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mmu_circZmynd8_1027
Basic information of circular RNA
PanCircBase ID:
mmu_circZmynd8_1027
mm39_Chr. Position ID:
chr2|165670127|165684797|-
Gene name:
Zmynd8
Transcript:
ENSMUST00000109266.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
10,9,8,7,6,5,4
Exon/intron offsets:
0,5101,6682,9073,10604,11790,14556
Genomic length:
14670
Exon/intron sizes in nt:
482,116,78,56,88,93,114
Flanking exon/introns:
chr2:165662608-165670127|chr2:165684797-165687940
Splice length:
1027
Other database IDs:
CIRCpedia: MMU_CIRCpedia_11558, circAtlas: mmu-Zmynd8_0004
circAtlas: hsa-ZMYND8_0016, CIRCpedia: HSA_CIRCpedia_34440
Human Ortholog IDs:
Mature spliced Sequence:
AAGATTACAGTAGCAGAATGCATCGAGACGCAGAGCAAAGCCATGACCATGCTGACCATTGAACAACTGTCCTACCTGCTCAAGTTTGCCATTCAGAAAATGAAGCAGCCAGGGACGGATGCATTCCAGAAGCCTGTTCCATTGGAGCAACACCCTGACTATGCAGAATATATTTTCCACCCCATGGACCTTTGTACATTGGAAAAGAATGCAAAAAAGAAGATGTACGGCTGCACAGAAGCCTTCCTGGCCGATGCCAAGTGGATCCTGCACAACTGCATTATTTATAATGGGGGAAATCACAAGTTGACGCAAATAGCAAAAGTCGTCATCAAAATCTGTGAGCACGAGATGAATGAAATCGAAGTCTGTCCAGAATGTTATCTTGCAGCTTGCCAAAAACGAGACAACTGGTTCTGTGAGCCCTGTAGCAATCCGCACCCTTTGGTCTGGGCAAAACTGAAAGGATTTCCATTCTGGCCAGCGAAAGCTCTGAGGGACAAAGACGGGCAGGTTGACGCCCGTTTCTTTGGACAACATGACAGAGCCTGGGTTCCAGTCAATAATTGCTACCTCATGTCTAAAGAAATCCCCTTTTCTGTGAAAAAGACTAAAAGTATCTTCAACAGCGCCATGCAAGAGATGGAAGTTTACGTGGAGAACATACGGAGGAAGTTTGGGGTTTTTAATTACTCCCCGTTCAGGACGCCCTACACGCCCAACAACCAGTACCAAATGCTGCTGGATCCCAGCAACCCCAGCGCGGGCACAGCCAAGACAGACAAACAGGAGAAGGTGAAGCTTAATTTTGACATGACAGCGTCCCCCAAGATCCTTCTGAGCAAGCCCCTTCTGAGCGGGGGTGCCGGCCGCAGGATCTCCCTGTCCGACATGCCTCGCTCCCCCACCAGTACGAACTCTTCCGTGCACACGGGCTCCGATGTGGAGCAGGACCCCGAGAAGAAGGCCCCGTCCAGCCACTTCAGCGCAAGCGAGGAGTCCATGGACTTCCTTGATAAGAGCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCAGGACCCCGAGAAGAA
60.23
ATGGTCAGCATGGTCATGGC
60.75
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGCAGGACCCCGAGAAGAA
61.26
ATGGTCAGCATGGTCATGGC
60.75
141
PCR template sequence:
CACACGGGCTCCGATGTGGAGCAGGACCCCGAGAAGAAGGCCCCGTCCAGCCACTTCAGCGCAAGCGAGGAGTCCATGGACTTCCTTGATAAGAGCACAGAAGATTACAGTAGCAGAATGCATCGAGACGCAGAGCAAAGCCATGACCATGCTGACCATTGAACAACTGTCCTACCTGCTCAAGTTTGCCATTCAGAAAA
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-let-7e-5p(2), mmu-let-7a-5p(1), mmu-miR-16-5p(1), mmu-miR-103-3p(1), mmu-let-7b-5p(1), mmu-miR-135a-5p(1), mmu-let-7c-5p(1), mmu-miR-322-5p(1), mmu-let-7d-5p(1), mmu-miR-153-3p(1), mmu-miR-182-5p(1), mmu-miR-107-3p(1), mmu-miR-98-5p(1), mmu-miR-129-5p(1), mmu-miR-207(1), mmu-miR-5101(1), mmu-miR-484(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
GATAAGAGCACAGAAGATTACAGTAG
siRNA sets
CTACTGTAATCTTCTGTGC, TACTGTAATCTTCTGTGCT, AATCTTCTGTGCTCTTATC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCZMYND8_1027_ORF_1
1.0285
0.274919578
0.996912574
1113
ORF sequence:
ATGTGGAGCAGGACCCCGAGAAGAAGGCCCCGTCCAGCCACTTCAGCGCAAGCGAGGAGTCCATGGACTTCCTTGATAAGAGCACAGAAGATTACAGTAGCAGAATGCATCGAGACGCAGAGCAAAGCCATGACCATGCTGACCATTGAACAACTGTCCTACCTGCTCAAGTTTGCCATTCAGAAAATGAAGCAGCCAGGGACGGATGCATTCCAGAAGCCTGTTCCATTGGAGCAACACCCTGACTATGCAGAATATATTTTCCACCCCATGGACCTTTGTACATTGGAAAAGAATGCAAAAAAGAAGATGTACGGCTGCACAGAAGCCTTCCTGGCCGATGCCAAGTGGATCCTGCACAACTGCATTATTTATAATGGGGGAAATCACAAGTTGACGCAAATAGCAAAAGTCGTCATCAAAATCTGTGAGCACGAGATGAATGAAATCGAAGTCTGTCCAGAATGTTATCTTGCAGCTTGCCAAAAACGAGACAACTGGTTCTGTGAGCCCTGTAGCAATCCGCACCCTTTGGTCTGGGCAAAACTGAAAGGATTTCCATTCTGGCCAGCGAAAGCTCTGAGGGACAAAGACGGGCAGGTTGACGCCCGTTTCTTTGGACAACATGACAGAGCCTGGGTTCCAGTCAATAATTGCTACCTCATGTCTAAAGAAATCCCCTTTTCTGTGAAAAAGACTAAAAGTATCTTCAACAGCGCCATGCAAGAGATGGAAGTTTACGTGGAGAACATACGGAGGAAGTTTGGGGTTTTTAATTACTCCCCGTTCAGGACGCCCTACACGCCCAACAACCAGTACCAAATGCTGCTGGATCCCAGCAACCCCAGCGCGGGCACAGCCAAGACAGACAAACAGGAGAAGGTGAAGCTTAATTTTGACATGACAGCGTCCCCCAAGATCCTTCTGAGCAAGCCCCTTCTGAGCGGGGGTGCCGGCCGCAGGATCTCCCTGTCCGACATGCCTCGCTCCCCCACCAGTACGAACTCTTCCGTGCACACGGGCTCCGATGTGGAGCAGGACCCCGAGAAGAAGGCCCCGTCCAGCCACTTCAGCGCAAGCGAGGAGTCCATGGACTTCCTTGATAAGAGCACA
Peptide sequence:
MWSRTPRRRPRPATSAQARSPWTSLIRAQKITVAECIETQSKAMTMLTIEQLSYLLKFAIQKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAKVVIKICEHEMNEIEVCPECYLAACQKRDNWFCEPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPVNNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVENIRRKFGVFNYSPFRTPYTPNNQYQMLLDPSNPSAGTAKTDKQEKVKLNFDMTASPKILLSKPLLSGGAGRRISLSDMPRSPTSTNSSVHTGSDVEQDPEKKAPSSHFSASEESMDFLDKST
IRESfinder result
IRESfinder score
0.422635751
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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