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mmu_circAfg3l2_925
Basic information of circular RNA
PanCircBase ID:
mmu_circAfg3l2_925
mm39_Chr. Position ID:
chr18|67554055|67564848|-
Gene name:
Afg3l2
Transcript:
ENSMUST00000025408.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
12,11,10,9,8,7
Exon/intron offsets:
0,222,1959,4903,7995,10668
Genomic length:
10793
Exon/intron sizes in nt:
1,26,10,81,54,13,82,74,000
Flanking exon/introns:
chr18:67548679-67554055|chr18:67564848-67567224
Splice length:
925
Other database IDs:
circBase: hsa_circ_0046961, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_23146
Human Ortholog IDs:
Mature spliced Sequence:
CAATACGTCTGGTTTAATATTGGCAGTGTTGACACATTTGAGCGGAATCTGGAGACTTTGCAGCAAGAATTGGGCATAGAAGGGGAGAACCGGGTCCCTGTGGTTTATATTGCTGAGAGCGATGGCTCCTTCCTGCTGAGCATGTTGCCCACCGTACTCATTATCGCTTTTCTACTCTACACCATAAGAAGAGGGCCCGCTGGCATTGGTCGGACCGGCCGGGGAATGGGTGGACTCTTCAGCGTTGGGGAAACCACAGCCAAGGTCTTAAAGGATGAGATAGATGTGAAGTTTAAAGATGTGGCTGGCTGTGAGGAGGCCAAGCTAGAAATAATGGAATTCGTGAATTTCTTGAAAAACCCAAAGCAATATCAAGACCTAGGAGCAAAAATCCCAAAGGGTGCCATTCTCACCGGTCCCCCAGGTACTGGGAAGACGCTGCTAGCTAAGGCCACAGCTGGAGAAGCCAATGTCCCCTTTATCACTGTGAGCGGATCTGAGTTTCTGGAGATGTTTGTTGGCGTTGGTCCAGCCAGAGTCCGAGACTTATTTGCCCTTGCTCGGAAGAATGCGCCTTGCATTCTCTTCATTGATGAGATTGATGCTGTGGGAAGGAAGCGCGGCAGAGGCAACTTCGGTGGGCAGAGCGAGCAGGAGAACACACTCAACCAGCTGCTTGTGGAGATGGACGGCTTCAACACAACCACCAATGTGGTCATCCTGGCAGGCACAAATCGACCAGACATCCTGGATCCAGCTCTGTTGAGACCAGGCCGCTTTGACAGGCAGATTTTTATTGGACCCCCAGACATAAAAGGACGAGCCTCAATCTTCAAAGTTCACCTTCGACCATTGAAGCTGGACAGTGCCTTGGAAAAAGATAAATTGGCCAGAAAACTGGCGTCCTTAACTCCAGGGTTTTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGAAGCTGGACAGTGCCTT
59.82
CGGTTCTCCCCTTCTATGCC
59.89
165
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGAAGCTGGACAGTGCCTT
59.82
CCGGTTCTCCCCTTCTATGC
59.89
166
PCR template sequence:
TCAATCTTCAAAGTTCACCTTCGACCATTGAAGCTGGACAGTGCCTTGGAAAAAGATAAATTGGCCAGAAAACTGGCGTCCTTAACTCCAGGGTTTTCAGCAATACGTCTGGTTTAATATTGGCAGTGTTGACACATTTGAGCGGAATCTGGAGACTTTGCAGCAAGAATTGGGCATAGAAGGGGAGAACCGGGTCCCTG
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
CCAGGGTTTTCAGCAATACGTCTGGT
siRNA sets
ACGTATTGCTGAAAACCCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFG3L2_925_ORF_1
1.0067
0.25529509
0.968010014
801
ORF sequence:
ATGTTGCCCACCGTACTCATTATCGCTTTTCTACTCTACACCATAAGAAGAGGGCCCGCTGGCATTGGTCGGACCGGCCGGGGAATGGGTGGACTCTTCAGCGTTGGGGAAACCACAGCCAAGGTCTTAAAGGATGAGATAGATGTGAAGTTTAAAGATGTGGCTGGCTGTGAGGAGGCCAAGCTAGAAATAATGGAATTCGTGAATTTCTTGAAAAACCCAAAGCAATATCAAGACCTAGGAGCAAAAATCCCAAAGGGTGCCATTCTCACCGGTCCCCCAGGTACTGGGAAGACGCTGCTAGCTAAGGCCACAGCTGGAGAAGCCAATGTCCCCTTTATCACTGTGAGCGGATCTGAGTTTCTGGAGATGTTTGTTGGCGTTGGTCCAGCCAGAGTCCGAGACTTATTTGCCCTTGCTCGGAAGAATGCGCCTTGCATTCTCTTCATTGATGAGATTGATGCTGTGGGAAGGAAGCGCGGCAGAGGCAACTTCGGTGGGCAGAGCGAGCAGGAGAACACACTCAACCAGCTGCTTGTGGAGATGGACGGCTTCAACACAACCACCAATGTGGTCATCCTGGCAGGCACAAATCGACCAGACATCCTGGATCCAGCTCTGTTGAGACCAGGCCGCTTTGACAGGCAGATTTTTATTGGACCCCCAGACATAAAAGGACGAGCCTCAATCTTCAAAGTTCACCTTCGACCATTGAAGCTGGACAGTGCCTTGGAAAAAGATAAATTGGCCAGAAAACTGGCGTCCTTAACTCCAGGGTTTTCAGCAATACGTCTGGTTTAA
Peptide sequence:
MLPTVLIIAFLLYTIRRGPAGIGRTGRGMGGLFSVGETTAKVLKDEIDVKFKDVAGCEEAKLEIMEFVNFLKNPKQYQDLGAKIPKGAILTGPPGTGKTLLAKATAGEANVPFITVSGSEFLEMFVGVGPARVRDLFALARKNAPCILFIDEIDAVGRKRGRGNFGGQSEQENTLNQLLVEMDGFNTTTNVVILAGTNRPDILDPALLRPGRFDRQIFIGPPDIKGRASIFKVHLRPLKLDSALEKDKLARKLASLTPGFSAIRLV
IRESfinder result
IRESfinder score
0.508080102
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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