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mmu_circUlk2_371
Basic information of circular RNA
PanCircBase ID:
mmu_circUlk2_371
mm39_Chr. Position ID:
chr11|61698887|61710282|-
Gene name:
Ulk2
Transcript:
ENSMUST00000004920.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
15,14,13
Exon/intron offsets:
0,4656,11223
Genomic length:
11395
Exon/intron sizes in nt:
1,38,61,172
Flanking exon/introns:
chr11:61694613-61698887|chr11:61710282-61715464
Splice length:
371
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
TCCCTTCCAGATATGCAGCATATTCAGGAAGAAAACTTATCCTCCCCACCGTTGGGTCCTCCCAACTATCTACAGGTGTCCAAAGACTCTGCGAGTAATAGTAGCAAGAACTCTTCTTGTGACACGGATGACTTTGTTTTGGTTCCACACAACATCTCGTCAGACCACTCATATGACATGCCAATGGGGACTACGGCCAGACGTGCTTCAAATGAATTCTTTATGTGTGGAGGGCAGTGTCAACCTACTGTGTCACCTCACAGCGAAACAGCCCCAATTCCAGTTCCTACTCAAGTAAGGAATTATCAGCGCATAGAACAGAATCTTATATCCACTGCCAGCTCTGGCACAAACCCACATGGTTCTCCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCCAATTCCAGTTCCTACTCA
59.42
CCAACGGTGGGGAGGATAAG
59.82
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCCCAATTCCAGTTCCTACTCAA
59.99
CCAACGGTGGGGAGGATAAG
59.82
155
PCR template sequence:
CCCCAATTCCAGTTCCTACTCAAGTAAGGAATTATCAGCGCATAGAACAGAATCTTATATCCACTGCCAGCTCTGGCACAAACCCACATGGTTCTCCAAGTCCCTTCCAGATATGCAGCATATTCAGGAAGAAAACTTATCCTCCCCACCGTTGGGTCCTCCCAACTATCTACAGGTGTCCAAAGACTCTGCGAGTAATA
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-34c-5p(1), mmu-miR-34b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATGGTTCTCCAAGTCCCTTCCAGATA
siRNA sets
TATCTGGAAGGGACTTGGA, ATCTGGAAGGGACTTGGAG, TCTGGAAGGGACTTGGAGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCULK2_371_ORF_1
0.6096
-0.018722438
0.631284791
657
ORF sequence:
ATGCAGCATATTCAGGAAGAAAACTTATCCTCCCCACCGTTGGGTCCTCCCAACTATCTACAGGTGTCCAAAGACTCTGCGAGTAATAGTAGCAAGAACTCTTCTTGTGACACGGATGACTTTGTTTTGGTTCCACACAACATCTCGTCAGACCACTCATATGACATGCCAATGGGGACTACGGCCAGACGTGCTTCAAATGAATTCTTTATGTGTGGAGGGCAGTGTCAACCTACTGTGTCACCTCACAGCGAAACAGCCCCAATTCCAGTTCCTACTCAAGTAAGGAATTATCAGCGCATAGAACAGAATCTTATATCCACTGCCAGCTCTGGCACAAACCCACATGGTTCTCCAAGTCCCTTCCAGATATGCAGCATATTCAGGAAGAAAACTTATCCTCCCCACCGTTGGGTCCTCCCAACTATCTACAGGTGTCCAAAGACTCTGCGAGTAATAGTAGCAAGAACTCTTCTTGTGACACGGATGACTTTGTTTTGGTTCCACACAACATCTCGTCAGACCACTCATATGACATGCCAATGGGGACTACGGCCAGACGTGCTTCAAATGAATTCTTTATGTGTGGAGGGCAGTGTCAACCTACTGTGTCACCTCACAGCGAAACAGCCCCAATTCCAGTTCCTACTCAAGTAA
Peptide sequence:
MQHIQEENLSSPPLGPPNYLQVSKDSASNSSKNSSCDTDDFVLVPHNISSDHSYDMPMGTTARRASNEFFMCGGQCQPTVSPHSETAPIPVPTQVRNYQRIEQNLISTASSGTNPHGSPSPFQICSIFRKKTYPPHRWVLPTIYRCPKTLRVIVARTLLVTRMTLFWFHTTSRQTTHMTCQWGLRPDVLQMNSLCVEGSVNLLCHLTAKQPQFQFLLK
IRESfinder result
IRESfinder score
0.539058122
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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