top of page
mmu_circAfg3l2_1000
Basic information of circular RNA
PanCircBase ID:
mmu_circAfg3l2_1000
mm39_Chr. Position ID:
chr18|67554055|67567299|-
Gene name:
Afg3l2
Transcript:
ENSMUST00000025408.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
12,11,10,9,8,7,6
Exon/intron offsets:
0,222,1959,4903,7995,10668,13169
Genomic length:
13244
Exon/intron sizes in nt:
126,108,154,138,274,125,75
Flanking exon/introns:
chr18:67548679-67554055|chr18:67567299-67573251
Splice length:
1000
Other database IDs:
CIRCpedia: MMU_CIRCpedia_37002, circAtlas: mmu-Afg3l2_0007
circAtlas: hsa-AFG3L2_0015, CIRCpedia: HSA_CIRCpedia_162837
Human Ortholog IDs:
Mature spliced Sequence:
GTGGACAGACTAGAAGTTGTCAACAAGCGTTTTGTTCGTGTGACCTTTACACCAGGAAAAACTCCGGTTGATGGGCAATACGTCTGGTTTAATATTGGCAGTGTTGACACATTTGAGCGGAATCTGGAGACTTTGCAGCAAGAATTGGGCATAGAAGGGGAGAACCGGGTCCCTGTGGTTTATATTGCTGAGAGCGATGGCTCCTTCCTGCTGAGCATGTTGCCCACCGTACTCATTATCGCTTTTCTACTCTACACCATAAGAAGAGGGCCCGCTGGCATTGGTCGGACCGGCCGGGGAATGGGTGGACTCTTCAGCGTTGGGGAAACCACAGCCAAGGTCTTAAAGGATGAGATAGATGTGAAGTTTAAAGATGTGGCTGGCTGTGAGGAGGCCAAGCTAGAAATAATGGAATTCGTGAATTTCTTGAAAAACCCAAAGCAATATCAAGACCTAGGAGCAAAAATCCCAAAGGGTGCCATTCTCACCGGTCCCCCAGGTACTGGGAAGACGCTGCTAGCTAAGGCCACAGCTGGAGAAGCCAATGTCCCCTTTATCACTGTGAGCGGATCTGAGTTTCTGGAGATGTTTGTTGGCGTTGGTCCAGCCAGAGTCCGAGACTTATTTGCCCTTGCTCGGAAGAATGCGCCTTGCATTCTCTTCATTGATGAGATTGATGCTGTGGGAAGGAAGCGCGGCAGAGGCAACTTCGGTGGGCAGAGCGAGCAGGAGAACACACTCAACCAGCTGCTTGTGGAGATGGACGGCTTCAACACAACCACCAATGTGGTCATCCTGGCAGGCACAAATCGACCAGACATCCTGGATCCAGCTCTGTTGAGACCAGGCCGCTTTGACAGGCAGATTTTTATTGGACCCCCAGACATAAAAGGACGAGCCTCAATCTTCAAAGTTCACCTTCGACCATTGAAGCTGGACAGTGCCTTGGAAAAAGATAAATTGGCCAGAAAACTGGCGTCCTTAACTCCAGGGTTTTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGAAGCTGGACAGTGCCTT
59.82
ATTGCCCATCAACCGGAGTT
59.96
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGAAGCTGGACAGTGCCTT
59.82
TGCCCATCAACCGGAGTTTT
60.18
150
PCR template sequence:
TCAATCTTCAAAGTTCACCTTCGACCATTGAAGCTGGACAGTGCCTTGGAAAAAGATAAATTGGCCAGAAAACTGGCGTCCTTAACTCCAGGGTTTTCAGGTGGACAGACTAGAAGTTGTCAACAAGCGTTTTGTTCGTGTGACCTTTACACCAGGAAAAACTCCGGTTGATGGGCAATACGTCTGGTTTAATATTGGCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-495-3p(1), mmu-miR-129-5p(1), mmu-miR-207(1), mmu-miR-300-3p(1), mmu-miR-452-3p(1), mmu-miR-3065-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCAGGGTTTTCAGGTGGACAGACTAG
siRNA sets
TCTGTCCACCTGAAAACCC, TGTCCACCTGAAAACCCTG, CTGTCCACCTGAAAACCCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFG3L2_1000_ORF_1
0.978
0.221883237
0.973558357
855
ORF sequence:
ATGTTGCCCACCGTACTCATTATCGCTTTTCTACTCTACACCATAAGAAGAGGGCCCGCTGGCATTGGTCGGACCGGCCGGGGAATGGGTGGACTCTTCAGCGTTGGGGAAACCACAGCCAAGGTCTTAAAGGATGAGATAGATGTGAAGTTTAAAGATGTGGCTGGCTGTGAGGAGGCCAAGCTAGAAATAATGGAATTCGTGAATTTCTTGAAAAACCCAAAGCAATATCAAGACCTAGGAGCAAAAATCCCAAAGGGTGCCATTCTCACCGGTCCCCCAGGTACTGGGAAGACGCTGCTAGCTAAGGCCACAGCTGGAGAAGCCAATGTCCCCTTTATCACTGTGAGCGGATCTGAGTTTCTGGAGATGTTTGTTGGCGTTGGTCCAGCCAGAGTCCGAGACTTATTTGCCCTTGCTCGGAAGAATGCGCCTTGCATTCTCTTCATTGATGAGATTGATGCTGTGGGAAGGAAGCGCGGCAGAGGCAACTTCGGTGGGCAGAGCGAGCAGGAGAACACACTCAACCAGCTGCTTGTGGAGATGGACGGCTTCAACACAACCACCAATGTGGTCATCCTGGCAGGCACAAATCGACCAGACATCCTGGATCCAGCTCTGTTGAGACCAGGCCGCTTTGACAGGCAGATTTTTATTGGACCCCCAGACATAAAAGGACGAGCCTCAATCTTCAAAGTTCACCTTCGACCATTGAAGCTGGACAGTGCCTTGGAAAAAGATAAATTGGCCAGAAAACTGGCGTCCTTAACTCCAGGGTTTTCAGGTGGACAGACTAGAAGTTGTCAACAAGCGTTTTGTTCGTGTGACCTTTACACCAGGAAAAACTCCGGTTGA
Peptide sequence:
MLPTVLIIAFLLYTIRRGPAGIGRTGRGMGGLFSVGETTAKVLKDEIDVKFKDVAGCEEAKLEIMEFVNFLKNPKQYQDLGAKIPKGAILTGPPGTGKTLLAKATAGEANVPFITVSGSEFLEMFVGVGPARVRDLFALARKNAPCILFIDEIDAVGRKRGRGNFGGQSEQENTLNQLLVEMDGFNTTTNVVILAGTNRPDILDPALLRPGRFDRQIFIGPPDIKGRASIFKVHLRPLKLDSALEKDKLARKLASLTPGFSGGQTRSCQQAFCSCDLYTRKNSG
IRESfinder result
IRESfinder score
0.504932608
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page