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mmu_circItsn2_1222
Basic information of circular RNA
PanCircBase ID:
mmu_circItsn2_1222
mm39_Chr. Position ID:
chr12|4708014|4723607|+
Gene name:
Itsn2
Transcript:
ENSMUST00000062580.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
20,21,22,23,24,25,26,27,28
Exon/intron offsets:
0,427,3844,6522,8145,13258,13387,14722,15401
Genomic length:
15593
Exon/intron sizes in nt:
1,76,13,02,06,86,16,74,00,00,00,000
Flanking exon/introns:
chr12:4703543-4708014|chr12:4723607-4747141
Splice length:
1222
Other database IDs:
circAtlas: mmu-Itsn2_0013
circBase: hsa_circ_0119536, circAtlas: hsa-ITSN2_0014, CIRCpedia: HSA_CIRCpedia_40417
Human Ortholog IDs:
Mature spliced Sequence:
GTTGATGAAAAAACTGTAGGAGAGCCTGGTTGGCTTTATGGTAGTTTTCAGGGAAAGTTTGGCTGGTTCCCGTGCAACTATGTAGAAAAAGTGCTGTCAAGTGAAAAAGCTCTGTCTCCTAAGAAGGCCTTACTTCCTCCTACAGTGTCTCTCTCTGCTACCTCAACTTCTTCCCAGCCACCAGCATCAGTGACTGATTATCACAATGTATCCTTCTCAAACCTTACTGTTAATACAACATGGCAGCAGAAGTCAGCTTTTACCCGCACTGTGTCCCCTGGATCTGTGTCCCCCATTCACGGACAGGGGCAGGCTGTAGAAAACCTGAAAGCCCAGGCCCTTTGTTCCTGGACGGCAAAGAAGGAGAACCACCTGAACTTCTCAAAGCACGACGTCATCACTGTCCTGGAGCAGCAGGAAAACTGGTGGTTTGGGGAGGTGCACGGAGGAAGAGGATGGTTCCCCAAGTCTTATGTCAAGCTCATTCCTGGGAATGAAGTACAGCGAGGAGAGCCAGAAGCTTTGTATGCAGCTGTGACTAAGAAACCTACCTCCACAGCCTATCCAGTTACCTCCACAGCCTATCCAGTTGGAGAAGACTACATTGCACTTTATTCATACTCAAGTGTAGAGCCCGGGGATTTGACTTTCACTGAAGGTGAAGAAATTCTAGTGACCCAGAAAGATGGAGAGTGGTGGACAGGAAGTATTGGAGAGAGAACTGGAATCTTCCCGTCCAACTACGTCAGACCAAAGGATCAAGAGAATTTTGGGAATGCTAGCAAATCTGGAGCATCAAACAAAAAACCCGAGATCGCTCAAGTAACTTCAGCATATGCTGCTTCAGGGACTGAGCAGCTCAGCCTTGCGCCAGGACAGTTAATATTAATCTTAAAGAAAAACACAAGCGGGTGGTGGCAAGGAGAGCTACAGGCCAGAGGGAAGAAACGACAGAAGGGATGGTTTCCTGCCAGCCATGTAAAGCTGCTAGGTCCAAGCAGTGAAAGAACCATGCCTACTTTTCACGCTGTATGTCAAGTGATTGCTATGTATGACTACATGGCGAATAACGAAGATGAGCTCAATTTCTCCAAAGGACAGCTGATTAATGTTATGAACAAAGATGACCCTGACTGGTGGCAAGGAGAAACCAATGGTCTGACTGGTCTCTTTCCTTCAAACTATGTTAAGATGACAACAGACTCAGATCCAAGTCAACAGT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGGTGGCAAGGAGAAACC
60.18
ACCAGCCAAACTTTCCCTGA
59.44
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGTGGCAAGGAGAAACCA
60.18
ACCAGCCAAACTTTCCCTGA
59.44
156
PCR template sequence:
GATGACCCTGACTGGTGGCAAGGAGAAACCAATGGTCTGACTGGTCTCTTTCCTTCAAACTATGTTAAGATGACAACAGACTCAGATCCAAGTCAACAGTGTTGATGAAAAAACTGTAGGAGAGCCTGGTTGGCTTTATGGTAGTTTTCAGGGAAAGTTTGGCTGGTTCCCGTGCAACTATGTAGAAAAAGTGCTGTCAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
21
Interacting miRNAs (#binding sites)
mmu-let-7d-5p(2), mmu-miR-9-5p(1), mmu-let-7a-5p(1), mmu-miR-15a-5p(1), mmu-miR-20a-5p(1), mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-15b-5p(1), mmu-miR-130a-3p(1), mmu-miR-138-5p(1), mmu-miR-149-5p(1), mmu-miR-130b-3p(1), mmu-miR-301b-3p(1), mmu-miR-301a-3p(1), mmu-miR-466d-3p(1), mmu-miR-98-5p(1), mmu-miR-499-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-5101(1), mmu-miR-670-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
CCAAGTCAACAGTGTTGATGAAAAAA
siRNA sets
TTTTTCATCAACACTGTTG,TTTTTTCATCAACACTGTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCITSN2_1222_ORF_3
1.0831
0.117712341
0.223386841
216
ORF sequence:
ATGCCTACTTTTCACGCTGTATGTCAAGTGATTGCTATGTATGACTACATGGCGAATAACGAAGATGAGCTCAATTTCTCCAAAGGACAGCTGATTAATGTTATGAACAAAGATGACCCTGACTGGTGGCAAGGAGAAACCAATGGTCTGACTGGTCTCTTTCCTTCAAACTATGTTAAGATGACAACAGACTCAGATCCAAGTCAACAGTGTTGA
Peptide sequence:
MPTFHAVCQVIAMYDYMANNEDELNFSKGQLINVMNKDDPDWWQGETNGLTGLFPSNYVKMTTDSDPSQQC
IRESfinder result
IRESfinder score
0.555411067
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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