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mmu_circSatb1_428
Basic information of circular RNA
PanCircBase ID:
mmu_circSatb1_428
mm39_Chr. Position ID:
chr17|52110458|52112401|-
Gene name:
Satb1
Transcript:
ENSMUST00000144331.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
5,4,3
Exon/intron offsets:
0,883,1766
Genomic length:
1943
Exon/intron sizes in nt:
12,41,27,177
Flanking exon/introns:
chr17:52092668-52110458|chr17:52112401-52116070
Splice length:
428
Other database IDs:
CIRCpedia: MMU_CIRCpedia_22212, circAtlas: mmu-Satb1_0003
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_104096
Human Ortholog IDs:
Mature spliced Sequence:
GAACCATGTTACCAGTTTTCTGCGTGGTGGAACATTATGAAAACGCCATTGAGTATGATTGCAAGGAGGAGCACGCGGAATTTGTATTGGTGAGAAAGGATATGCTTTTCAACCAGCTGATAGAGATGGCGTTGCTGTCTCTAGGCTATTCACACAGCTCTGCTGCCCAAGCCAAAGGGCTCATCCAGGTTGGGAAGTGGAATCCAGTTCCACTGTCGTATGTGACAGATGCCCCTGATGCCACGGTGGCAGACATGCTTCAAGATGTGTATCATGTGGTCACCCTCAAAATTCAGTTACACAGTTGCCCTAAACTAGAAGACTTGCCTCCTGAACAATGGTCGCACACCACAGTAAGGAATGCTCTGAAGGACTTACTGAAAGATATGAACCAGAGTTCGTTGGCCAAGGAGTGCCCCCTTTCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTCGCACACCACAGTAAGGA
59.97
TACAAATTCCGCGTGCTCCT
60.04
174
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTCGCACACCACAGTAAGGA
59.97
CGTGCTCCTCCTTGCAATCA
60.67
163
PCR template sequence:
TCCTGAACAATGGTCGCACACCACAGTAAGGAATGCTCTGAAGGACTTACTGAAAGATATGAACCAGAGTTCGTTGGCCAAGGAGTGCCCCCTTTCACAGGAACCATGTTACCAGTTTTCTGCGTGGTGGAACATTATGAAAACGCCATTGAGTATGATTGCAAGGAGGAGCACGCGGAATTTGTATTGGTGAGAAAGGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-680(1), mmu-miR-335-3p(1), mmu-miR-490-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCCCCTTTCACAGGAACCATGTTACC
siRNA sets
AACATGGTTCCTGTGAAAG, ACATGGTTCCTGTGAAAGG, TAACATGGTTCCTGTGAAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSATB1_428_ORF_1
1.0312
0.211160307
0.779569043
519
ORF sequence:
ATGGTCGCACACCACAGTAAGGAATGCTCTGAAGGACTTACTGAAAGATATGAACCAGAGTTCGTTGGCCAAGGAGTGCCCCCTTTCACAGGAACCATGTTACCAGTTTTCTGCGTGGTGGAACATTATGAAAACGCCATTGAGTATGATTGCAAGGAGGAGCACGCGGAATTTGTATTGGTGAGAAAGGATATGCTTTTCAACCAGCTGATAGAGATGGCGTTGCTGTCTCTAGGCTATTCACACAGCTCTGCTGCCCAAGCCAAAGGGCTCATCCAGGTTGGGAAGTGGAATCCAGTTCCACTGTCGTATGTGACAGATGCCCCTGATGCCACGGTGGCAGACATGCTTCAAGATGTGTATCATGTGGTCACCCTCAAAATTCAGTTACACAGTTGCCCTAAACTAGAAGACTTGCCTCCTGAACAATGGTCGCACACCACAGTAAGGAATGCTCTGAAGGACTTACTGAAAGATATGAACCAGAGTTCGTTGGCCAAGGAGTGCCCCCTTTCACAG
Peptide sequence:
MVAHHSKECSEGLTERYEPEFVGQGVPPFTGTMLPVFCVVEHYENAIEYDCKEEHAEFVLVRKDMLFNQLIEMALLSLGYSHSSAAQAKGLIQVGKWNPVPLSYVTDAPDATVADMLQDVYHVVTLKIQLHSCPKLEDLPPEQWSHTTVRNALKDLLKDMNQSSLAKECPLSQ
IRESfinder result
IRESfinder score
0.412181453
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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