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mmu_circSlf2_981
Basic information of circular RNA
PanCircBase ID:
mmu_circSlf2_981
mm39_Chr. Position ID:
chr19|44947443|44964154|+
Gene name:
Slf2
Transcript:
ENSMUST00000096053.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
10,11,12,13,14,15,16,17,18
Exon/intron offsets:
0,1729,7962,8498,10032,12593,14129,14603,16624
Genomic length:
16711
Exon/intron sizes in nt:
76,142,103,177,98,88,132,78,87
Flanking exon/introns:
chr19:44940610-44947443|chr19:44964154-44967599
Splice length:
981
Other database IDs:
CIRCpedia: MMU_CIRCpedia_20461, circAtlas: mmu-Fam178a_0013
circAtlas: hsa-SLF2_0016, CIRCpedia: HSA_CIRCpedia_76839
Human Ortholog IDs:
Mature spliced Sequence:
ATGATGTCGGTTCACACAGATTGTATTGTGTCGGTGCAGATTTTAAGTACATTGATGGAAATAACCATTAGAAATGATACTTTCAGTGACTCTCCAGTTTGGCCCTGGATCCCATCTTTGTCTGATATAGCAGCTGTATTCTTCAACATGGGCGTTGGTTTTGGATCTTTGTTTCCTCTGGAGACTCTTCAGCCTGACTTTAATGAAGAAAATCTAATTTCTGAAACACAGAAAACACTGGGGGGAAAAGAAAGTGAAGATTCACCTTATAGTCCAGTATTTTCAGCTCTTCCTGAAACCAACATTTTAAATGTGGTTAAGTTCCTAGGTCTGTGCACATCTATACATCCAGAAGGTTACCAAGATGGAGAATTAATGCTGCTGATTTTAATGCTGTTTAAAATGAGTTTGGAAAAAGAGCTTAAACAGATTCCATTAGTAGACTTTCAGAGCCTCCTGATAAATCTCATGAAAAACATCAGAGATTGGAACACAAAGGTTCATGAACTCTGTCTGGGCATAAATGAACTCTCCAGTCATCCCCATAACCTTCTTTGGTTGGTACAGCTAGTCCCTAACTGGACATCTCGTGGAAGGCAGCTGAGGCAGTGCCTCAGTCTGGTGATGATGTCAAAGCTTTTGGATGAAAAGCATGAAGATATTCCTAATGCCAATAACCTTCAGATCTCGGTCCTGCATCGATATCTTGTGCAGATGAAGCCTTCTGATTTGTTGAAGAAAATGGTCTTGAAGAAAAGGGCCGAACAGCCAAATGAAACTATTGATGACAGTCTTCATTTAGAACTTGAAAAGCAGGCATATTACCTGACCTACATCCTTCTTCATTTAGTTGGGGAAGTTAGTTGCTCTCATTCTCTTTCTTCTGGACAACGGAAACACTTCGTGCTGCTTTGTGGGGCTTTGGAAAAGCATGTTAAGTGTGATATTAGGGAAGATGCAAGACTTTTCTACAGAACTAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACAACGGAAACACTTCGTGC
59.62
ACTTAAAATCTGCACCGACACA
58.53
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AACGGAAACACTTCGTGCTG
59.34
ACTTAAAATCTGCACCGACACA
58.53
140
PCR template sequence:
TTCTGGACAACGGAAACACTTCGTGCTGCTTTGTGGGGCTTTGGAAAAGCATGTTAAGTGTGATATTAGGGAAGATGCAAGACTTTTCTACAGAACTAAAATGATGTCGGTTCACACAGATTGTATTGTGTCGGTGCAGATTTTAAGTACATTGATGGAAATAACCATTAGAAATGATACTTTCAGTGACTCTCCAGTTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-15a-5p(2), mmu-miR-322-5p(2), mmu-miR-16-5p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-15b-5p(1), mmu-miR-324-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-3065-5p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTACAGAACTAAAATGATGTCGGTTC
siRNA sets
GAACCGACATCATTTTAGT, AACCGACATCATTTTAGTT, CATCATTTTAGTTCTGTAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSLF2_981_ORF_1
1.0098
-0.000125586
0.999978487
1962
ORF sequence:
ATGATGTCGGTTCACACAGATTGTATTGTGTCGGTGCAGATTTTAAGTACATTGATGGAAATAACCATTAGAAATGATACTTTCAGTGACTCTCCAGTTTGGCCCTGGATCCCATCTTTGTCTGATATAGCAGCTGTATTCTTCAACATGGGCGTTGGTTTTGGATCTTTGTTTCCTCTGGAGACTCTTCAGCCTGACTTTAATGAAGAAAATCTAATTTCTGAAACACAGAAAACACTGGGGGGAAAAGAAAGTGAAGATTCACCTTATAGTCCAGTATTTTCAGCTCTTCCTGAAACCAACATTTTAAATGTGGTTAAGTTCCTAGGTCTGTGCACATCTATACATCCAGAAGGTTACCAAGATGGAGAATTAATGCTGCTGATTTTAATGCTGTTTAAAATGAGTTTGGAAAAAGAGCTTAAACAGATTCCATTAGTAGACTTTCAGAGCCTCCTGATAAATCTCATGAAAAACATCAGAGATTGGAACACAAAGGTTCATGAACTCTGTCTGGGCATAAATGAACTCTCCAGTCATCCCCATAACCTTCTTTGGTTGGTACAGCTAGTCCCTAACTGGACATCTCGTGGAAGGCAGCTGAGGCAGTGCCTCAGTCTGGTGATGATGTCAAAGCTTTTGGATGAAAAGCATGAAGATATTCCTAATGCCAATAACCTTCAGATCTCGGTCCTGCATCGATATCTTGTGCAGATGAAGCCTTCTGATTTGTTGAAGAAAATGGTCTTGAAGAAAAGGGCCGAACAGCCAAATGAAACTATTGATGACAGTCTTCATTTAGAACTTGAAAAGCAGGCATATTACCTGACCTACATCCTTCTTCATTTAGTTGGGGAAGTTAGTTGCTCTCATTCTCTTTCTTCTGGACAACGGAAACACTTCGTGCTGCTTTGTGGGGCTTTGGAAAAGCATGTTAAGTGTGATATTAGGGAAGATGCAAGACTTTTCTACAGAACTAAAATGATGTCGGTTCACACAGATTGTATTGTGTCGGTGCAGATTTTAAGTACATTGATGGAAATAACCATTAGAAATGATACTTTCAGTGACTCTCCAGTTTGGCCCTGGATCCCATCTTTGTCTGATATAGCAGCTGTATTCTTCAACATGGGCGTTGGTTTTGGATCTTTGTTTCCTCTGGAGACTCTTCAGCCTGACTTTAATGAAGAAAATCTAATTTCTGAAACACAGAAAACACTGGGGGGAAAAGAAAGTGAAGATTCACCTTATAGTCCAGTATTTTCAGCTCTTCCTGAAACCAACATTTTAAATGTGGTTAAGTTCCTAGGTCTGTGCACATCTATACATCCAGAAGGTTACCAAGATGGAGAATTAATGCTGCTGATTTTAATGCTGTTTAAAATGAGTTTGGAAAAAGAGCTTAAACAGATTCCATTAGTAGACTTTCAGAGCCTCCTGATAAATCTCATGAAAAACATCAGAGATTGGAACACAAAGGTTCATGAACTCTGTCTGGGCATAAATGAACTCTCCAGTCATCCCCATAACCTTCTTTGGTTGGTACAGCTAGTCCCTAACTGGACATCTCGTGGAAGGCAGCTGAGGCAGTGCCTCAGTCTGGTGATGATGTCAAAGCTTTTGGATGAAAAGCATGAAGATATTCCTAATGCCAATAACCTTCAGATCTCGGTCCTGCATCGATATCTTGTGCAGATGAAGCCTTCTGATTTGTTGAAGAAAATGGTCTTGAAGAAAAGGGCCGAACAGCCAAATGAAACTATTGATGACAGTCTTCATTTAGAACTTGAAAAGCAGGCATATTACCTGACCTACATCCTTCTTCATTTAGTTGGGGAAGTTAGTTGCTCTCATTCTCTTTCTTCTGGACAACGGAAACACTTCGTGCTGCTTTGTGGGGCTTTGGAAAAGCATGTTAAGTGTGATATTAGGGAAGATGCAAGACTTTTCTACAGAACTAAA
Peptide sequence:
MMSVHTDCIVSVQILSTLMEITIRNDTFSDSPVWPWIPSLSDIAAVFFNMGVGFGSLFPLETLQPDFNEENLISETQKTLGGKESEDSPYSPVFSALPETNILNVVKFLGLCTSIHPEGYQDGELMLLILMLFKMSLEKELKQIPLVDFQSLLINLMKNIRDWNTKVHELCLGINELSSHPHNLLWLVQLVPNWTSRGRQLRQCLSLVMMSKLLDEKHEDIPNANNLQISVLHRYLVQMKPSDLLKKMVLKKRAEQPNETIDDSLHLELEKQAYYLTYILLHLVGEVSCSHSLSSGQRKHFVLLCGALEKHVKCDIREDARLFYRTKMMSVHTDCIVSVQILSTLMEITIRNDTFSDSPVWPWIPSLSDIAAVFFNMGVGFGSLFPLETLQPDFNEENLISETQKTLGGKESEDSPYSPVFSALPETNILNVVKFLGLCTSIHPEGYQDGELMLLILMLFKMSLEKELKQIPLVDFQSLLINLMKNIRDWNTKVHELCLGINELSSHPHNLLWLVQLVPNWTSRGRQLRQCLSLVMMSKLLDEKHEDIPNANNLQISVLHRYLVQMKPSDLLKKMVLKKRAEQPNETIDDSLHLELEKQAYYLTYILLHLVGEVSCSHSLSSGQRKHFVLLCGALEKHVKCDIREDARLFYRTK
IRESfinder result
IRESfinder score
0.794061203
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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