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mmu_circSec23b_429
Basic information of circular RNA
PanCircBase ID:
mmu_circSec23b_429
mm39_Chr. Position ID:
chr2|144420251|144425688|+
Gene name:
Sec23b
Transcript:
ENSMUST00000028916.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
12,13,14,15
Exon/intron offsets:
0,965,3612,5359
Genomic length:
5437
Exon/intron sizes in nt:
90,107,154,78
Flanking exon/introns:
chr2:144416667-144420251|chr2:144425688-144427517
Splice length:
429
Other database IDs:
circAtlas: mmu-Sec23b_0004
Human Ortholog IDs:
Mature spliced Sequence:
GAGCTTGGTGTTGGTGGCACAAGTCAGTGGAAGATCTGTGGCCTGGATCCCTCATCTACTCTTGGCATCTACTTTGAAGTTGTCAATCAGCACAATGCTCCAGTTCCCCAGGGAGGCAGAGGTGCCATCCAGTTTGTCACACAGTATCAGCATTCCAGCACTCAGAAGCGCATCCGAGTGACCACCATTGCCCGCAATTGGGCAGATGCACAGAGTCAGCTGAGGCACATAGAAGCAGCATTTGACCAGGAGGCCGCAGCAGTCCTGATGGCACGGCTTGGAGTGTTCCGCGCAGAGTCAGAGGAGGGGCCTGACGTGCTTCGGTGGCTGGATCGGCAACTCATCAGACTGTGTCAGAAGTTTGGGCAGTATAACAAAGAAGACCCTACGTCTTTCAGATTGTCAGACTCCTTTTCTCTGTATCCTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCGGCAACTCATCAGACTGT
59.03
CCAGGCCACAGATCTTCCAC
60.39
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGGCAACTCATCAGACTGTG
58.93
CCAGGCCACAGATCTTCCAC
60.39
142
PCR template sequence:
GGATCGGCAACTCATCAGACTGTGTCAGAAGTTTGGGCAGTATAACAAAGAAGACCCTACGTCTTTCAGATTGTCAGACTCCTTTTCTCTGTATCCTCAGGAGCTTGGTGTTGGTGGCACAAGTCAGTGGAAGATCTGTGGCCTGGATCCCTCATCTACTCTTGGCATCTACTTTGAAGTTGTCAATCAGCACAATGCTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
NA
Interacting miRNAs (#binding sites)
NA
siRNAs for circular RNA silencing
Junction sequence
TCTGTATCCTCAGGAGCTTGGTGTTG
siRNA sets
AACACCAAGCTCCTGAGGA, CAACACCAAGCTCCTGAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSEC23B_429_ORF_1
0.9892
0.264534812
0.872450256
591
ORF sequence:
ATGGCACGGCTTGGAGTGTTCCGCGCAGAGTCAGAGGAGGGGCCTGACGTGCTTCGGTGGCTGGATCGGCAACTCATCAGACTGTGTCAGAAGTTTGGGCAGTATAACAAAGAAGACCCTACGTCTTTCAGATTGTCAGACTCCTTTTCTCTGTATCCTCAGGAGCTTGGTGTTGGTGGCACAAGTCAGTGGAAGATCTGTGGCCTGGATCCCTCATCTACTCTTGGCATCTACTTTGAAGTTGTCAATCAGCACAATGCTCCAGTTCCCCAGGGAGGCAGAGGTGCCATCCAGTTTGTCACACAGTATCAGCATTCCAGCACTCAGAAGCGCATCCGAGTGACCACCATTGCCCGCAATTGGGCAGATGCACAGAGTCAGCTGAGGCACATAGAAGCAGCATTTGACCAGGAGGCCGCAGCAGTCCTGATGGCACGGCTTGGAGTGTTCCGCGCAGAGTCAGAGGAGGGGCCTGACGTGCTTCGGTGGCTGGATCGGCAACTCATCAGACTGTGTCAGAAGTTTGGGCAGTATAACAAAGAAGACCCTACGTCTTTCAGATTGTCAGACTCCTTTTCTCTGTATCCTCAG
Peptide sequence:
MARLGVFRAESEEGPDVLRWLDRQLIRLCQKFGQYNKEDPTSFRLSDSFSLYPQELGVGGTSQWKICGLDPSSTLGIYFEVVNQHNAPVPQGGRGAIQFVTQYQHSSTQKRIRVTTIARNWADAQSQLRHIEAAFDQEAAAVLMARLGVFRAESEEGPDVLRWLDRQLIRLCQKFGQYNKEDPTSFRLSDSFSLYPQ
IRESfinder result
IRESfinder score
0.5892504
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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