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mmu_circB4galt6_544
Basic information of circular RNA
PanCircBase ID:
mmu_circB4galt6_544
mm39_Chr. Position ID:
chr18|20825448|20853199|-
Gene name:
B4galt6
Transcript:
ENSMUST00000070080.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,5,4,3
Exon/intron offsets:
0,8347,14013,27637
Genomic length:
27751
Exon/intron sizes in nt:
1,88,11,71,25,114
Flanking exon/introns:
chr18:20822400-20825448|chr18:20853199-20861018
Splice length:
544
Other database IDs:
circBase: hsa_circ_0047347, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_23624
Human Ortholog IDs:
Mature spliced Sequence:
ATTATCCTGAAGGCAATAATACAAGTGACTATCTTGTTCAAACAACAACGTATCTTCCGCAAAACTTCACGTATTTGCCACACCTCCCCTGTCCAGAGAAGCTGCCTTACATGCGGGGATTCCTCAGTGTCAATGTGAGTGAGATCAGTTTTGATGAAGTCCATCAGCTCTTCTCCAAGGACTCAGAGATTGGGCCAGGAGGCCACTGGAGGCCCAAAGACTGCAAGCCCAGATGGAAGGTGGCAGTTCTCATCCCCTTCCGTAACCGCCATGAACATCTTCCGATTTTTTTCCTGCACCTGATTCCGATGCTCCAGAAACAGCGGCTGGAATTTGCCTTTTATGTCATCGAACAGACCGGCACACAACCATTCAATCGTGCGATGCTCTTTAATGTGGGTTTCAAAGAGGCCATGAAAGACAGAGCCTGGGACTGTGTGATCTTCCATGATGTGGATCATCTGCCTGAAAATGATCGGAACTACTACGGATGTGGAGAGATGCCGCGGCACTTTGCAGCGAAGCTGGACAAGTACATGTACAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTACGGATGTGGAGAGATGCC
60
GGGAGGTGTGGCAAATACGT
60.32
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTACGGATGTGGAGAGATGCC
60
CAGGGGAGGTGTGGCAAATA
59.67
151
PCR template sequence:
TCCATGATGTGGATCATCTGCCTGAAAATGATCGGAACTACTACGGATGTGGAGAGATGCCGCGGCACTTTGCAGCGAAGCTGGACAAGTACATGTACATATTATCCTGAAGGCAATAATACAAGTGACTATCTTGTTCAAACAACAACGTATCTTCCGCAAAACTTCACGTATTTGCCACACCTCCCCTGTCCAGAGAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-miR-146a-5p(1), mmu-miR-23a-3p(1), mmu-miR-680(1), mmu-miR-484(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGTACATGTACATATTATCCTGAAGG
siRNA sets
CTTCAGGATAATATGTACA, TTCAGGATAATATGTACAT, GATAATATGTACATGTACT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCB4GALT6_544_ORF_1
0.9431
0.225155656
0.882578056
639
ORF sequence:
ATGATGTGGATCATCTGCCTGAAAATGATCGGAACTACTACGGATGTGGAGAGATGCCGCGGCACTTTGCAGCGAAGCTGGACAAGTACATGTACATATTATCCTGAAGGCAATAATACAAGTGACTATCTTGTTCAAACAACAACGTATCTTCCGCAAAACTTCACGTATTTGCCACACCTCCCCTGTCCAGAGAAGCTGCCTTACATGCGGGGATTCCTCAGTGTCAATGTGAGTGAGATCAGTTTTGATGAAGTCCATCAGCTCTTCTCCAAGGACTCAGAGATTGGGCCAGGAGGCCACTGGAGGCCCAAAGACTGCAAGCCCAGATGGAAGGTGGCAGTTCTCATCCCCTTCCGTAACCGCCATGAACATCTTCCGATTTTTTTCCTGCACCTGATTCCGATGCTCCAGAAACAGCGGCTGGAATTTGCCTTTTATGTCATCGAACAGACCGGCACACAACCATTCAATCGTGCGATGCTCTTTAATGTGGGTTTCAAAGAGGCCATGAAAGACAGAGCCTGGGACTGTGTGATCTTCCATGATGTGGATCATCTGCCTGAAAATGATCGGAACTACTACGGATGTGGAGAGATGCCGCGGCACTTTGCAGCGAAGCTGGACAAGTACATGTAC
Peptide sequence:
MMWIICLKMIGTTTDVERCRGTLQRSWTSTCTYYPEGNNTSDYLVQTTTYLPQNFTYLPHLPCPEKLPYMRGFLSVNVSEISFDEVHQLFSKDSEIGPGGHWRPKDCKPRWKVAVLIPFRNRHEHLPIFFLHLIPMLQKQRLEFAFYVIEQTGTQPFNRAMLFNVGFKEAMKDRAWDCVIFHDVDHLPENDRNYYGCGEMPRHFAAKLDKYMY
IRESfinder result
IRESfinder score
0.474191278
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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