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mmu_circArfgef1_647
Basic information of circular RNA
PanCircBase ID:
mmu_circArfgef1_647
mm39_Chr. Position ID:
chr1|10264481|10275134|-
Gene name:
Arfgef1
Transcript:
ENSMUST00000088615.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
10,9,8,7
Exon/intron offsets:
0,4586,5472,10551
Genomic length:
10653
Exon/intron sizes in nt:
2,35,13,41,76,102
Flanking exon/introns:
chr1:10259903-10264481|chr1:10275134-10279649
Splice length:
647
Other database IDs:
circAtlas: mmu-Arfgef1_0007
circAtlas: hsa-ARFGEF1_0003, CIRCpedia: HSA_CIRCpedia_69425
Human Ortholog IDs:
Mature spliced Sequence:
CATTATCTAAAAATGATATCTTGTATGATGGAGACTATGAAGAAAAGCCACTTGATATTGTCCAGAGCATTGTAGAAGAAATGGTGAACATCATTGTTGGAGACATGGGAGAAGGGATGGCTATCAGTGCAAGTACAGAAGGCAACACTGGAACTGTAGAAGATGGTAGTGACAGTGAAAACATCCAAGCAAATGGAATCCCAGGAACACCCATTTCTGTTGCATATACACCATCGTTACCTGACGACAGGTTATCTGTCTCCTCCAATGATACTCAGGAATCTGGAAATTCTTCAGGACCTTCACCTGGTGCTAAGTTTTCCCACATTTTACAAAAGGATGCCTTTCTAGTGTTCAGGTCATTGTGTAAGCTGTCAATGAAACCACTGTCAGATGGACCACCAGATCCAAAGTCTCATGAGTTACGGTCCAAGATTCTTTCATTGCAGTTGCTTCTGTCCATTCTGCAGAATGCAGGACCTGTTTTCAGGACAAATGAGATGTTTATTAATGCTATCAAGCAGTATCTATGTGTTGCACTCTCAAAAAACGGAGTCTCATCTGTTCCAGAGGTTTTTGAGCTTTCTCTTTCCATATTTCTTACTTTGTTGTCAAACTTCAAGACACATCTGAAGATGCAAATTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACGGAGTCTCATCTGTTCCAG
59.18
GCTCTGGACAATATCAAGTGGC
59.38
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACGGAGTCTCATCTGTTCCA
58.08
GCTCTGGACAATATCAAGTGGC
59.38
166
PCR template sequence:
AAACGGAGTCTCATCTGTTCCAGAGGTTTTTGAGCTTTCTCTTTCCATATTTCTTACTTTGTTGTCAAACTTCAAGACACATCTGAAGATGCAAATTGAGCATTATCTAAAAATGATATCTTGTATGATGGAGACTATGAAGAAAAGCCACTTGATATTGTCCAGAGCATTGTAGAAGAAATGGTGAACATCATTGTTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-140-5p(2), mmu-miR-199a-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-139-5p(1), mmu-miR-136-5p(1), mmu-miR-363-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-130b-3p(1), mmu-miR-301a-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-207(1), mmu-miR-3065-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GATGCAAATTGAGCATTATCTAAAAA
siRNA sets
TTTTTAGATAATGCTCAAT, TTTTAGATAATGCTCAATT, TTTAGATAATGCTCAATTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARFGEF1_647_ORF_1
0.8723
-0.019356714
0.711473035
642
ORF sequence:
ATGGTGAACATCATTGTTGGAGACATGGGAGAAGGGATGGCTATCAGTGCAAGTACAGAAGGCAACACTGGAACTGTAGAAGATGGTAGTGACAGTGAAAACATCCAAGCAAATGGAATCCCAGGAACACCCATTTCTGTTGCATATACACCATCGTTACCTGACGACAGGTTATCTGTCTCCTCCAATGATACTCAGGAATCTGGAAATTCTTCAGGACCTTCACCTGGTGCTAAGTTTTCCCACATTTTACAAAAGGATGCCTTTCTAGTGTTCAGGTCATTGTGTAAGCTGTCAATGAAACCACTGTCAGATGGACCACCAGATCCAAAGTCTCATGAGTTACGGTCCAAGATTCTTTCATTGCAGTTGCTTCTGTCCATTCTGCAGAATGCAGGACCTGTTTTCAGGACAAATGAGATGTTTATTAATGCTATCAAGCAGTATCTATGTGTTGCACTCTCAAAAAACGGAGTCTCATCTGTTCCAGAGGTTTTTGAGCTTTCTCTTTCCATATTTCTTACTTTGTTGTCAAACTTCAAGACACATCTGAAGATGCAAATTGAGCATTATCTAAAAATGATATCTTGTATGATGGAGACTATGAAGAAAAGCCACTTGATATTGTCCAGAGCATTGTAG
Peptide sequence:
MVNIIVGDMGEGMAISASTEGNTGTVEDGSDSENIQANGIPGTPISVAYTPSLPDDRLSVSSNDTQESGNSSGPSPGAKFSHILQKDAFLVFRSLCKLSMKPLSDGPPDPKSHELRSKILSLQLLLSILQNAGPVFRTNEMFINAIKQYLCVALSKNGVSSVPEVFELSLSIFLTLLSNFKTHLKMQIEHYLKMISCMMETMKKSHLILSRAL
IRESfinder result
IRESfinder score
0.74186691
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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