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mmu_circAlms1_737
Basic information of circular RNA
PanCircBase ID:
mmu_circAlms1_737
mm39_Chr. Position ID:
chr6|85618300|85644938|+
Gene name:
Alms1
Transcript:
ENSMUST00000072018.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
11,12,13,14,15
Exon/intron offsets:
0,1839,9944,15076,26548
Genomic length:
26638
Exon/intron sizes in nt:
230,126,156,135,90
Flanking exon/introns:
chr6:85606696-85618300|chr6:85644938-85654537
Splice length:
737
Other database IDs:
CIRCpedia: MMU_CIRCpedia_32112, circAtlas: mmu-Alms1_0002
Human Ortholog IDs:
Mature spliced Sequence:
TTCACAAGAACAGAGTAAGGTTTCCTTTACTACGTCCTTTGGAAAGTTATCATCTGATGCCATCACTCAGATAACAACAGAAAGTCCAGAAAAGACCACATTTTCATCTGAAATTTTTATTCATGCGGATGATCGTGGACAGGGCATTCTAGACCCCATGGCCCAAAAGCCATCCAGGTTTGCCTCATCATCCTCAGTGCAGCAAATCCCAGCTTCTCATGGCAAAGACGCCCAGCCTGTGCTGTTACCATATAAGCCATCTGGTAGTTCGAAGATGTATTATGTTCCACTGTTAAAAAGAGTTCCTTCATATCTGGATTCCAAATCTGATACCACTGTTGAGAGCTCACATTCAGGCTCAAATGATGCTATTGCCCCAGACTTTCCACCTCAAATGCTAGGCACAAGAGACGATGACCTCTCCAACACTGTAAACATTAAGCACAAAGAAGGGATTTATAGCAAGAGGGCTGCAACAAAGGGGAAAAACCCCTCTCAGAAAGGTGATGCAGCGGCCCCAGTTCAAATGCCTATAACTTGGGATGAGAATGTCTTGGACGAAAACCAAGAAGAGGTCATCAGTAGAGGAGTTGTGATCAAGATGGCAGGACCTGAAGAAATGTCATCCCTGGAGAAGGACCTTGCAGGTCCCAGTGATATCACTGTACAAGACAGAAAAACTGAAAATCTGCCAGACACTAAATCCATTAAACAGAAGGAAGGATCCTTAGAGATAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTTGCAGGTCCCAGTGATA
59.09
TCTGAGTGATGGCATCAGATGA
58.96
169
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTTGCAGGTCCCAGTGATA
59.09
CTGAGTGATGGCATCAGATGA
57.53
168
PCR template sequence:
GACCTTGCAGGTCCCAGTGATATCACTGTACAAGACAGAAAAACTGAAAATCTGCCAGACACTAAATCCATTAAACAGAAGGAAGGATCCTTAGAGATAGTTCACAAGAACAGAGTAAGGTTTCCTTTACTACGTCCTTTGGAAAGTTATCATCTGATGCCATCACTCAGATAACAACAGAAAGTCCAGAAAAGACCACA
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-339-5p(1), mmu-miR-194-5p(1), mmu-miR-218-5p(1), mmu-miR-369-3p(1), mmu-miR-490-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCCTTAGAGATAGTTCACAAGAACAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCALMS1_737_ORF_1
0.9097
0.079829403
0.811535233
654
ORF sequence:
ATGGCCCAAAAGCCATCCAGGTTTGCCTCATCATCCTCAGTGCAGCAAATCCCAGCTTCTCATGGCAAAGACGCCCAGCCTGTGCTGTTACCATATAAGCCATCTGGTAGTTCGAAGATGTATTATGTTCCACTGTTAAAAAGAGTTCCTTCATATCTGGATTCCAAATCTGATACCACTGTTGAGAGCTCACATTCAGGCTCAAATGATGCTATTGCCCCAGACTTTCCACCTCAAATGCTAGGCACAAGAGACGATGACCTCTCCAACACTGTAAACATTAAGCACAAAGAAGGGATTTATAGCAAGAGGGCTGCAACAAAGGGGAAAAACCCCTCTCAGAAAGGTGATGCAGCGGCCCCAGTTCAAATGCCTATAACTTGGGATGAGAATGTCTTGGACGAAAACCAAGAAGAGGTCATCAGTAGAGGAGTTGTGATCAAGATGGCAGGACCTGAAGAAATGTCATCCCTGGAGAAGGACCTTGCAGGTCCCAGTGATATCACTGTACAAGACAGAAAAACTGAAAATCTGCCAGACACTAAATCCATTAAACAGAAGGAAGGATCCTTAGAGATAGTTCACAAGAACAGAGTAAGGTTTCCTTTACTACGTCCTTTGGAAAGTTATCATCTGATGCCATCACTCAGATAA
Peptide sequence:
MAQKPSRFASSSSVQQIPASHGKDAQPVLLPYKPSGSSKMYYVPLLKRVPSYLDSKSDTTVESSHSGSNDAIAPDFPPQMLGTRDDDLSNTVNIKHKEGIYSKRAATKGKNPSQKGDAAAPVQMPITWDENVLDENQEEVISRGVVIKMAGPEEMSSLEKDLAGPSDITVQDRKTENLPDTKSIKQKEGSLEIVHKNRVRFPLLRPLESYHLMPSLR
IRESfinder result
IRESfinder score
0.448183631
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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