top of page
mmu_circAff4_632
Basic information of circular RNA
PanCircBase ID:
mmu_circAff4_632
mm39_Chr. Position ID:
chr11|53298706|53302883|+
Gene name:
Aff4
Transcript:
ENSMUST00000060945.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
15,16,17,18,19,20
Exon/intron offsets:
0,177,519,1388,3036,3956
Genomic length:
4177
Exon/intron sizes in nt:
6,41,37,72,94,44,221
Flanking exon/introns:
chr11:53297502-53298706|chr11:53302883-53306214
Splice length:
632
Other database IDs:
circBase: hsa_circ_0007806, circAtlas: hsa-AFF4_0030, CIRCpedia: HSA_CIRCpedia_50150
Human Ortholog IDs:
Mature spliced Sequence:
AAATTATTCAGCAGACCATTATTTACAAGAAGCAAAAAAACTCAAACACAATGCAGATGCTTTGTCTGACAGGTTTGAGAAAGCCGTGTACTACCTTGATGCTGTAGTGTCTTTCATTGAGTGTGGGAATGCATTAGAGAAGAACGCTCAGGAATCCAAGTCCCCATTCCCTATGTACTCAGACACGGTGGAGCTCATTAAGTACACTATGAAACTAAAGAATTATTTGGCACCAGATGCTACAGCTGCAGACAAGAGACTCACAGTACTTTGCCTGAGATGCCAGTCATTATTGTACCTGAGGCTGTTCAAACTGAAGAAGGAGAACGCTCTCAAGTACTCCAAGACGCTAACTGAGCACCTGAAGAATTCTTACAGTAATTCTCAAGCACCTTCACCCGGCTTGGGGAGCAAAGCTGTTGGGATGCCCTCCCCTGTTTCTCCAAAACTGTCACCAGGCAATTCTGGAAGTTACTCTTCTGGGGGAAGTAGTGCTTCAGCAAGTGGTTCTTCAGTGACCATTCCACAGAAAATCCACCAGATGGCAGCAAGCTATGTCCAGGTTACATCTAACTTCCTCTATGCCACAGAAATTTGGGACCAAGCTGAACAGCTTTCCAAAGAACAAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGGCAGCAAGCTATGTCCA
59.74
ACGGCTTTCTCAAACCTGTCA
60.13
178
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATGGCAGCAAGCTATGTCCA
59.74
CACGGCTTTCTCAAACCTGTC
59.74
179
PCR template sequence:
ATCCACCAGATGGCAGCAAGCTATGTCCAGGTTACATCTAACTTCCTCTATGCCACAGAAATTTGGGACCAAGCTGAACAGCTTTCCAAAGAACAAAAAGAAATTATTCAGCAGACCATTATTTACAAGAAGCAAAAAAACTCAAACACAATGCAGATGCTTTGTCTGACAGGTTTGAGAAAGCCGTGTACTACCTTGAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-33-5p(1), mmu-miR-324-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-188-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AAAGAACAAAAAGAAATTATTCAGCA
siRNA sets
AATAATTTCTTTTTGTTCT, TAATTTCTTTTTGTTCTTT, ATAATTTCTTTTTGTTCTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFF4_632_ORF_1
0.8087
0.089097642
0.66533547
567
ORF sequence:
ATGTACTCAGACACGGTGGAGCTCATTAAGTACACTATGAAACTAAAGAATTATTTGGCACCAGATGCTACAGCTGCAGACAAGAGACTCACAGTACTTTGCCTGAGATGCCAGTCATTATTGTACCTGAGGCTGTTCAAACTGAAGAAGGAGAACGCTCTCAAGTACTCCAAGACGCTAACTGAGCACCTGAAGAATTCTTACAGTAATTCTCAAGCACCTTCACCCGGCTTGGGGAGCAAAGCTGTTGGGATGCCCTCCCCTGTTTCTCCAAAACTGTCACCAGGCAATTCTGGAAGTTACTCTTCTGGGGGAAGTAGTGCTTCAGCAAGTGGTTCTTCAGTGACCATTCCACAGAAAATCCACCAGATGGCAGCAAGCTATGTCCAGGTTACATCTAACTTCCTCTATGCCACAGAAATTTGGGACCAAGCTGAACAGCTTTCCAAAGAACAAAAAGAAATTATTCAGCAGACCATTATTTACAAGAAGCAAAAAAACTCAAACACAATGCAGATGCTTTGTCTGACAGGTTTGAGAAAGCCGTGTACTACCTTGATGCTGTAG
Peptide sequence:
MYSDTVELIKYTMKLKNYLAPDATAADKRLTVLCLRCQSLLYLRLFKLKKENALKYSKTLTEHLKNSYSNSQAPSPGLGSKAVGMPSPVSPKLSPGNSGSYSSGGSSASASGSSVTIPQKIHQMAASYVQVTSNFLYATEIWDQAEQLSKEQKEIIQQTIIYKKQKNSNTMQMLCLTGLRKPCTTLML
IRESfinder result
IRESfinder score
0.565020006
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page