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mmu_circEp400_567
Basic information of circular RNA
PanCircBase ID:
mmu_circEp400_567
mm39_Chr. Position ID:
chr5|110866952|110872377|-
Gene name:
Ep400
Transcript:
ENSMUST00000041558.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
15,14,13,12
Exon/intron offsets:
0,346,1649,5335
Genomic length:
5425
Exon/intron sizes in nt:
178,191,108,90
Flanking exon/introns:
chr5:110859033-110866952|chr5:110872377-110874756
Splice length:
567
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TGGAAGATGAAGAAGAGACCATTGAAGAGGAGGAAGCACACGAAGGGCTTGTAGACCACCACACAGAACTTACTAATCTGGCCAAAGAAGCTGAGTTGCCCTTAATCGATTTGATGAAGTTGTATGAAGGTGCCTTTCTGCCAAATTTTCAGTGGCCACAGCCTGAACCTGATCATGAAGAGTCAAGTGGGGAAGAAGATGTAGAAGACTGTCCTAGTGACAGGGAGAGCCGGAGGGACTCCGTTCTCATTGACTCACTCTTCATCATGGATCAGTTTAAAGCTGCAGAGAGAATGAGCATTGGAAAATCCAACACCAAGGACATCACAGAAGTTACTGCTGTGGCTGAAGCCATCCTCCCTAAGGGCAGTGCCCGAGTCACAACTGCGGTGAAGTTTAGTGCTCCATCTTTGTTGTATGGTGCTCTCCGAGACTATCAGAAGATAGGCCTGGACTGGTTGGCCAAGCTATACCGGAAGAATCTCAATGGCATATTGGCTGATGAAGCAGGGCTTGGGAAAACTGTGCAGATCATTGCTTTTTTTGCTCACCTTGCCTGTAATGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCTTGGGAAAACTGTGCAG
59.97
GCAACTCAGCTTCTTTGGCC
60.04
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCTTGGGAAAACTGTGCAG
59.97
GGCAACTCAGCTTCTTTGGC
60.04
157
PCR template sequence:
CTATACCGGAAGAATCTCAATGGCATATTGGCTGATGAAGCAGGGCTTGGGAAAACTGTGCAGATCATTGCTTTTTTTGCTCACCTTGCCTGTAATGAAGTGGAAGATGAAGAAGAGACCATTGAAGAGGAGGAAGCACACGAAGGGCTTGTAGACCACCACACAGAACTTACTAATCTGGCCAAAGAAGCTGAGTTGCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-339-5p(1), mmu-miR-495-3p(1), mmu-miR-758-3p(1), mmu-miR-410-3p(1), mmu-miR-542-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCCTGTAATGAAGTGGAAGATGAAGA
siRNA sets
ATCTTCCACTTCATTACAG, CATCTTCCACTTCATTACA, CTTCCACTTCATTACAGGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCEP400_567_ORF_1
1.2092
0.280704231
0.995878494
1020
ORF sequence:
ATGAAGTTGTATGAAGGTGCCTTTCTGCCAAATTTTCAGTGGCCACAGCCTGAACCTGATCATGAAGAGTCAAGTGGGGAAGAAGATGTAGAAGACTGTCCTAGTGACAGGGAGAGCCGGAGGGACTCCGTTCTCATTGACTCACTCTTCATCATGGATCAGTTTAAAGCTGCAGAGAGAATGAGCATTGGAAAATCCAACACCAAGGACATCACAGAAGTTACTGCTGTGGCTGAAGCCATCCTCCCTAAGGGCAGTGCCCGAGTCACAACTGCGGTGAAGTTTAGTGCTCCATCTTTGTTGTATGGTGCTCTCCGAGACTATCAGAAGATAGGCCTGGACTGGTTGGCCAAGCTATACCGGAAGAATCTCAATGGCATATTGGCTGATGAAGCAGGGCTTGGGAAAACTGTGCAGATCATTGCTTTTTTTGCTCACCTTGCCTGTAATGAAGTGGAAGATGAAGAAGAGACCATTGAAGAGGAGGAAGCACACGAAGGGCTTGTAGACCACCACACAGAACTTACTAATCTGGCCAAAGAAGCTGAGTTGCCCTTAATCGATTTGATGAAGTTGTATGAAGGTGCCTTTCTGCCAAATTTTCAGTGGCCACAGCCTGAACCTGATCATGAAGAGTCAAGTGGGGAAGAAGATGTAGAAGACTGTCCTAGTGACAGGGAGAGCCGGAGGGACTCCGTTCTCATTGACTCACTCTTCATCATGGATCAGTTTAAAGCTGCAGAGAGAATGAGCATTGGAAAATCCAACACCAAGGACATCACAGAAGTTACTGCTGTGGCTGAAGCCATCCTCCCTAAGGGCAGTGCCCGAGTCACAACTGCGGTGAAGTTTAGTGCTCCATCTTTGTTGTATGGTGCTCTCCGAGACTATCAGAAGATAGGCCTGGACTGGTTGGCCAAGCTATACCGGAAGAATCTCAATGGCATATTGGCTGATGAAGCAGGGCTTGGGAAAACTGTGCAGATCATTGCTTTTTTTGCTCACCTTGCCTGTAATGAA
Peptide sequence:
MKLYEGAFLPNFQWPQPEPDHEESSGEEDVEDCPSDRESRRDSVLIDSLFIMDQFKAAERMSIGKSNTKDITEVTAVAEAILPKGSARVTTAVKFSAPSLLYGALRDYQKIGLDWLAKLYRKNLNGILADEAGLGKTVQIIAFFAHLACNEVEDEEETIEEEEAHEGLVDHHTELTNLAKEAELPLIDLMKLYEGAFLPNFQWPQPEPDHEESSGEEDVEDCPSDRESRRDSVLIDSLFIMDQFKAAERMSIGKSNTKDITEVTAVAEAILPKGSARVTTAVKFSAPSLLYGALRDYQKIGLDWLAKLYRKNLNGILADEAGLGKTVQIIAFFAHLACNE
IRESfinder result
IRESfinder score
0.560388056
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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