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mmu_circItsn1_709
Basic information of circular RNA
PanCircBase ID:
mmu_circItsn1_709
mm39_Chr. Position ID:
chr16|91579048|91609041|+
Gene name:
Itsn1
Transcript:
ENSMUST00000114001.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
2,3,4,5,6,7,8,9
Exon/intron offsets:
0,1902,3127,11446,19477,20874,23932,29929
Genomic length:
29993
Exon/intron sizes in nt:
60,93,64,161,69,97,101,64
Flanking exon/introns:
chr16:91526487-91579048|chr16:91609041-91612289
Splice length:
709
Other database IDs:
CIRCpedia: MMU_CIRCpedia_34202, circAtlas: mmu-Itsn1_0019
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GCGTCGATCAGCAAGGTGAACGTAATAGAACCATGGCTCAGTTTCCCACACCTTTCGGTGGTAGCCTGGATGTCTGGGCCATAACTGTGGAGGAAAGGGCCAAGCATGACCAGCAGTTCCTTAGCCTGAAGCCGATAGCGGGATTTATTACTGGTGATCAAGCGAGGAACTTTTTTTTCCAATCTGGGTTACCTCAGCCTGTCTTAGCACAAATATGGGCGCTAGCGGACATGAATAACGATGGAAGGATGGATCAAGTGGAATTTTCCATAGCCATGAAGCTTATCAAACTGAAGCTACAAGGATATCAGCTCCCCTCCACACTTCCCCCTGTCATGAAACAGCAACCAGTGGCTATTTCCAGTGCACCAGCATTTGCAGCAGTGCCTCCCCTGGCTAACGGGGCTCCTCCCGTCATACAGCCTCTGCCTGCGTTTGCGCATCCTGCAGCCACATTGCCAAAGAGTTCTTCCTTCAGCAGATCTGGTCCAGGGTCACAATTAAACACTAAGTTACAGAAGGCACAATCATTCGATGTCGCCAGCGCCCCTCCAGCAGCAGAATGGGCTGTGCCTCAGTCATCAAGGCTGAAATACAGGCAGTTATTCAACAGCCACGACAAAACTATGAGTGGACACTTAACAGGTCCCCAGGCAAGAACTATTCTCATGCAATCAAGTTTACCCCAGGCTCAGCTGGCTTCAATATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGTCCCCAGGCAAGAACTA
60.18
CCTCCACAGTTATGGCCCAG
60.11
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGTCCCCAGGCAAGAACTA
60.18
CAGACATCCAGGCTACCACC
59.82
142
PCR template sequence:
ACAGCCACGACAAAACTATGAGTGGACACTTAACAGGTCCCCAGGCAAGAACTATTCTCATGCAATCAAGTTTACCCCAGGCTCAGCTGGCTTCAATATGGCGTCGATCAGCAAGGTGAACGTAATAGAACCATGGCTCAGTTTCCCACACCTTTCGGTGGTAGCCTGGATGTCTGGGCCATAACTGTGGAGGAAAGGGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-328-3p(1), mmu-miR-138-5p(1), mmu-miR-182-5p(1), mmu-miR-758-3p(1), mmu-miR-362-5p(1), mmu-miR-666-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
TGGCTTCAATATGGCGTCGATCAGCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCITSN1_709_ORF_1
0.9319
0.033634589
0.834357369
696
ORF sequence:
ATGGCTCAGTTTCCCACACCTTTCGGTGGTAGCCTGGATGTCTGGGCCATAACTGTGGAGGAAAGGGCCAAGCATGACCAGCAGTTCCTTAGCCTGAAGCCGATAGCGGGATTTATTACTGGTGATCAAGCGAGGAACTTTTTTTTCCAATCTGGGTTACCTCAGCCTGTCTTAGCACAAATATGGGCGCTAGCGGACATGAATAACGATGGAAGGATGGATCAAGTGGAATTTTCCATAGCCATGAAGCTTATCAAACTGAAGCTACAAGGATATCAGCTCCCCTCCACACTTCCCCCTGTCATGAAACAGCAACCAGTGGCTATTTCCAGTGCACCAGCATTTGCAGCAGTGCCTCCCCTGGCTAACGGGGCTCCTCCCGTCATACAGCCTCTGCCTGCGTTTGCGCATCCTGCAGCCACATTGCCAAAGAGTTCTTCCTTCAGCAGATCTGGTCCAGGGTCACAATTAAACACTAAGTTACAGAAGGCACAATCATTCGATGTCGCCAGCGCCCCTCCAGCAGCAGAATGGGCTGTGCCTCAGTCATCAAGGCTGAAATACAGGCAGTTATTCAACAGCCACGACAAAACTATGAGTGGACACTTAACAGGTCCCCAGGCAAGAACTATTCTCATGCAATCAAGTTTACCCCAGGCTCAGCTGGCTTCAATATGGCGTCGATCAGCAAGGTGA
Peptide sequence:
MAQFPTPFGGSLDVWAITVEERAKHDQQFLSLKPIAGFITGDQARNFFFQSGLPQPVLAQIWALADMNNDGRMDQVEFSIAMKLIKLKLQGYQLPSTLPPVMKQQPVAISSAPAFAAVPPLANGAPPVIQPLPAFAHPAATLPKSSSFSRSGPGSQLNTKLQKAQSFDVASAPPAAEWAVPQSSRLKYRQLFNSHDKTMSGHLTGPQARTILMQSSLPQAQLASIWRRSAR
IRESfinder result
IRESfinder score
0.514314991
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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