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mmu_circSatb2_1004
Basic information of circular RNA
PanCircBase ID:
mmu_circSatb2_1004
mm39_Chr. Position ID:
chr1|56910470|56987414|-
Gene name:
Satb2
Transcript:
ENSMUST00000114415.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
7,6,5,4,3
Exon/intron offsets:
0,19851,26634,27679,76767
Genomic length:
76944
Exon/intron sizes in nt:
47,31,03,12,41,27,177
Flanking exon/introns:
chr1:56889542-56910470|chr1:56987414-57008811
Splice length:
1004
Other database IDs:
CIRCpedia: MMU_CIRCpedia_23661, circAtlas: mmu-Satb2_0016
circBase: hsa_circ_0008928, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_39066
Human Ortholog IDs:
Mature spliced Sequence:
GTTTGATGATTCCAGTTTTCTGTGTGGTGGAGCAGTTGGATGGCTCTCTTGAATACGACAACCGAGAAGAGCACGCTGAGTTCGTCTTGGTGCGGAAAGATGTGCTTTTTAGCCAGCTGGTGGAGACCGCGCTCCTGGCCCTGGGGTATTCCCACAGCTCTGCAGCGCAGGCCCAAGGAATAATCAAGCTAGGGAGGTGGAACCCCCTCCCCCTCAGTTATGTGACAGACGCCCCTGATGCGACTGTGGCCGACATGCTGCAAGATGTCTATCACGTTGTGACGCTGAAGATCCAATTACAAAGTTGTTCAAAGTTGGAAGACTTGCCTGCGGAGCAATGGAACCACGCCACCGTCCGCAATGCCTTAAAGGAACTGCTCAAAGAAATGAACCAGAGCACATTAGCCAAAGAATGCCCTCTCTCCCAGAGTATGATTTCATCCATTGTAAATAGCACATACTATGCCAATGTGTCAGCAACCAAGTGCCAGGAGTTTGGGAGATGGTACAAAAAGTATAAGAAGATAAAAGTGGAAAGAGTGGAGCGAGAGAACCTTTCAGACTATTGTGTTCTGGGCCAGCGGCCAATGCATTTACCAAATATGAACCAGCTGGCATCCCTGGGCAAAACCAACGAACAGTCTCCTCATAGCCAAATCCACCACAGTACTCCAATCCGAAACCAAGTGCCCGCACTCCAGCCCATCATGAGCCCTGGTCTTCTCTCACCGCAGCTCAGTCCTCAGCTTGTCAGGCAGCAAATAGCCATGGCCCATCTGATAAACCAACAGATAGCCGTTAGCCGACTCCTGGCTCACCAGCATCCTCAAGCCATCAACCAGCAGTTCTTGAACCACCCACCCATTCCCAGAGCAGTTAAGCCAGAGCCAACAAACTCCTCTGTGGAAGTCTCTCCTGATATCTACCAGCAAGTTAGAGATGAGTTGAAGAGGGCTAGTGTGTCTCAAGCTGTCTTTGCAAGAGTGGCATTCAACCGCACACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGGCTAGTGTGTCTCAAGCT
59.39
TCTTTCCGCACCAAGACGAA
59.89
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGGCTAGTGTGTCTCAAGC
59.39
TCTTTCCGCACCAAGACGAA
59.89
154
PCR template sequence:
GGAAGTCTCTCCTGATATCTACCAGCAAGTTAGAGATGAGTTGAAGAGGGCTAGTGTGTCTCAAGCTGTCTTTGCAAGAGTGGCATTCAACCGCACACAGGTTTGATGATTCCAGTTTTCTGTGTGGTGGAGCAGTTGGATGGCTCTCTTGAATACGACAACCGAGAAGAGCACGCTGAGTTCGTCTTGGTGCGGAAAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-150-5p(1), mmu-miR-138-5p(1), mmu-miR-185-5p(1), mmu-miR-433-3p(1), mmu-miR-27a-5p(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CAACCGCACACAGGTTTGATGATTCC
siRNA sets
AATCATCAAACCTGTGTGC, ATCATCAAACCTGTGTGCG, GAATCATCAAACCTGTGTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSATB2_1004_ORF_1
1.1345
0.225886969
0.993278488
1005
ORF sequence:
ATGATTCCAGTTTTCTGTGTGGTGGAGCAGTTGGATGGCTCTCTTGAATACGACAACCGAGAAGAGCACGCTGAGTTCGTCTTGGTGCGGAAAGATGTGCTTTTTAGCCAGCTGGTGGAGACCGCGCTCCTGGCCCTGGGGTATTCCCACAGCTCTGCAGCGCAGGCCCAAGGAATAATCAAGCTAGGGAGGTGGAACCCCCTCCCCCTCAGTTATGTGACAGACGCCCCTGATGCGACTGTGGCCGACATGCTGCAAGATGTCTATCACGTTGTGACGCTGAAGATCCAATTACAAAGTTGTTCAAAGTTGGAAGACTTGCCTGCGGAGCAATGGAACCACGCCACCGTCCGCAATGCCTTAAAGGAACTGCTCAAAGAAATGAACCAGAGCACATTAGCCAAAGAATGCCCTCTCTCCCAGAGTATGATTTCATCCATTGTAAATAGCACATACTATGCCAATGTGTCAGCAACCAAGTGCCAGGAGTTTGGGAGATGGTACAAAAAGTATAAGAAGATAAAAGTGGAAAGAGTGGAGCGAGAGAACCTTTCAGACTATTGTGTTCTGGGCCAGCGGCCAATGCATTTACCAAATATGAACCAGCTGGCATCCCTGGGCAAAACCAACGAACAGTCTCCTCATAGCCAAATCCACCACAGTACTCCAATCCGAAACCAAGTGCCCGCACTCCAGCCCATCATGAGCCCTGGTCTTCTCTCACCGCAGCTCAGTCCTCAGCTTGTCAGGCAGCAAATAGCCATGGCCCATCTGATAAACCAACAGATAGCCGTTAGCCGACTCCTGGCTCACCAGCATCCTCAAGCCATCAACCAGCAGTTCTTGAACCACCCACCCATTCCCAGAGCAGTTAAGCCAGAGCCAACAAACTCCTCTGTGGAAGTCTCTCCTGATATCTACCAGCAAGTTAGAGATGAGTTGAAGAGGGCTAGTGTGTCTCAAGCTGTCTTTGCAAGAGTGGCATTCAACCGCACACAGGTTTGA
Peptide sequence:
MIPVFCVVEQLDGSLEYDNREEHAEFVLVRKDVLFSQLVETALLALGYSHSSAAQAQGIIKLGRWNPLPLSYVTDAPDATVADMLQDVYHVVTLKIQLQSCSKLEDLPAEQWNHATVRNALKELLKEMNQSTLAKECPLSQSMISSIVNSTYYANVSATKCQEFGRWYKKYKKIKVERVERENLSDYCVLGQRPMHLPNMNQLASLGKTNEQSPHSQIHHSTPIRNQVPALQPIMSPGLLSPQLSPQLVRQQIAMAHLINQQIAVSRLLAHQHPQAINQQFLNHPPIPRAVKPEPTNSSVEVSPDIYQQVRDELKRASVSQAVFARVAFNRTQV
IRESfinder result
IRESfinder score
0.425179635
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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