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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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Institute of Life sciences, Bhubaneswar, India

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