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mmu_circSafb2_1160
Basic information of circular RNA
PanCircBase ID:
mmu_circSafb2_1160
mm39_Chr. Position ID:
chr17|56878209|56884905|-
Gene name:
Safb2
Transcript:
ENSMUST00000075510.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
11,10,9,8,7,6,5
Exon/intron offsets:
0,190,2992,3693,4145,5668,6633
Genomic length:
6696
Exon/intron sizes in nt:
110,150,101,50,658,28,63
Flanking exon/introns:
chr17:56876022-56878209|chr17:56884905-56885640
Splice length:
1160
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGGATGAGGAGGTCTTCAAGAACACTCTGGAAGCTTCCGTGTCAGACCTTAAAGTAACTCTGGCTGATGAAGAAGCCCCCATGGAACCAGAAAATGAGAAAATACTCGACATTTTGGGGGAAACTTGTAAATCTGAGCCAGTAAAAGAAGAAGGTTCGGAGCTGGAGCAGCCCTTTGCCCAGGCCACGAGTAGCGTGGGGCCAGACAGGAAGCTGGCGGAGGAAGAGGACCTATTTGAGAGCTGCGGCCACCCGGAAGAGGAAGAGGAAGAGGAGGAAGAAGATCAGGAAGAGGAGCAGGAGGAGGAGGGAGATTTAGCTTTGGCCAGCAGCAGCAAGTCTGAGTCTCCAAGCACTCGGTGTCAGTGGAGCGAGGCAGATGCCCCGTTAGCAGTAGTGAAAAGGGAGCTGGCAGATGCGCCGGGTGGAGGTGGAGGTACTCGGCACAGGCGGAAGCGCAAGCGAAGGCGGAAGCATCAGGCGCAGGCAGAAGCTCTGGGCACAGGTGGAGGTGCCGGGATGAACTGCGAGCCTGTAGGGCTAGAGGAGCCAGTTGAACAGAGTAGCACGGCTGCCCAGCTCCCGGAGGCCACCAGCCAGGAGCTGGTGCGAGCGCCCACGGCAGCCCTGAGCCCTGAGCCCCAAGATAGCAAAGAAGACGTGAAGAAGTTTGCTTTTGACGCTTGTAATGACGTCCCTGCGCCTCCTAAAGAGTCCTCAGCCAGTGAGGGCGCTGATCAGAAAATGAGCTCTGTTAAGGAAGAACAAGATATAAAGCCAGTCATTAAAGATGAAAAAGGCCGTGCCAGCTGTAGCTCAGGAAGGAACCTGTGGGTCAGTGGGCTGTCCTCCAGCACCCGTGCTGCTGACCTCAAGAGCCTCTTCAGCAAGCATGGGAAGGTCATCGGAGCCAAGGTGGTCACCAATGCCCGCAGTCCAGGGGCTCGGTGCTATGGATTTGTGACAATGTCCACGTCAGATGAGGCCACCAAATGCATTAGCCACCTGCACAGAACTGAACTACATGGGAGGATGATCTCTGTGGAGAAGGCCAAGAATGAACCCTCTGAGAAGAAGTCGTCAGACAGGAGAGCATGTGACCAAAAGGAGAAGGTGCCAGGGCCGGACAGGCCTCACCCTGTGAAGATCAAGACGGAGAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAAAGGAGAAGGTGCCAGGG
59.89
GTTCCATGGGGGCTTCTTCA
59.96
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAAAGGAGAAGGTGCCAGGG
59.89
ATGGGGGCTTCTTCATCAGC
60.11
141
PCR template sequence:
AACCCTCTGAGAAGAAGTCGTCAGACAGGAGAGCATGTGACCAAAAGGAGAAGGTGCCAGGGCCGGACAGGCCTCACCCTGTGAAGATCAAGACGGAGAAGTGGATGAGGAGGTCTTCAAGAACACTCTGGAAGCTTCCGTGTCAGACCTTAAAGTAACTCTGGCTGATGAAGAAGCCCCCATGGAACCAGAAAATGAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-207(2), mmu-miR-335-3p(2), mmu-miR-16-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-24-3p(1), mmu-miR-149-5p(1), mmu-miR-680(1), mmu-miR-29b-2-5p(1), mmu-miR-129-5p(1), mmu-miR-484(1), mmu-miR-350-3p(1), mmu-miR-193b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCAAGACGGAGAAGTGGATGAGGAGG
siRNA sets
CTCCTCATCCACTTCTCCG, CCTCCTCATCCACTTCTCC, ATCCACTTCTCCGTCTTGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSAFB2_1160_ORF_1
0.9751
0.366045763
0.998009869
1137
ORF sequence:
ATGGAACCAGAAAATGAGAAAATACTCGACATTTTGGGGGAAACTTGTAAATCTGAGCCAGTAAAAGAAGAAGGTTCGGAGCTGGAGCAGCCCTTTGCCCAGGCCACGAGTAGCGTGGGGCCAGACAGGAAGCTGGCGGAGGAAGAGGACCTATTTGAGAGCTGCGGCCACCCGGAAGAGGAAGAGGAAGAGGAGGAAGAAGATCAGGAAGAGGAGCAGGAGGAGGAGGGAGATTTAGCTTTGGCCAGCAGCAGCAAGTCTGAGTCTCCAAGCACTCGGTGTCAGTGGAGCGAGGCAGATGCCCCGTTAGCAGTAGTGAAAAGGGAGCTGGCAGATGCGCCGGGTGGAGGTGGAGGTACTCGGCACAGGCGGAAGCGCAAGCGAAGGCGGAAGCATCAGGCGCAGGCAGAAGCTCTGGGCACAGGTGGAGGTGCCGGGATGAACTGCGAGCCTGTAGGGCTAGAGGAGCCAGTTGAACAGAGTAGCACGGCTGCCCAGCTCCCGGAGGCCACCAGCCAGGAGCTGGTGCGAGCGCCCACGGCAGCCCTGAGCCCTGAGCCCCAAGATAGCAAAGAAGACGTGAAGAAGTTTGCTTTTGACGCTTGTAATGACGTCCCTGCGCCTCCTAAAGAGTCCTCAGCCAGTGAGGGCGCTGATCAGAAAATGAGCTCTGTTAAGGAAGAACAAGATATAAAGCCAGTCATTAAAGATGAAAAAGGCCGTGCCAGCTGTAGCTCAGGAAGGAACCTGTGGGTCAGTGGGCTGTCCTCCAGCACCCGTGCTGCTGACCTCAAGAGCCTCTTCAGCAAGCATGGGAAGGTCATCGGAGCCAAGGTGGTCACCAATGCCCGCAGTCCAGGGGCTCGGTGCTATGGATTTGTGACAATGTCCACGTCAGATGAGGCCACCAAATGCATTAGCCACCTGCACAGAACTGAACTACATGGGAGGATGATCTCTGTGGAGAAGGCCAAGAATGAACCCTCTGAGAAGAAGTCGTCAGACAGGAGAGCATGTGACCAAAAGGAGAAGGTGCCAGGGCCGGACAGGCCTCACCCTGTGAAGATCAAGACGGAGAAGTGGATGAGGAGGTCTTCAAGAACACTCTGGAAGCTTCCGTGTCAGACCTTAAAGTAA
Peptide sequence:
MEPENEKILDILGETCKSEPVKEEGSELEQPFAQATSSVGPDRKLAEEEDLFESCGHPEEEEEEEEEDQEEEQEEEGDLALASSSKSESPSTRCQWSEADAPLAVVKRELADAPGGGGGTRHRRKRKRRRKHQAQAEALGTGGGAGMNCEPVGLEEPVEQSSTAAQLPEATSQELVRAPTAALSPEPQDSKEDVKKFAFDACNDVPAPPKESSASEGADQKMSSVKEEQDIKPVIKDEKGRASCSSGRNLWVSGLSSSTRAADLKSLFSKHGKVIGAKVVTNARSPGARCYGFVTMSTSDEATKCISHLHRTELHGRMISVEKAKNEPSEKKSSDRRACDQKEKVPGPDRPHPVKIKTEKWMRRSSRTLWKLPCQTLK
IRESfinder result
IRESfinder score
0.20338905
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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