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mmu_circSmchd1_1201
Basic information of circular RNA
PanCircBase ID:
mmu_circSmchd1_1201
mm39_Chr. Position ID:
chr17|71665131|71677991|-
Gene name:
Smchd1
Transcript:
ENSMUST00000127430.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
44,43,42,41,40,39,38,37,36,35
Exon/intron offsets:
0,211,1890,3704,4883,6952,7209,11671,12087,12772
Genomic length:
12860
Exon/intron sizes in nt:
71,110,191,123,86,120,127,153,132,88
Flanking exon/introns:
chr17:71660552-71665131|chr17:71677991-71684008
Splice length:
1201
Other database IDs:
circAtlas: mmu-Smchd1_0018
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_88151
Human Ortholog IDs:
Mature spliced Sequence:
GGAGAAAACTATCCCTAACAAGGTGGGAGCATATTGTATCCAGTTTGATTTCATGATTGATAAGACAAATATTCTAAGCAGCCAACAGGTTATAGTTGATGTTCTCCCCAACCAGCCTATGAAGTTGGTTCCTGACAGCCAACCAGCTACCCCAGCTGTTTCTAATGTCCGTTCAATTGCCAGCAGGACCTTGGTCAAAGACCTGCGCCTCAGTATCACAGATAATTATGGTAATCACACTGGAATGGATCTGGTTGGCACTGTAGTAGCAACCATTAAAGGCTTTAATGAGGAGGACACTGATACCCCACTCTTCATCGGGAAGGTTAGGACGCTTGAGTTTCCCTTTGTGAAAGGCTCTGCTGAAATCACGACTCTAGTGCTGGCAGAAAATAGTCCTGGAAGGGATAGTACTGAATACTTTATTATCTTTGAGCCTCGGCTGTCAACTGTATCAGGAACATTAGAATCATATAGCCTGCCATTTATGTTTTACAATGATGTTAAGAAGCAGCAACAAATGGCAGCGCTTACGAAGGAGAAGGACGAGTTATCCAAGTCCATCACTATGTACAGAAGTCTCTTCGATGCCAACAAGCAGCTTGTGGATGAAATGAAATGCCAAGCTGAAGAAGCAAAGTTAAAAGAGACCCAGCTACGAAATGAACTAAAAGCGTACAATATTGATATTCCTGCGACACAACAGACAACTCATATTGAAGCACTTTTGGAAAAAAAGATAACAGAACAGAACGAGCTTAAAAAGAGGCCCAGAAGGTTGTGTACTCTTCCAAACTACACTAAACGCAGTGGAGATATTTTGGGAAAGATTGCACATCTAGCACAAATTGAAGATGATCGAGCTGCCATGGTTATCTCTTGGCATCTGGCAAGTGACATGGACTGTGTGGTTACCCTAACCACTGATGCCGCACGCGCTATCTATGACGAAACTCAAGGTCGCCAGCAAGTGTTGCCCCTTGATTCTATTTACAGGAAAACTCTTCCAGATTGGAAAAGACCTCTACCTCATTTCCGAAATGGTAAATTACACTTTAAGCCCTTTGGAAATCCAGTCTTTGCCCGAGATTTGTTAACATTCCCAGATAATATTGAACATTGTGAAACAGTTTTTGGTATGCTGTTAGGAGACACCATTATTTTGGATAATCTGGATGCAGCCAATCATTATAGAAAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGTATGCTGTTAGGAGACACCA
59.5
AACCTGTTGGCTGCTTAGAA
57.34
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGTATGCTGTTAGGAGACACC
59.5
AACCTGTTGGCTGCTTAGAA
57.34
158
PCR template sequence:
CCCAGATAATATTGAACATTGTGAAACAGTTTTTGGTATGCTGTTAGGAGACACCATTATTTTGGATAATCTGGATGCAGCCAATCATTATAGAAAAGAGGGAGAAAACTATCCCTAACAAGGTGGGAGCATATTGTATCCAGTTTGATTTCATGATTGATAAGACAAATATTCTAAGCAGCCAACAGGTTATAGTTGAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
18
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-199a-5p(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-miR-139-5p(1), mmu-let-7d-5p(1), mmu-miR-370-3p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTATAGAAAAGAGGGAGAAAACTATC
siRNA sets
TTTTCTCCCTCTTTTCTAT, TAGTTTTCTCCCTCTTTTC, AGTTTTCTCCCTCTTTTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMCHD1_1201_ORF_1
1.0153
0.132711908
0.99749233
1227
ORF sequence:
ATGCAGCCAATCATTATAGAAAAGAGGGAGAAAACTATCCCTAACAAGGTGGGAGCATATTGTATCCAGTTTGATTTCATGATTGATAAGACAAATATTCTAAGCAGCCAACAGGTTATAGTTGATGTTCTCCCCAACCAGCCTATGAAGTTGGTTCCTGACAGCCAACCAGCTACCCCAGCTGTTTCTAATGTCCGTTCAATTGCCAGCAGGACCTTGGTCAAAGACCTGCGCCTCAGTATCACAGATAATTATGGTAATCACACTGGAATGGATCTGGTTGGCACTGTAGTAGCAACCATTAAAGGCTTTAATGAGGAGGACACTGATACCCCACTCTTCATCGGGAAGGTTAGGACGCTTGAGTTTCCCTTTGTGAAAGGCTCTGCTGAAATCACGACTCTAGTGCTGGCAGAAAATAGTCCTGGAAGGGATAGTACTGAATACTTTATTATCTTTGAGCCTCGGCTGTCAACTGTATCAGGAACATTAGAATCATATAGCCTGCCATTTATGTTTTACAATGATGTTAAGAAGCAGCAACAAATGGCAGCGCTTACGAAGGAGAAGGACGAGTTATCCAAGTCCATCACTATGTACAGAAGTCTCTTCGATGCCAACAAGCAGCTTGTGGATGAAATGAAATGCCAAGCTGAAGAAGCAAAGTTAAAAGAGACCCAGCTACGAAATGAACTAAAAGCGTACAATATTGATATTCCTGCGACACAACAGACAACTCATATTGAAGCACTTTTGGAAAAAAAGATAACAGAACAGAACGAGCTTAAAAAGAGGCCCAGAAGGTTGTGTACTCTTCCAAACTACACTAAACGCAGTGGAGATATTTTGGGAAAGATTGCACATCTAGCACAAATTGAAGATGATCGAGCTGCCATGGTTATCTCTTGGCATCTGGCAAGTGACATGGACTGTGTGGTTACCCTAACCACTGATGCCGCACGCGCTATCTATGACGAAACTCAAGGTCGCCAGCAAGTGTTGCCCCTTGATTCTATTTACAGGAAAACTCTTCCAGATTGGAAAAGACCTCTACCTCATTTCCGAAATGGTAAATTACACTTTAAGCCCTTTGGAAATCCAGTCTTTGCCCGAGATTTGTTAACATTCCCAGATAATATTGAACATTGTGAAACAGTTTTTGGTATGCTGTTAGGAGACACCATTATTTTGGATAATCTGGATGCAGCCAATCATTATAGAAAAGAG
Peptide sequence:
MQPIIIEKREKTIPNKVGAYCIQFDFMIDKTNILSSQQVIVDVLPNQPMKLVPDSQPATPAVSNVRSIASRTLVKDLRLSITDNYGNHTGMDLVGTVVATIKGFNEEDTDTPLFIGKVRTLEFPFVKGSAEITTLVLAENSPGRDSTEYFIIFEPRLSTVSGTLESYSLPFMFYNDVKKQQQMAALTKEKDELSKSITMYRSLFDANKQLVDEMKCQAEEAKLKETQLRNELKAYNIDIPATQQTTHIEALLEKKITEQNELKKRPRRLCTLPNYTKRSGDILGKIAHLAQIEDDRAAMVISWHLASDMDCVVTLTTDAARAIYDETQGRQQVLPLDSIYRKTLPDWKRPLPHFRNGKLHFKPFGNPVFARDLLTFPDNIEHCETVFGMLLGDTIILDNLDAANHYRKE
IRESfinder result
IRESfinder score
0.645363683
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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