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mmu_circAff1_1035
Basic information of circular RNA
PanCircBase ID:
mmu_circAff1_1035
mm39_Chr. Position ID:
chr5|103863215|103932379|+
Gene name:
Aff1
Transcript:
ENSMUST00000126335.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
2,3,4
Exon/intron offsets:
0,67774,68306
Genomic length:
69164
Exon/intron sizes in nt:
5,61,21,858
Flanking exon/introns:
chr5:103840469-103863215|chr5:103932379-103958928
Splice length:
1035
Other database IDs:
circAtlas: mmu-Aff1_0010
circBase: hsa_circ_0070373, circAtlas: hsa-AFF1_0009, CIRCpedia: HSA_CIRCpedia_49485
Human Ortholog IDs:
Mature spliced Sequence:
ATGAGCACCTTCCACTGACCAGCAGCAATGGCTTTTAAGGACAGCAGCAGCAGCAGCTTGTACAATGAAGATAGAAACCTGCTTCGAATCAGAGAGAAGGAAAGACGCAACCAAGAAGCTCACCAGGAGAAGGAGGCATTTCCCGAGAAGGCTCCCCTGTTTCCAGAGCCTTACAAGACTGCAAAAGGCGATGAGCTATCAAGTCGGATCCAGACCATGCTGGGTGACTATGAGGAGATGAAGGAGTTCCTGAGCAGCAAGTCCCACCCCCACCGCCTGGATGGCTCTGAAGACAGGCCCGGGAAGCCCAGATATCCCTTAGGTCATGACAGGGGGAACGGGGCTGCATCCAGCTCCCTCCGCACACATGTCTACCACCAGCCTATCCACACTTCTGCTCCCGGATCACGTCCTGTCGGTAACATTAGCCACAGTCCAAAGATGGCACAGCCAAGGATGGAGCCAAGTCTCCACACCAAAATCTATGATGGCCCACGTCTGACTCAAGACCACCTCAGTCAGGGACATTGTTCCAGAAAGTGTGACCGAAGAGCTGAAGGAGACTCTGCTCCCGAGAGGAAGCTCTCGCCCTTGATCTCCTCTTTGCCATCCCCGGTGCCCCCTCTATCACCTGTACATTCCAGGCTGCAGGGAACCAGCAAGGCTCACAGCAGTGGCGTTAGCAGTAAAAGCTGCTGTGTGGCCAAGTCTTCCAAGGACTTGGTGGCGAAGGCCCAAGATAAAGAGACTCCTCATGACGGTTTGGTGGCAGTTACCAGCCTTGGATCAGCCCCTCCTCAGCCACCTTGCCAGACATTTCCACCCCCTCCTCTCCCCTCAAAAAGTGCTGCAATGCAGCAGAAGCCCACGGCATATGTCCGTCCCATGGACGGTCAGGATCAGGCTCCCAGTGAGTCCCCCGAGCTGAAGCTGCCACTGGAGGACTATGGTCAGCAAAGCTTTGAGAAACCAGACCTTAAAGTGCCTGCCAAAGCCAAGCTCACCAGACTAAGGATGCCCTCTCAGTCGGTGGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGGAGGACTATGGTCAGCA
60.27
GCTGCTGCTGCTGTCCTTAA
60.96
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGAGGACTATGGTCAGCA
58.51
GCTGCTGCTGCTGTCCTTAA
60.96
153
PCR template sequence:
ACTGGAGGACTATGGTCAGCAAAGCTTTGAGAAACCAGACCTTAAAGTGCCTGCCAAAGCCAAGCTCACCAGACTAAGGATGCCCTCTCAGTCGGTGGAGATGAGCACCTTCCACTGACCAGCAGCAATGGCTTTTAAGGACAGCAGCAGCAGCAGCTTGTACAATGAAGATAGAAACCTGCTTCGAATCAGAGAGAAGG
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-1a-3p(1), mmu-miR-7b-5p(1), mmu-miR-206-3p(1), mmu-miR-205-5p(1), mmu-miR-33-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-207(1), mmu-miR-670-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
TCAGTCGGTGGAGATGAGCACCTTCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFF1_1035_ORF_1
0.8483
0.268102674
0.991724417
1026
ORF sequence:
ATGGCTTTTAAGGACAGCAGCAGCAGCAGCTTGTACAATGAAGATAGAAACCTGCTTCGAATCAGAGAGAAGGAAAGACGCAACCAAGAAGCTCACCAGGAGAAGGAGGCATTTCCCGAGAAGGCTCCCCTGTTTCCAGAGCCTTACAAGACTGCAAAAGGCGATGAGCTATCAAGTCGGATCCAGACCATGCTGGGTGACTATGAGGAGATGAAGGAGTTCCTGAGCAGCAAGTCCCACCCCCACCGCCTGGATGGCTCTGAAGACAGGCCCGGGAAGCCCAGATATCCCTTAGGTCATGACAGGGGGAACGGGGCTGCATCCAGCTCCCTCCGCACACATGTCTACCACCAGCCTATCCACACTTCTGCTCCCGGATCACGTCCTGTCGGTAACATTAGCCACAGTCCAAAGATGGCACAGCCAAGGATGGAGCCAAGTCTCCACACCAAAATCTATGATGGCCCACGTCTGACTCAAGACCACCTCAGTCAGGGACATTGTTCCAGAAAGTGTGACCGAAGAGCTGAAGGAGACTCTGCTCCCGAGAGGAAGCTCTCGCCCTTGATCTCCTCTTTGCCATCCCCGGTGCCCCCTCTATCACCTGTACATTCCAGGCTGCAGGGAACCAGCAAGGCTCACAGCAGTGGCGTTAGCAGTAAAAGCTGCTGTGTGGCCAAGTCTTCCAAGGACTTGGTGGCGAAGGCCCAAGATAAAGAGACTCCTCATGACGGTTTGGTGGCAGTTACCAGCCTTGGATCAGCCCCTCCTCAGCCACCTTGCCAGACATTTCCACCCCCTCCTCTCCCCTCAAAAAGTGCTGCAATGCAGCAGAAGCCCACGGCATATGTCCGTCCCATGGACGGTCAGGATCAGGCTCCCAGTGAGTCCCCCGAGCTGAAGCTGCCACTGGAGGACTATGGTCAGCAAAGCTTTGAGAAACCAGACCTTAAAGTGCCTGCCAAAGCCAAGCTCACCAGACTAAGGATGCCCTCTCAGTCGGTGGAGATGAGCACCTTCCACTGA
Peptide sequence:
MAFKDSSSSSLYNEDRNLLRIREKERRNQEAHQEKEAFPEKAPLFPEPYKTAKGDELSSRIQTMLGDYEEMKEFLSSKSHPHRLDGSEDRPGKPRYPLGHDRGNGAASSSLRTHVYHQPIHTSAPGSRPVGNISHSPKMAQPRMEPSLHTKIYDGPRLTQDHLSQGHCSRKCDRRAEGDSAPERKLSPLISSLPSPVPPLSPVHSRLQGTSKAHSSGVSSKSCCVAKSSKDLVAKAQDKETPHDGLVAVTSLGSAPPQPPCQTFPPPPLPSKSAAMQQKPTAYVRPMDGQDQAPSESPELKLPLEDYGQQSFEKPDLKVPAKAKLTRLRMPSQSVEMSTFH
IRESfinder result
IRESfinder score
0.331630537
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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