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mmu_circDdx5_284

Basic information of circular RNA
PanCircBase ID:

mmu_circDdx5_284

mm39_Chr. Position ID:

chr11|106675239|106675878|-

Gene name:

Ddx5

Transcript:

ENSMUST00000021062.12

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

2

Exon/intron indexes:

9,8

Exon/intron offsets:

0,466

Genomic length:

639

Exon/intron sizes in nt:

1,11,173

Flanking exon/introns:

chr11:106674988-106675239|chr11:106675878-106675961

Splice length:

284

Other database IDs:

Human Ortholog IDs:
Mature spliced Sequence:

CCTGATAGGCAAACACTAATGTGGAGTGCAACTTGGCCAAAAGAAGTAAGACAGCTTGCTGAAGATTTCCTGAAAGACTATATTCATATCAATATTGGTGCACTGGAACTGAGTGCAAACCATAACATTCTTCAGATTGTGGATGTATGTCATGATGTCGAAAAGGATGAAAAGCTTATTCGTCTGATGGAAGAAATCATGAGTGAGAAGGAGAATAAAACTATTGTTTTTGTTGAAACCAAAAGAAGATGTGATGAACTTACCAGAAAAATGAGGAGAGATGG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

ATGGAAGAAATCATGAGTGAGAAGGA

60.07

TTTTGGCCAAGTTGCACTCC

59.54

140

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

ATGGAAGAAATCATGAGTGAGAAGG

58.88

TTTTGGCCAAGTTGCACTCC

59.54

140

PCR template sequence:

TGATGGAAGAAATCATGAGTGAGAAGGAGAATAAAACTATTGTTTTTGTTGAAACCAAAAGAAGATGTGATGAACTTACCAGAAAAATGAGGAGAGATGGCCTGATAGGCAAACACTAATGTGGAGTGCAACTTGGCCAAAAGAAGTAAGACAGCTTGCTGAAGATTTCCTGAAAGACTATATTCATATCAATATTGGTG

Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs

5

Interacting miRNAs (#binding sites)

mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-433-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-3065-5p(1)

siRNAs for circular RNA silencing
Junction sequence

TGAGGAGAGATGGCCTGATAGGCAAA

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCDDX5_284_ORF_1

1.0566

0.079427496

0.28698157

285

ORF sequence:

ATGTGGAGTGCAACTTGGCCAAAAGAAGTAAGACAGCTTGCTGAAGATTTCCTGAAAGACTATATTCATATCAATATTGGTGCACTGGAACTGAGTGCAAACCATAACATTCTTCAGATTGTGGATGTATGTCATGATGTCGAAAAGGATGAAAAGCTTATTCGTCTGATGGAAGAAATCATGAGTGAGAAGGAGAATAAAACTATTGTTTTTGTTGAAACCAAAAGAAGATGTGATGAACTTACCAGAAAAATGAGGAGAGATGGCCTGATAGGCAAACACTAA

Peptide sequence:

MWSATWPKEVRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHDVEKDEKLIRLMEEIMSEKENKTIVFVETKRRCDELTRKMRRDGLIGKH

IRESfinder result

IRESfinder score

0.391132757

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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