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mmu_circSmchd1_495
Basic information of circular RNA
PanCircBase ID:
mmu_circSmchd1_495
mm39_Chr. Position ID:
chr17|71665131|71668958|-
Gene name:
Smchd1
Transcript:
ENSMUST00000127430.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
44,43,42,41
Exon/intron offsets:
0,211,1890,3704
Genomic length:
3827
Exon/intron sizes in nt:
71,11,01,91,123
Flanking exon/introns:
chr17:71660552-71665131|chr17:71668958-71670014
Splice length:
495
Other database IDs:
CIRCpedia: MMU_CIRCpedia_27777, circAtlas: mmu-Smchd1_0055
Human Ortholog IDs:
Mature spliced Sequence:
ACAACTCATATTGAAGCACTTTTGGAAAAAAAGATAACAGAACAGAACGAGCTTAAAAAGAGGCCCAGAAGGTTGTGTACTCTTCCAAACTACACTAAACGCAGTGGAGATATTTTGGGAAAGATTGCACATCTAGCACAAATTGAAGATGATCGAGCTGCCATGGTTATCTCTTGGCATCTGGCAAGTGACATGGACTGTGTGGTTACCCTAACCACTGATGCCGCACGCGCTATCTATGACGAAACTCAAGGTCGCCAGCAAGTGTTGCCCCTTGATTCTATTTACAGGAAAACTCTTCCAGATTGGAAAAGACCTCTACCTCATTTCCGAAATGGTAAATTACACTTTAAGCCCTTTGGAAATCCAGTCTTTGCCCGAGATTTGTTAACATTCCCAGATAATATTGAACATTGTGAAACAGTTTTTGGTATGCTGTTAGGAGACACCATTATTTTGGATAATCTGGATGCAGCCAATCATTATAGAAAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGTATGCTGTTAGGAGACACCA
59.5
CACAACCTTCTGGGCCTCTT
59.89
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGTATGCTGTTAGGAGACACC
59.5
CACAACCTTCTGGGCCTCTT
59.89
144
PCR template sequence:
CCCAGATAATATTGAACATTGTGAAACAGTTTTTGGTATGCTGTTAGGAGACACCATTATTTTGGATAATCTGGATGCAGCCAATCATTATAGAAAAGAGACAACTCATATTGAAGCACTTTTGGAAAAAAAGATAACAGAACAGAACGAGCTTAAAAAGAGGCCCAGAAGGTTGTGTACTCTTCCAAACTACACTAAAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-140-5p(1), mmu-let-7a-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-1a-3p(1), mmu-miR-206-3p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-106b-5p(1), mmu-let-7d-5p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTATAGAAAAGAGACAACTCATATTG
siRNA sets
ATATGAGTTGTCTCTTTTC, TATGAGTTGTCTCTTTTCT, AATATGAGTTGTCTCTTTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMCHD1_495_ORF_1
0.9918
0.041764676
0.938429385
828
ORF sequence:
ATGGTTATCTCTTGGCATCTGGCAAGTGACATGGACTGTGTGGTTACCCTAACCACTGATGCCGCACGCGCTATCTATGACGAAACTCAAGGTCGCCAGCAAGTGTTGCCCCTTGATTCTATTTACAGGAAAACTCTTCCAGATTGGAAAAGACCTCTACCTCATTTCCGAAATGGTAAATTACACTTTAAGCCCTTTGGAAATCCAGTCTTTGCCCGAGATTTGTTAACATTCCCAGATAATATTGAACATTGTGAAACAGTTTTTGGTATGCTGTTAGGAGACACCATTATTTTGGATAATCTGGATGCAGCCAATCATTATAGAAAAGAGACAACTCATATTGAAGCACTTTTGGAAAAAAAGATAACAGAACAGAACGAGCTTAAAAAGAGGCCCAGAAGGTTGTGTACTCTTCCAAACTACACTAAACGCAGTGGAGATATTTTGGGAAAGATTGCACATCTAGCACAAATTGAAGATGATCGAGCTGCCATGGTTATCTCTTGGCATCTGGCAAGTGACATGGACTGTGTGGTTACCCTAACCACTGATGCCGCACGCGCTATCTATGACGAAACTCAAGGTCGCCAGCAAGTGTTGCCCCTTGATTCTATTTACAGGAAAACTCTTCCAGATTGGAAAAGACCTCTACCTCATTTCCGAAATGGTAAATTACACTTTAAGCCCTTTGGAAATCCAGTCTTTGCCCGAGATTTGTTAACATTCCCAGATAATATTGAACATTGTGAAACAGTTTTTGGTATGCTGTTAGGAGACACCATTATTTTGGATAATCTGGATGCAGCCAATCATTATAGAAAAGAG
Peptide sequence:
MVISWHLASDMDCVVTLTTDAARAIYDETQGRQQVLPLDSIYRKTLPDWKRPLPHFRNGKLHFKPFGNPVFARDLLTFPDNIEHCETVFGMLLGDTIILDNLDAANHYRKETTHIEALLEKKITEQNELKKRPRRLCTLPNYTKRSGDILGKIAHLAQIEDDRAAMVISWHLASDMDCVVTLTTDAARAIYDETQGRQQVLPLDSIYRKTLPDWKRPLPHFRNGKLHFKPFGNPVFARDLLTFPDNIEHCETVFGMLLGDTIILDNLDAANHYRKE
IRESfinder result
IRESfinder score
0.726135905
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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