCTTCTGACAGCAGCTGCAGGACTCCAGGGACGGACTTAGGGCTTCCCTCAAAAGAAGGGGAGCCAGGGATGGACGCTGAGCTCCAAGAGAGGGAAAATGGGGTGAACACCATGGGATTGGATACGTTGGACCAGCACCATGAAGTGAAGGAGACTAATGAACAGAAACTTCACAAAATAGCCACTGAACTTTTACTTACAGAAAGAGCTTATGTCAGCCGGCTCGACCTCCTAGATCAGGTATTTTATTGCAAACTATTAGAAGAAGCAAACCGAGGCTCATTTCCTGCAGAGATGGTGAATAAAATCTTTTCTAACATTTCATCAATAAATGCCTTCCATAGTAAATTCCTATTACCTGAGCTGGAGAAACGAATGCAAGAATGGGAAACTACACCCAGAATTGGAGATATCCTGCAAAAGTTGGCGCCATTCCTTAAGATGTATGGAGAATACGTGAAGGGATTTGATAATGCAGTGGAACTGGTTAAAACCATGACAGAGCGTGTTCCCCAGTTTAAATCAGTGACTGAAGAGATTCAGAAACAGAAGATCTGTGGAAGCTTAACGCTGCAGCATCACATGCTGGAGCCTATTCAGCGCATTCCTCGCTATGAGATGCTCCTGAAGGACTACCTGAAGAAGTTGTCTCCTGACTCCCCAGACTGGAATGATGCAAAAAAGTCACTTGAAATTATATCTACAGCAGCAAGCCATTCTAATAGTGCAATAAGAAAAATGGAGAACCTGAAGAAACTTTTAGAAATTTATGAGATGTTGGGAGAAGAAGAGGATATTGTAAATCCCTCAAATGAACTAATAAAAGAAGGACAAATCCTCAAACTAGCAGCTCGGAACACATCAGCACAAGAGCGCTACCTCTTCTTATGCCTCCAAAACCATTATATCTGCAGAATTCACCTTCATCCCATATTCCCCAAGTCCCCAGGCATAAAGCTTTACCTAGTGCAAAGCCAAGGATGGAGGAGTCTAATCCGGCCCCTACTTCTTGTACCTCAAAAGGGAAGCATAGTAAGGTATCGGATCTCATCAGCCACTTTGAAGGAGGCAGTGTTTTGTCAAGTTACATTGATTTGCAGAAAGATTCTACTATGA
Peptide sequence:
MEESNPAPTSCTSKGKHSKVSDLISHFEGGSVLSSYIDLQKDSTMNLNIPQTLGQPGLTSSPPRKFLPQHSPQKQENDPDQTQGQHGCLANGVVAAQNQMECEDEKETTLSPEMAIQTAAASPDTHVLNGERNETITDSASSIANSHDENASDSSCRTPGTDLGLPSKEGEPGMDAELQERENGVNTMGLDTLDQHHEVKETNEQKLHKIATELLLTERAYVSRLDLLDQVFYCKLLEEANRGSFPAEMVNKIFSNISSINAFHSKFLLPELEKRMQEWETTPRIGDILQKLAPFLKMYGEYVKGFDNAVELVKTMTERVPQFKSVTEEIQKQKICGSLTLQHHMLEPIQRIPRYEMLLKDYLKKLSPDSPDWNDAKKSLEIISTAASHSNSAIRKMENLKKLLEIYEMLGEEEDIVNPSNELIKEGQILKLAARNTSAQERYLFLCLQNHYICRIHLHPIFPKSPGIKLYLVQSQGWRSLIRPLLLVPQKGSIVRYRISSATLKEAVFCQVTLICRKILL
IRESfinder result
IRESfinder score
0.537333178
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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