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mmu_circSlf2_990
Basic information of circular RNA
PanCircBase ID:
mmu_circSlf2_990
mm39_Chr. Position ID:
chr19|44936368|44957573|+
Gene name:
Slf2
Transcript:
ENSMUST00000096053.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
7,8,9,10,11,12,13,14
Exon/intron offsets:
0,1042,4139,11075,12804,19037,19573,21107
Genomic length:
21205
Exon/intron sizes in nt:
123,168,103,76,142,103,177,98
Flanking exon/introns:
chr19:44931958-44936368|chr19:44957573-44960036
Splice length:
990
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_120004
Human Ortholog IDs:
Mature spliced Sequence:
GCTAGATGAACTACAGAAGAAGCTACAGGAAGACATAAGACAAGGCCGTGGCATTAAATCTCCTCTCAGAACTGGCGATCAGGATAGTACAGATGATGGTGATGGCCTCTTGGAAGAACACAGGGAATTTCTAAAGAAATTTTCAGTTACAGTTGATGCTATTCCTGATCATCATCCAGGTGAAGAAATATTTAATTTCCTCAATTCTGGAAAAATTTTCAATCAGTATACCTTAGATTTAAGAGACTCTGGTTTTATTGGAGAAAGTGCTGTGGAAAAGCTTATTCTCAAATCAGGAAAAACAGATCAGATTTTTTTGACAACACAAGGCTTCCTTACCACTGCATATCACTACGTCCAATGTCCTGTACCTGTGTTAAAGTGGCTGTTTCGGATGATGTCGGTTCACACAGATTGTATTGTGTCGGTGCAGATTTTAAGTACATTGATGGAAATAACCATTAGAAATGATACTTTCAGTGACTCTCCAGTTTGGCCCTGGATCCCATCTTTGTCTGATATAGCAGCTGTATTCTTCAACATGGGCGTTGGTTTTGGATCTTTGTTTCCTCTGGAGACTCTTCAGCCTGACTTTAATGAAGAAAATCTAATTTCTGAAACACAGAAAACACTGGGGGGAAAAGAAAGTGAAGATTCACCTTATAGTCCAGTATTTTCAGCTCTTCCTGAAACCAACATTTTAAATGTGGTTAAGTTCCTAGGTCTGTGCACATCTATACATCCAGAAGGTTACCAAGATGGAGAATTAATGCTGCTGATTTTAATGCTGTTTAAAATGAGTTTGGAAAAAGAGCTTAAACAGATTCCATTAGTAGACTTTCAGAGCCTCCTGATAAATCTCATGAAAAACATCAGAGATTGGAACACAAAGGTTCATGAACTCTGTCTGGGCATAAATGAACTCTCCAGTCATCCCCATAACCTTCTTTGGTTGGTACAGCTAGTCCCTAACTGGACATCTCGTGGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGAACTCTCCAGTCATCCCCA
60.2
TCGCCAGTTCTGAGAGGAGA
59.96
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCATGAACTCTGTCTGGGCA
58.65
AATGCCACGGCCTTGTCTTA
59.96
151
PCR template sequence:
AGGTTCATGAACTCTGTCTGGGCATAAATGAACTCTCCAGTCATCCCCATAACCTTCTTTGGTTGGTACAGCTAGTCCCTAACTGGACATCTCGTGGAAGGCTAGATGAACTACAGAAGAAGCTACAGGAAGACATAAGACAAGGCCGTGGCATTAAATCTCCTCTCAGAACTGGCGATCAGGATAGTACAGATGATGGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-15a-5p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-322-5p(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CATCTCGTGGAAGGCTAGATGAACTA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSLF2_990_ORF_1
0.8906
-0.046607495
0.999503248
1584
ORF sequence:
ATGATGTCGGTTCACACAGATTGTATTGTGTCGGTGCAGATTTTAAGTACATTGATGGAAATAACCATTAGAAATGATACTTTCAGTGACTCTCCAGTTTGGCCCTGGATCCCATCTTTGTCTGATATAGCAGCTGTATTCTTCAACATGGGCGTTGGTTTTGGATCTTTGTTTCCTCTGGAGACTCTTCAGCCTGACTTTAATGAAGAAAATCTAATTTCTGAAACACAGAAAACACTGGGGGGAAAAGAAAGTGAAGATTCACCTTATAGTCCAGTATTTTCAGCTCTTCCTGAAACCAACATTTTAAATGTGGTTAAGTTCCTAGGTCTGTGCACATCTATACATCCAGAAGGTTACCAAGATGGAGAATTAATGCTGCTGATTTTAATGCTGTTTAAAATGAGTTTGGAAAAAGAGCTTAAACAGATTCCATTAGTAGACTTTCAGAGCCTCCTGATAAATCTCATGAAAAACATCAGAGATTGGAACACAAAGGTTCATGAACTCTGTCTGGGCATAAATGAACTCTCCAGTCATCCCCATAACCTTCTTTGGTTGGTACAGCTAGTCCCTAACTGGACATCTCGTGGAAGGCTAGATGAACTACAGAAGAAGCTACAGGAAGACATAAGACAAGGCCGTGGCATTAAATCTCCTCTCAGAACTGGCGATCAGGATAGTACAGATGATGGTGATGGCCTCTTGGAAGAACACAGGGAATTTCTAAAGAAATTTTCAGTTACAGTTGATGCTATTCCTGATCATCATCCAGGTGAAGAAATATTTAATTTCCTCAATTCTGGAAAAATTTTCAATCAGTATACCTTAGATTTAAGAGACTCTGGTTTTATTGGAGAAAGTGCTGTGGAAAAGCTTATTCTCAAATCAGGAAAAACAGATCAGATTTTTTTGACAACACAAGGCTTCCTTACCACTGCATATCACTACGTCCAATGTCCTGTACCTGTGTTAAAGTGGCTGTTTCGGATGATGTCGGTTCACACAGATTGTATTGTGTCGGTGCAGATTTTAAGTACATTGATGGAAATAACCATTAGAAATGATACTTTCAGTGACTCTCCAGTTTGGCCCTGGATCCCATCTTTGTCTGATATAGCAGCTGTATTCTTCAACATGGGCGTTGGTTTTGGATCTTTGTTTCCTCTGGAGACTCTTCAGCCTGACTTTAATGAAGAAAATCTAATTTCTGAAACACAGAAAACACTGGGGGGAAAAGAAAGTGAAGATTCACCTTATAGTCCAGTATTTTCAGCTCTTCCTGAAACCAACATTTTAAATGTGGTTAAGTTCCTAGGTCTGTGCACATCTATACATCCAGAAGGTTACCAAGATGGAGAATTAATGCTGCTGATTTTAATGCTGTTTAAAATGAGTTTGGAAAAAGAGCTTAAACAGATTCCATTAGTAGACTTTCAGAGCCTCCTGATAAATCTCATGAAAAACATCAGAGATTGGAACACAAAGGTTCATGAACTCTGTCTGGGCATAAATGAACTCTCCAGTCATCCCCATAACCTTCTTTGGTTGGTACAGCTAGTCCCTAACTGGACATCTCGTGGA
Peptide sequence:
MMSVHTDCIVSVQILSTLMEITIRNDTFSDSPVWPWIPSLSDIAAVFFNMGVGFGSLFPLETLQPDFNEENLISETQKTLGGKESEDSPYSPVFSALPETNILNVVKFLGLCTSIHPEGYQDGELMLLILMLFKMSLEKELKQIPLVDFQSLLINLMKNIRDWNTKVHELCLGINELSSHPHNLLWLVQLVPNWTSRGRLDELQKKLQEDIRQGRGIKSPLRTGDQDSTDDGDGLLEEHREFLKKFSVTVDAIPDHHPGEEIFNFLNSGKIFNQYTLDLRDSGFIGESAVEKLILKSGKTDQIFLTTQGFLTTAYHYVQCPVPVLKWLFRMMSVHTDCIVSVQILSTLMEITIRNDTFSDSPVWPWIPSLSDIAAVFFNMGVGFGSLFPLETLQPDFNEENLISETQKTLGGKESEDSPYSPVFSALPETNILNVVKFLGLCTSIHPEGYQDGELMLLILMLFKMSLEKELKQIPLVDFQSLLINLMKNIRDWNTKVHELCLGINELSSHPHNLLWLVQLVPNWTSRG
IRESfinder result
IRESfinder score
0.815202589
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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