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mmu_circArel1_677
Basic information of circular RNA
PanCircBase ID:
mmu_circArel1_677
mm39_Chr. Position ID:
chr12|84978472|84981897|-
Gene name:
Arel1
Transcript:
ENSMUST00000163231.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
9,8,7,6
Exon/intron offsets:
0,2453,2871,3255
Genomic length:
3425
Exon/intron sizes in nt:
78,248,181,170
Flanking exon/introns:
chr12:84977264-84978472|chr12:84981897-84986933
Splice length:
677
Other database IDs:
circAtlas: mmu-Arel1_0013
Human Ortholog IDs:
Mature spliced Sequence:
GAATGGTGGTTCCTTCCAAAACAAAAATTGTGTGCCATTTTTCTACTCTGGTGTTGACGTGTGGGCAGCCACACACTCTGCAGATAGTGCCCCGAGATGAGTATGACAACCCAACCAACAATTCCATGTCCCTGAGAGATGAGCACAGCTACAGCTTAGCCATTCACGAGCTTGGTCCTCAAGAAGAAGAGAATAATGAAGTCTCATTTGAGAAGTCAGTGACGTCCAACAGGCAGACTTGCCAGGTGTTCTTGCGGCTCACCCTGCATTCCCGAGGTTGCTTCCATGCCTGCATTTCATATCAGAACCAACCCATCAATAATGGCGAATTTGACATTATTGTCCTTAGTGAGAATGAGAAGAATATTGTTGAACGAAATGTGTCCACCTCAGGAGTGAGCATTTACTTTGAGGCTTACCTTTACAATGCTAACAACTGTACCAGCACACCATGGCATCTTCCTCCCATGCACATGAGCTCTTCTCAACGCCGGCCCTCCACTGCTATTGAGGAGGACGATGAAGACTCACCCTCAGAGTGTCACACCCCTGAGAAGGTGAAGAAACCGAAGAAGGTGTACTGCTATGTGTCACCAAAGCAATTCTCTGTGAAGGAATTCTACCTGAAAATCATCCCCTGGCGCCTCTACACCTTCCGAGTGTGCCCAGGAACAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGAAAATCATCCCCTGGCG
58.97
CATCTCGGGGCACTATCTGC
60.32
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGAAAATCATCCCCTGGCGC
61.04
CATCTCGGGGCACTATCTGC
60.32
152
PCR template sequence:
GTACTGCTATGTGTCACCAAAGCAATTCTCTGTGAAGGAATTCTACCTGAAAATCATCCCCTGGCGCCTCTACACCTTCCGAGTGTGCCCAGGAACAAAGGAATGGTGGTTCCTTCCAAAACAAAAATTGTGTGCCATTTTTCTACTCTGGTGTTGACGTGTGGGCAGCCACACACTCTGCAGATAGTGCCCCGAGATGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCCAGGAACAAAGGAATGGTGGTTCC
siRNA sets
CCATTCCTTTGTTCCTGGG, ACCATTCCTTTGTTCCTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAREL1_677_ORF_1
0.7
0.198936379
0.893087921
732
ORF sequence:
ATGGTGGTTCCTTCCAAAACAAAAATTGTGTGCCATTTTTCTACTCTGGTGTTGACGTGTGGGCAGCCACACACTCTGCAGATAGTGCCCCGAGATGAGTATGACAACCCAACCAACAATTCCATGTCCCTGAGAGATGAGCACAGCTACAGCTTAGCCATTCACGAGCTTGGTCCTCAAGAAGAAGAGAATAATGAAGTCTCATTTGAGAAGTCAGTGACGTCCAACAGGCAGACTTGCCAGGTGTTCTTGCGGCTCACCCTGCATTCCCGAGGTTGCTTCCATGCCTGCATTTCATATCAGAACCAACCCATCAATAATGGCGAATTTGACATTATTGTCCTTAGTGAGAATGAGAAGAATATTGTTGAACGAAATGTGTCCACCTCAGGAGTGAGCATTTACTTTGAGGCTTACCTTTACAATGCTAACAACTGTACCAGCACACCATGGCATCTTCCTCCCATGCACATGAGCTCTTCTCAACGCCGGCCCTCCACTGCTATTGAGGAGGACGATGAAGACTCACCCTCAGAGTGTCACACCCCTGAGAAGGTGAAGAAACCGAAGAAGGTGTACTGCTATGTGTCACCAAAGCAATTCTCTGTGAAGGAATTCTACCTGAAAATCATCCCCTGGCGCCTCTACACCTTCCGAGTGTGCCCAGGAACAAAGGAATGGTGGTTCCTTCCAAAACAAAAATTGTGTGCCATTTTTCTACTCTGGTGTTGA
Peptide sequence:
MVVPSKTKIVCHFSTLVLTCGQPHTLQIVPRDEYDNPTNNSMSLRDEHSYSLAIHELGPQEEENNEVSFEKSVTSNRQTCQVFLRLTLHSRGCFHACISYQNQPINNGEFDIIVLSENEKNIVERNVSTSGVSIYFEAYLYNANNCTSTPWHLPPMHMSSSQRRPSTAIEEDDEDSPSECHTPEKVKKPKKVYCYVSPKQFSVKEFYLKIIPWRLYTFRVCPGTKEWWFLPKQKLCAIFLLWC
IRESfinder result
IRESfinder score
0.542795615
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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