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mmu_circBabam2_519
Basic information of circular RNA
PanCircBase ID:
mmu_circBabam2_519
mm39_Chr. Position ID:
chr5|31859169|31978016|+
Gene name:
Babam2
Transcript:
ENSMUST00000201352.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
2,3,4,5
Exon/intron offsets:
0,29141,83752,118652
Genomic length:
118847
Exon/intron sizes in nt:
1,52,77,95,195
Flanking exon/introns:
chr5:31855421-31859169|chr5:31978016-31988428
Splice length:
519
Other database IDs:
circAtlas: hsa-BRE_0004, CIRCpedia: HSA_CIRCpedia_150481
Human Ortholog IDs:
Mature spliced Sequence:
TGGTAACTCATAAATCAAGTTAAAATGTCTCCAGAAATTGCCTTGAACCGAATTTCTCCAATGCTCTCCCCATTCATATCAAGCGTGGTCCGAAATGGGAAGGTGGGACTGGATGCTACAAACTGTTTGAGAATTACGGACTTGAAGTCTGGCTGTACATCATTGACTCCTGGACCCAACTGTGACCGCTTCAAACTGCACATCCCGTACGCTGGGGAGACGTTAAAATGGGACATAATTTTCAATGCTCAGTACCCAGAGCTGCCTCCTGATTTCATCTTTGGAGAGGATGCTGAGTTTCTGCCAGACCCCTCTGCGCTGCACAACCTTGCCTCCTGGAACCCTTCAAACCCTGAGTGCCTGTTGCTCGTGGTGAAGGAGCTGGTGCAGCAGTACCACCAGTTCCAGTGCGGCCGCCTCCGTGAGAGCTCGCGCCTCATGTTTGAGTACCAGACGCTCCTGGAAGAGCCTCAGTATGGAGAGAACATGGAAATTTATGCTGGAAAGAAAAACAACTGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCGCGCCTCATGTTTGAGTA
59.75
TGAATGGGGAGAGCATTGGAG
59.79
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCGCGCCTCATGTTTGAGTA
59.75
TGAATGGGGAGAGCATTGGA
58.7
166
PCR template sequence:
CCGTGAGAGCTCGCGCCTCATGTTTGAGTACCAGACGCTCCTGGAAGAGCCTCAGTATGGAGAGAACATGGAAATTTATGCTGGAAAGAAAAACAACTGGTGGTAACTCATAAATCAAGTTAAAATGTCTCCAGAAATTGCCTTGAACCGAATTTCTCCAATGCTCTCCCCATTCATATCAAGCGTGGTCCGAAATGGGA
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-298-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAAAAACAACTGGTGGTAACTCATAA
siRNA sets
TATGAGTTACCACCAGTTG, ATGAGTTACCACCAGTTGT, TTATGAGTTACCACCAGTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCBABAM2_519_ORF_1
0.9204
0.31483307
0.793609095
501
ORF sequence:
ATGTCTCCAGAAATTGCCTTGAACCGAATTTCTCCAATGCTCTCCCCATTCATATCAAGCGTGGTCCGAAATGGGAAGGTGGGACTGGATGCTACAAACTGTTTGAGAATTACGGACTTGAAGTCTGGCTGTACATCATTGACTCCTGGACCCAACTGTGACCGCTTCAAACTGCACATCCCGTACGCTGGGGAGACGTTAAAATGGGACATAATTTTCAATGCTCAGTACCCAGAGCTGCCTCCTGATTTCATCTTTGGAGAGGATGCTGAGTTTCTGCCAGACCCCTCTGCGCTGCACAACCTTGCCTCCTGGAACCCTTCAAACCCTGAGTGCCTGTTGCTCGTGGTGAAGGAGCTGGTGCAGCAGTACCACCAGTTCCAGTGCGGCCGCCTCCGTGAGAGCTCGCGCCTCATGTTTGAGTACCAGACGCTCCTGGAAGAGCCTCAGTATGGAGAGAACATGGAAATTTATGCTGGAAAGAAAAACAACTGGTGGTAA
Peptide sequence:
MSPEIALNRISPMLSPFISSVVRNGKVGLDATNCLRITDLKSGCTSLTPGPNCDRFKLHIPYAGETLKWDIIFNAQYPELPPDFIFGEDAEFLPDPSALHNLASWNPSNPECLLLVVKELVQQYHQFQCGRLRESSRLMFEYQTLLEEPQYGENMEIYAGKKNNWW
IRESfinder result
IRESfinder score
0.665653694
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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