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mmu_circSafb_1007
Basic information of circular RNA
PanCircBase ID:
mmu_circSafb_1007
mm39_Chr. Position ID:
chr17|56908047|56912399|+
Gene name:
Safb
Transcript:
ENSMUST00000182533.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
11,12,13,14,15,16,17,18
Exon/intron offsets:
0,179,395,1829,2484,3098,3318,4236
Genomic length:
4352
Exon/intron sizes in nt:
83,14,08,91,07,29,11,30,00,000
Flanking exon/introns:
chr17:56907971-56908047|chr17:56912399-56912550
Splice length:
1007
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GCCAAAAGTGAGCCCACTGGCAAAAGAGTGCCTGACAGGCGAGATGGGGACAGCAAGAAGGAGAAGGCCAGCACCAGTGACAGATCTGCAAACCTTAAGAGGGAGGAGAAAGGTGAGAGAAAAGACGATGCCAAGAAGACAGATGATGGGAGCACAGAGAAGAGCAAAGACGCAGATGACCAGAAACCTGGGCCTTCAGAGCGCTCGCGAACGACCAAGTCAGGAAGCCGTGGCACTGAGCGCACTGTGGTGATGGACAAGTCCAAAGGTGTGCCTGTCATCAGTGTGAAAACATCTGGGTCTAAAGAGAGAGCCTCCAAAAGTCAGGACCGGAAGTCAGCCAGCCGGGAGAAGCGGTCTGTTGTGTCCTTTGACAAAGTTAAAGAGTCTCGAAAGTCCAGAGACTCAGAGTCTCGGAGGGAACGGGAGCGCAGTGAGCGGGAGCAGAGGCTGCAGGCCCAGTGGGAGCGGGAGGAGCGAGAGCGGCTGGAGATTGCTCGTGAGCGCTTGGCATTCCACCGCCATCGGCTAGAGCGTGAACGCATGGAGCGGGAGCGGCTGGAGCGGGAGCGGATGCATGTAGAACAGGAGCGGAGGCGTGAGCAAGAGCGCATTCACCGAGAGCGAGAGGAGCTTCGGCGTCAGCAGGAGCTGCGCTATGAACAGGAGCGCCGGCCTGCTGTGCGCAGGCCCTATGAAGTGGATGGCCGGCGAGATGATGCCTATTGGCCAGAAGCTAAACGGGCTGCTCTGGATGACCGTTACCACTCAGACTTCAGCCGCCAGGACCGCTTTCACGACTTCGACCACAGAGACAGAGGCCGTTATCCCAACCATTCTGTGGATAGGAGAGAAGGTTCACGGTCGATGATGGGAGACAGAGAAGGACAGCATTACCCTGAACGCCATGGAGGACCTGAACGCCATGGCCGGGACTCTCGAGATGGCTGGGGCTATGGTTCGAACAAGAGATTGAGTGAAGGCCGGGGGCTGCCCCCTCCTCCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGGGCTATGGTTCGAACA
59.75
GCAGATCTGTCACTGGTGCT
60.04
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGGGCTATGGTTCGAACA
59.75
TGCAGATCTGTCACTGGTGC
60.32
150
PCR template sequence:
ATGGAGGACCTGAACGCCATGGCCGGGACTCTCGAGATGGCTGGGGCTATGGTTCGAACAAGAGATTGAGTGAAGGCCGGGGGCTGCCCCCTCCTCCCAGGCCAAAAGTGAGCCCACTGGCAAAAGAGTGCCTGACAGGCGAGATGGGGACAGCAAGAAGGAGAAGGCCAGCACCAGTGACAGATCTGCAAACCTTAAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-207(2), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-370-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCCCTCCTCCCAGGCCAAAAGTGAGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSAFB_1007_ORF_1
0.818
0.421129577
0.994658285
1008
ORF sequence:
ATGGACAAGTCCAAAGGTGTGCCTGTCATCAGTGTGAAAACATCTGGGTCTAAAGAGAGAGCCTCCAAAAGTCAGGACCGGAAGTCAGCCAGCCGGGAGAAGCGGTCTGTTGTGTCCTTTGACAAAGTTAAAGAGTCTCGAAAGTCCAGAGACTCAGAGTCTCGGAGGGAACGGGAGCGCAGTGAGCGGGAGCAGAGGCTGCAGGCCCAGTGGGAGCGGGAGGAGCGAGAGCGGCTGGAGATTGCTCGTGAGCGCTTGGCATTCCACCGCCATCGGCTAGAGCGTGAACGCATGGAGCGGGAGCGGCTGGAGCGGGAGCGGATGCATGTAGAACAGGAGCGGAGGCGTGAGCAAGAGCGCATTCACCGAGAGCGAGAGGAGCTTCGGCGTCAGCAGGAGCTGCGCTATGAACAGGAGCGCCGGCCTGCTGTGCGCAGGCCCTATGAAGTGGATGGCCGGCGAGATGATGCCTATTGGCCAGAAGCTAAACGGGCTGCTCTGGATGACCGTTACCACTCAGACTTCAGCCGCCAGGACCGCTTTCACGACTTCGACCACAGAGACAGAGGCCGTTATCCCAACCATTCTGTGGATAGGAGAGAAGGTTCACGGTCGATGATGGGAGACAGAGAAGGACAGCATTACCCTGAACGCCATGGAGGACCTGAACGCCATGGCCGGGACTCTCGAGATGGCTGGGGCTATGGTTCGAACAAGAGATTGAGTGAAGGCCGGGGGCTGCCCCCTCCTCCCAGGCCAAAAGTGAGCCCACTGGCAAAAGAGTGCCTGACAGGCGAGATGGGGACAGCAAGAAGGAGAAGGCCAGCACCAGTGACAGATCTGCAAACCTTAAGAGGGAGGAGAAAGGTGAGAGAAAAGACGATGCCAAGAAGACAGATGATGGGAGCACAGAGAAGAGCAAAGACGCAGATGACCAGAAACCTGGGCCTTCAGAGCGCTCGCGAACGACCAAGTCAGGAAGCCGTGGCACTGAGCGCACTGTGGTGA
Peptide sequence:
MDKSKGVPVISVKTSGSKERASKSQDRKSASREKRSVVSFDKVKESRKSRDSESRRERERSEREQRLQAQWEREERERLEIARERLAFHRHRLERERMERERLERERMHVEQERRREQERIHREREELRRQQELRYEQERRPAVRRPYEVDGRRDDAYWPEAKRAALDDRYHSDFSRQDRFHDFDHRDRGRYPNHSVDRREGSRSMMGDREGQHYPERHGGPERHGRDSRDGWGYGSNKRLSEGRGLPPPPRPKVSPLAKECLTGEMGTARRRRPAPVTDLQTLRGRRKVREKTMPRRQMMGAQRRAKTQMTRNLGLQSARERPSQEAVALSALW
IRESfinder result
IRESfinder score
0.123903933
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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