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mmu_circNelfb_495
Basic information of circular RNA
PanCircBase ID:
mmu_circNelfb_495
mm39_Chr. Position ID:
chr2|25099865|25100884|-
Gene name:
Nelfb
Transcript:
ENSMUST00000059849.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
4,3,2
Exon/intron offsets:
0,584,855
Genomic length:
1019
Exon/intron sizes in nt:
23,11,00,164
Flanking exon/introns:
chr2:25096357-25099865|chr2:25100884-25101113
Splice length:
495
Other database IDs:
circAtlas: mmu-Nelfb_0009
circBase: hsa_circ_0089667, CIRCpedia: HSA_CIRCpedia_63486
Human Ortholog IDs:
Mature spliced Sequence:
ACAGAGAATGGCGTGTTGCTGCCTTCCCTGCAGTCGGCCCTGCCCTTCTTGGATCTACACGGGACACCGCGGCTGGAGTTCCATCAGTCAGTGTTTGATGAACTACGTGACAAACTTCTGGAACGAGTGTCAGCAATTGCCTCTGAGGGAAAGGCAGAGGAGAGGTACAAGAAGCTGGAAGACCTTCTGGAAAAGAGCTTTTCTTTGGTCAAGATGCCATCCCTACAACCAGTGGTGATGTGTGTTATGAAACACTTGCCCAAGGTTCCTGAGAAGAAGCTGAAGCTGGTGATGGCTGACAAGGAGTTGTACCGGGCATGTGCTGTGGAAGTGAAGAGGCAGATTTGGCAAGACAACCAGGCTCTCTTTGGTGATGAAGTCTCACCACTGCTGAAGCAGTATATCCTAGAGAAAGAGAGTGCGCTCTTCAGCACAGAGCTCTCTGTGCTGCACAACTTCTTCAGCCCTTCCCCCAAGACCCGGCGCCAAGGAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTAGAGAAAGAGAGTGCGC
59.25
GGTGTCCCGTGTAGATCCAA
59.1
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTAGAGAAAGAGAGTGCGCT
59.25
GGTGTCCCGTGTAGATCCAA
59.1
159
PCR template sequence:
GCAGTATATCCTAGAGAAAGAGAGTGCGCTCTTCAGCACAGAGCTCTCTGTGCTGCACAACTTCTTCAGCCCTTCCCCCAAGACCCGGCGCCAAGGAGAGACAGAGAATGGCGTGTTGCTGCCTTCCCTGCAGTCGGCCCTGCCCTTCTTGGATCTACACGGGACACCGCGGCTGGAGTTCCATCAGTCAGTGTTTGATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-382-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCGCCAAGGAGAGACAGAGAATGGCG
siRNA sets
ATTCTCTGTCTCTCCTTGG, TTCTCTGTCTCTCCTTGGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNELFB_495_ORF_1
1.1757
0.373724982
0.982963567
777
ORF sequence:
ATGCCATCCCTACAACCAGTGGTGATGTGTGTTATGAAACACTTGCCCAAGGTTCCTGAGAAGAAGCTGAAGCTGGTGATGGCTGACAAGGAGTTGTACCGGGCATGTGCTGTGGAAGTGAAGAGGCAGATTTGGCAAGACAACCAGGCTCTCTTTGGTGATGAAGTCTCACCACTGCTGAAGCAGTATATCCTAGAGAAAGAGAGTGCGCTCTTCAGCACAGAGCTCTCTGTGCTGCACAACTTCTTCAGCCCTTCCCCCAAGACCCGGCGCCAAGGAGAGACAGAGAATGGCGTGTTGCTGCCTTCCCTGCAGTCGGCCCTGCCCTTCTTGGATCTACACGGGACACCGCGGCTGGAGTTCCATCAGTCAGTGTTTGATGAACTACGTGACAAACTTCTGGAACGAGTGTCAGCAATTGCCTCTGAGGGAAAGGCAGAGGAGAGGTACAAGAAGCTGGAAGACCTTCTGGAAAAGAGCTTTTCTTTGGTCAAGATGCCATCCCTACAACCAGTGGTGATGTGTGTTATGAAACACTTGCCCAAGGTTCCTGAGAAGAAGCTGAAGCTGGTGATGGCTGACAAGGAGTTGTACCGGGCATGTGCTGTGGAAGTGAAGAGGCAGATTTGGCAAGACAACCAGGCTCTCTTTGGTGATGAAGTCTCACCACTGCTGAAGCAGTATATCCTAGAGAAAGAGAGTGCGCTCTTCAGCACAGAGCTCTCTGTGCTGCACAACTTCTTCAGCCCTTCCCCCAAGACCCGGCGCCAAGGAGAG
Peptide sequence:
MPSLQPVVMCVMKHLPKVPEKKLKLVMADKELYRACAVEVKRQIWQDNQALFGDEVSPLLKQYILEKESALFSTELSVLHNFFSPSPKTRRQGETENGVLLPSLQSALPFLDLHGTPRLEFHQSVFDELRDKLLERVSAIASEGKAEERYKKLEDLLEKSFSLVKMPSLQPVVMCVMKHLPKVPEKKLKLVMADKELYRACAVEVKRQIWQDNQALFGDEVSPLLKQYILEKESALFSTELSVLHNFFSPSPKTRRQGE
IRESfinder result
IRESfinder score
0.395791588
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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