top of page

mmu_ciDdx5_1187

Basic information of circular RNA
PanCircBase ID:

mmu_ciDdx5_1187

mm39_Chr. Position ID:

chr11|106673597|106674784|-

Gene name:

Ddx5

Transcript:

ENSMUST00000021062.12

CircRNA type:

Circular intronic (ci)RNA

Exon/Intron count:

1

Exon/intron indexes:

11

Exon/intron offsets:

0

Genomic length:

1187

Exon/intron sizes in nt:

1187

Flanking exon/introns:

chr11:106673519-106674784

Splice length:

1187

Other database IDs:

Human Ortholog IDs:
Mature spliced Sequence:

GTTAGTACAAACTCGAATTCATGGCTTGGTTTCCCAGAAGATCTCCATGTAGTTTTTTTTAAAGAAAGTTTATTGCTTTCTTTAACCTGCATTTTTTCTAAGTTTTTTTCACATAAAGGTGCAGTCTTTGTGGCAAGGCCTAGGCATGACAATCGGAGGACTCGAGGGGGATGGAGGACTAGTGATCGGCTGGCTGCTTCCAGTCGATTAGAGAGGTGAAAAGCTGAAAGTGTGCCAGTAATCTTCAAAGGGCAGAACATACCACCTCTGCCCCATAAACTGTTCTCTCCGGGGGAAAAAAATGGAAGTTACCTCACAGTTCACTGCCGTGGTATTTCATCTGTCCCATGCTTTGCATGATTGCCATGGTACAGCATTGTTTCAAACTGTTCACTGTGATCTGTGGGTCTTTGAGTTTCAGTGAGTTTGCTGAAATGTCGAAGAAATATTTCCAAACTTCAATGTTCAATGAAATTTTTGTTCAAGTTTGAAATGGAGAGAGCAGCTTTAAAAGCCTTTTACAAATTGGTGAGTACTGGCACATGAGACCTAGAGCAGGACCAACTTCTCACACATAGTCAGTGGGAAAAGAAAGTGCCTTGAAAGTTCCTCCCTCACCTACACAGTAGTCGTCATGTCGAGACCTGCCAGAGAGAGACACATTCTCAAGTGAATCCTGGCTTCTTGGAAGCGCTTGCCTAGACGAGACACAGTGCATTAAAACAACTTTTGGGGGACAGGTATGTTTTTCTTGCAGCTGCAGTTGTAAGGTCTTGGCAAGACAAGCAGTGTGGCCAGAGTTTTGAACTTCTGATGAGTGTAATGCAAAGGACCTTTACATTTTTGTTAAAAGGTCCTCAAAAATGAGCACATGAAGAGATTGCTGAGAAACTTTTAATTGGCCCTACTGCGCAGAAGCATTCAGATGTCACTTGATGATCTGTAAGGGGACTGTCAATTTGGGAATGTGCTAAGGAGAACACACATTCCCTTGATAGGCTGTCAGTGGGTGGGTGTTAAGACAGCTGACATGTGCAAATTTTTTTGTTGTTTTTTGGGTGTTTTGGTTTTTTTTTTTTCCTACCCTGCCCTTTTTTCCTACCTCAATGGTGTTCCTACAGGAAATGGATAACCATTTTAACTGTATTTTTTTCAGCCCGTACCTTCTTGGGAATACAATTGTCTAA

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CCTCAATGGTGTTCCTACAGGA

59.43

AACTACATGGAGATCTTCTGGGA

58.38

140

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

CCTCAATGGTGTTCCTACAGGA

59.43

AACTACATGGAGATCTTCTGGGAA

58.97

140

PCR template sequence:

GCCCTTTTTTCCTACCTCAATGGTGTTCCTACAGGAAATGGATAACCATTTTAACTGTATTTTTTTCAGCCCGTACCTTCTTGGGAATACAATTGTCTAAGTTAGTACAAACTCGAATTCATGGCTTGGTTTCCCAGAAGATCTCCATGTAGTTTTTTTTAAAGAAAGTTTATTGCTTTCTTTAACCTGCATTTTTTCTA

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

17

Interacting miRNAs (#binding sites)

mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-let-7e-5p(1), mmu-miR-34c-5p(1), mmu-miR-205-5p(1), mmu-miR-298-5p(1), mmu-miR-185-5p(1), mmu-miR-339-5p(1), mmu-miR-128-3p(1), mmu-miR-136-5p(1), mmu-miR-431-5p(1), mmu-miR-382-5p(1), mmu-miR-34b-5p(1), mmu-miR-466a-5p(1), mmu-miR-1198-5p(1), mmu-miR-466p-5p(1), mmu-miR-3087-3p(1)

siRNAs for circular RNA silencing
Junction sequence

TACAATTGTCTAAGTTAGTACAAACT

siRNA sets

TACTAACTTAGACAATTGT, GTACTAACTTAGACAATTG

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

NA

NA

NA

NA

NA

ORF sequence:

NA

Peptide sequence:

NA

IRESfinder result

IRESfinder score

0.842629069

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

bottom of page