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mmu_circMap3k13_557

Basic information of circular RNA
PanCircBase ID:

mmu_circMap3k13_557

mm39_Chr. Position ID:

chr16|21710633|21711190|+

Gene name:

Map3k13

Transcript:

ENSMUST00000231988.2

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

1

Exon/intron indexes:

3

Exon/intron offsets:

0

Genomic length:

557

Exon/intron sizes in nt:

557

Flanking exon/introns:

chr16:21614725-21710633|chr16:21711190-21717238

Splice length:

557

Other database IDs:

circAtlas: mmu-Map3k13_0001

circBase: hsa_circ_0123036, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_117977

Human Ortholog IDs:
Mature spliced Sequence:

GTTTTGGAGTCCTCTCTTGCATCAAACCTCTGTTGCTGCAATCTTCTGACTGTCATCTCAGGACCTGGGTCACCCTCATGGCACAATGGCCAACCCTCAGGAGCACCTGAGCTGCTCCTCTTTGCCACACTTGCCCTTGACTGAGAACAAAACCTCTGGTGGACGAAATGAGCTTGCAGCTATGGGGAACCACCCTTCACCCAAGCTCCCTGAGGACCCTCAGGAGAGGGGGGCTATACAGTCAGAGCTGATGGAGATCACAGGCAGCCCGATCTCCACAACAGTGTTGACCAGTGTAAGCGAGGATTCTAGGGGCCAGTTTGAGAACAGTGTTCTTCAGCTAAGGGAACAGGATGAGTCAGAGATGACCCTGTCTCTGGGGAACAGCAACACTGTGGATGGAGAGAACACGAACGGACCAGAAGACATCAAGATTCAGTTCAGCAGGTCAGGCAGCGGCAGCGGCGGGTTTCTCGAAGGACTGTTTGGATGTCTCAGGCCCGTGTGGAATATCATTGGGAAGGCATATTCCACTGATTACAAGCTGCAGCAGCAAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

TGTTTGGATGTCTCAGGCCC

59.96

ACCCAGGTCCTGAGATGACA

59.88

145

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TGTTTGGATGTCTCAGGCCC

59.96

CCATTGTGCCATGAGGGTGA

60.32

164

PCR template sequence:

GGCAGCGGCGGGTTTCTCGAAGGACTGTTTGGATGTCTCAGGCCCGTGTGGAATATCATTGGGAAGGCATATTCCACTGATTACAAGCTGCAGCAGCAAGGTTTTGGAGTCCTCTCTTGCATCAAACCTCTGTTGCTGCAATCTTCTGACTGTCATCTCAGGACCTGGGTCACCCTCATGGCACAATGGCCAACCCTCAG

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-141-3p(2), mmu-miR-200a-3p(1), mmu-miR-136-5p(1), mmu-miR-370-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-207(1), mmu-miR-300-3p(1), mmu-miR-193b-3p(1)

siRNAs for circular RNA silencing
Junction sequence

CTGCAGCAGCAAGGTTTTGGAGTCCT

siRNA sets

GACTCCAAAACCTTGCTGC, ACTCCAAAACCTTGCTGCT, AGGACTCCAAAACCTTGCT

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCMAP3K13_557_ORF_1

0.8948

0.203812233

0.806596861

582

ORF sequence:

ATGGCCAACCCTCAGGAGCACCTGAGCTGCTCCTCTTTGCCACACTTGCCCTTGACTGAGAACAAAACCTCTGGTGGACGAAATGAGCTTGCAGCTATGGGGAACCACCCTTCACCCAAGCTCCCTGAGGACCCTCAGGAGAGGGGGGCTATACAGTCAGAGCTGATGGAGATCACAGGCAGCCCGATCTCCACAACAGTGTTGACCAGTGTAAGCGAGGATTCTAGGGGCCAGTTTGAGAACAGTGTTCTTCAGCTAAGGGAACAGGATGAGTCAGAGATGACCCTGTCTCTGGGGAACAGCAACACTGTGGATGGAGAGAACACGAACGGACCAGAAGACATCAAGATTCAGTTCAGCAGGTCAGGCAGCGGCAGCGGCGGGTTTCTCGAAGGACTGTTTGGATGTCTCAGGCCCGTGTGGAATATCATTGGGAAGGCATATTCCACTGATTACAAGCTGCAGCAGCAAGGTTTTGGAGTCCTCTCTTGCATCAAACCTCTGTTGCTGCAATCTTCTGACTGTCATCTCAGGACCTGGGTCACCCTCATGGCACAATGGCCAACCCTCAGGAGCACCTGA

Peptide sequence:

MANPQEHLSCSSLPHLPLTENKTSGGRNELAAMGNHPSPKLPEDPQERGAIQSELMEITGSPISTTVLTSVSEDSRGQFENSVLQLREQDESEMTLSLGNSNTVDGENTNGPEDIKIQFSRSGSGSGGFLEGLFGCLRPVWNIIGKAYSTDYKLQQQGFGVLSCIKPLLLQSSDCHLRTWVTLMAQWPTLRST

IRESfinder result

IRESfinder score

0.490237257

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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