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mmu_circStam2_674
Basic information of circular RNA
PanCircBase ID:
mmu_circStam2_674
mm39_Chr. Position ID:
chr2|52599607|52609989|-
Gene name:
Stam2
Transcript:
ENSMUST00000102759.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
8,7,6,5,4,3
Exon/intron offsets:
0,5222,6092,6829,10101,10306
Genomic length:
10382
Exon/intron sizes in nt:
95,187,70,147,99,76
Flanking exon/introns:
chr2:52598237-52599607|chr2:52609989-52610895
Splice length:
674
Other database IDs:
CIRCpedia: MMU_CIRCpedia_38633
Human Ortholog IDs:
Mature spliced Sequence:
AGCAAAAGATTGCCTAAAAGCCATAATGAAAAGGGTAAACCATAAGGTCCCTCACGTTGCTCTGCAGGCATTGACCCTTCTTGGAGCTTGTGTGGCAAACTGTGGAAAGATATTTCATTTAGAAGTATGTTCCCGTGATTTTGCAACGGAAGTACGTTCTGTGATAAAAAATAAGGCTCATCCTAAAGTATGTGAAAAACTAAAATCTCTAATGGTGGAATGGTCAGAAGAATTCCAGAAGGACCCCCAATTTAGTCTGATATCTGCAACTATTAAGTCTATGAAAGAAGAAGGGGTTACTTTTCCTTCCGCAGGCTCCCAGACTGTCGCGGCTGCTGCCAAAAACGGGACATCATTGAACAAAAACAAAGAAGATGAGGACATAGCTAAAGCTATTGAGTTATCGTTGCAAGAGCAGAAGCAGCAGTACACGGAGACAAAGGCTTTGTACCCACCCGCAGAGAGTCAGCTCAATAACAAGGCTGCACGGAGAGTCAGAGCTTTATACGACTTTGAAGCTGTTGAGGACAACGAGCTCACCTTTAAACATGGTGAGCTCATTACTGTTTTGGATGACAGTGACGCCAACTGGTGGCAAGGAGAAAATCACAGAGGAACAGGACTCTTCCCCTCCAACTTTGTAACGACTGACTTAAGCACAGAGGTTGAGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCAACTGGTGGCAAGGAGAA
60.18
GTCAATGCCTGCAGAGCAAC
60.11
165
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCAACTGGTGGCAAGGAGAA
60.18
AAGAAGGGTCAATGCCTGCA
59.89
172
PCR template sequence:
GACAGTGACGCCAACTGGTGGCAAGGAGAAAATCACAGAGGAACAGGACTCTTCCCCTCCAACTTTGTAACGACTGACTTAAGCACAGAGGTTGAGACAGAGCAAAAGATTGCCTAAAAGCCATAATGAAAAGGGTAAACCATAAGGTCCCTCACGTTGCTCTGCAGGCATTGACCCTTCTTGGAGCTTGTGTGGCAAAC
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-135a-5p(1), mmu-miR-340-5p(1), mmu-miR-325-3p(1), mmu-miR-335-3p(1), mmu-miR-1904(1), mmu-miR-544-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GAGGTTGAGACAGAGCAAAAGATTGC
siRNA sets
CTTTTGCTCTGTCTCAACC, AATCTTTTGCTCTGTCTCA, TTTTGCTCTGTCTCAACCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSTAM2_674_ORF_1
0.9202
0.10244849
0.840447598
666
ORF sequence:
ATGAAAAGGGTAAACCATAAGGTCCCTCACGTTGCTCTGCAGGCATTGACCCTTCTTGGAGCTTGTGTGGCAAACTGTGGAAAGATATTTCATTTAGAAGTATGTTCCCGTGATTTTGCAACGGAAGTACGTTCTGTGATAAAAAATAAGGCTCATCCTAAAGTATGTGAAAAACTAAAATCTCTAATGGTGGAATGGTCAGAAGAATTCCAGAAGGACCCCCAATTTAGTCTGATATCTGCAACTATTAAGTCTATGAAAGAAGAAGGGGTTACTTTTCCTTCCGCAGGCTCCCAGACTGTCGCGGCTGCTGCCAAAAACGGGACATCATTGAACAAAAACAAAGAAGATGAGGACATAGCTAAAGCTATTGAGTTATCGTTGCAAGAGCAGAAGCAGCAGTACACGGAGACAAAGGCTTTGTACCCACCCGCAGAGAGTCAGCTCAATAACAAGGCTGCACGGAGAGTCAGAGCTTTATACGACTTTGAAGCTGTTGAGGACAACGAGCTCACCTTTAAACATGGTGAGCTCATTACTGTTTTGGATGACAGTGACGCCAACTGGTGGCAAGGAGAAAATCACAGAGGAACAGGACTCTTCCCCTCCAACTTTGTAACGACTGACTTAAGCACAGAGGTTGAGACAGAGCAAAAGATTGCCTAA
Peptide sequence:
MKRVNHKVPHVALQALTLLGACVANCGKIFHLEVCSRDFATEVRSVIKNKAHPKVCEKLKSLMVEWSEEFQKDPQFSLISATIKSMKEEGVTFPSAGSQTVAAAAKNGTSLNKNKEDEDIAKAIELSLQEQKQQYTETKALYPPAESQLNNKAARRVRALYDFEAVEDNELTFKHGELITVLDDSDANWWQGENHRGTGLFPSNFVTTDLSTEVETEQKIA
IRESfinder result
IRESfinder score
0.59702021
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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