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mmu_circLamc1_622
Basic information of circular RNA
PanCircBase ID:
mmu_circLamc1_622
mm39_Chr. Position ID:
chr1|153109230|153116241|-
Gene name:
Lamc1
Transcript:
ENSMUST00000027752.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
20,19,18,17
Exon/intron offsets:
0,963,5770,6832
Genomic length:
7011
Exon/intron sizes in nt:
80,20,61,57,179
Flanking exon/introns:
chr1:153107617-153109230|chr1:153116241-153117622
Splice length:
622
Other database IDs:
CIRCpedia: MMU_CIRCpedia_224089, circAtlas: mmu-Lamc1_0007
Human Ortholog IDs:
Mature spliced Sequence:
CTTGTGACTGTCACCATGAAGGATCCCTTTCACTCCAGTGTAAAGAGGACGGCCGTTGTGAATGCAGGGAAGGCTTTGTGGGCAATCGCTGTGACCAGTGTGAAGAGAACTATTTCTACAATCGGTCCTGGCCTGGCTGCCAGGAGTGTCCGGCTTGTTACCGACTGGTGAAGGATAAGGTTGCTGAGCATCGAGTGAAACTCCAGGAGTTAGAGAGCCTCATCGCCAACCTTGGCACTGGGGATGACATGGTGACAGATCAAGCCTTTGAGGACAGACTTAAGGAAGCAGAAAGGGAGGTGACAGACCTTCTCCGTGAGGCTCAGGAAGTCAAAGATGTAGATCAAAATCTGATGGATCGCCTTCAGAGAGTAAATAGCAGCCTGCATAGCCAAATTAGCCGACTGCAGAATATCCGGAATACTATCGAAGAGACCGGGATCTTGGCTGAGCGAGCACGGTCCCGAGTGGAGAGTACAGAGCAGCTGATTGAGATCGCCTCCAGGGAGCTCGAGAAAGCAAAAATGGCTGCCGCCAATGTGTCAATCACTCAGCCAGAGTCTACAGGGGAGCCAAACAACATGACCCTCTTGGCAGAAGAAGCCCGAAAGCTTGCAGAGCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCCAGAGTCTACAGGGGAG
60.03
CGATTGCCCACAAAGCCTTC
60.11
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCCAGAGTCTACAGGGGAG
60.03
AGCCTTCCCTGCATTCACAA
59.89
145
PCR template sequence:
AAATGGCTGCCGCCAATGTGTCAATCACTCAGCCAGAGTCTACAGGGGAGCCAAACAACATGACCCTCTTGGCAGAAGAAGCCCGAAAGCTTGCAGAGCGCTTGTGACTGTCACCATGAAGGATCCCTTTCACTCCAGTGTAAAGAGGACGGCCGTTGTGAATGCAGGGAAGGCTTTGTGGGCAATCGCTGTGACCAGTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-541-5p(1), mmu-miR-129-5p(1), mmu-miR-673-5p(1), mmu-miR-5101(1), mmu-miR-1904(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGCTTGCAGAGCGCTTGTGACTGTCA
siRNA sets
TGACAGTCACAAGCGCTCT, GACAGTCACAAGCGCTCTG, TCACAAGCGCTCTGCAAGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCLAMC1_622_ORF_1
1.0682
0.389821686
0.742213747
381
ORF sequence:
ATGGTGACAGATCAAGCCTTTGAGGACAGACTTAAGGAAGCAGAAAGGGAGGTGACAGACCTTCTCCGTGAGGCTCAGGAAGTCAAAGATGTAGATCAAAATCTGATGGATCGCCTTCAGAGAGTAAATAGCAGCCTGCATAGCCAAATTAGCCGACTGCAGAATATCCGGAATACTATCGAAGAGACCGGGATCTTGGCTGAGCGAGCACGGTCCCGAGTGGAGAGTACAGAGCAGCTGATTGAGATCGCCTCCAGGGAGCTCGAGAAAGCAAAAATGGCTGCCGCCAATGTGTCAATCACTCAGCCAGAGTCTACAGGGGAGCCAAACAACATGACCCTCTTGGCAGAAGAAGCCCGAAAGCTTGCAGAGCGCTTGTGA
Peptide sequence:
MVTDQAFEDRLKEAEREVTDLLREAQEVKDVDQNLMDRLQRVNSSLHSQISRLQNIRNTIEETGILAERARSRVESTEQLIEIASRELEKAKMAAANVSITQPESTGEPNNMTLLAEEARKLAERL
IRESfinder result
IRESfinder score
0.312208405
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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