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mmu_ciCsde1_698

Basic information of circular RNA
PanCircBase ID:

mmu_ciCsde1_698

mm39_Chr. Position ID:

chr3|102951247|102951945|+

Gene name:

Csde1

Transcript:

ENSMUST00000198174.2

CircRNA type:

Circular intronic (ci)RNA

Exon/Intron count:

1

Exon/intron indexes:

3

Exon/intron offsets:

0

Genomic length:

698

Exon/intron sizes in nt:

698

Flanking exon/introns:

chr3:102951247-102952074

Splice length:

698

Other database IDs:

Human Ortholog IDs:
Mature spliced Sequence:

GTAAATTGTCTTTATCAGCAATGTCTTCTTCTGACCAATCAGTACAATATTATGATGATACACTAAAGGTGGAGTCTGTTTGATTGATGTAGTTGTGTGTAGTGGGGTGTATCTTTTAATAGGTATTTTAATTAAAAAAAAAAAAAAAACAAAAAACAAAATAGATGCTGATGGTGTGGTTCAGTGGCAGAGGGCTGACCTAGCATGCAAAAGGCCCCCAGTACTGCAGAAAGAAAAGAGACACTAATGAACGGTAGGTTGATGGGTATGTTTTTGCTTATTTGATTTTCACTGAGTGATTAAGATTAAAAGAAACTGTTACCTGAACTGGGGAAGGTCCTACTGAATTGGACTGCATGTGCTACTTCTCTGTTCCCCCGTCTTACCATTTGTTAACTGGTGGGAAGTAAGGTGAAAGGCATCATTGCTGGATAAATGTGAGATCCAAAGGGCTGAAATGTTTTTCCTTAGCAGTTCTTGATATCACAGTGCAGTGTTAACAACAGTGCTTGATTTATGGTTGTCATGGGACCTTAGATGATGAAGCTTTTATATTGGGCTTATATTGTCAGCACTTTTTTCCCCTTCAGGCTACTACTATATTATAAATAAGCTATTTACTGTGTGTTCTTCTTGTTTGACTTAGAGCTAAAAGGATGAGAAATCTCCAGCTAAAATCGTTTTTCCTTCTCATCAGA

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

ACTGTGTGTTCTTCTTGTTTGACT

59

ACATCAATCAAACAGACTCCACC

58.93

169

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GCTAAAAGGATGAGAAATCTCCAGC

59.99

ACATCAATCAAACAGACTCCACC

58.93

141

PCR template sequence:

TATATTATAAATAAGCTATTTACTGTGTGTTCTTCTTGTTTGACTTAGAGCTAAAAGGATGAGAAATCTCCAGCTAAAATCGTTTTTCCTTCTCATCAGAGTAAATTGTCTTTATCAGCAATGTCTTCTTCTGACCAATCAGTACAATATTATGATGATACACTAAAGGTGGAGTCTGTTTGATTGATGTAGTTGTGTGT

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

15

Interacting miRNAs (#binding sites)

mmu-miR-23b-3p(1), mmu-miR-20b-5p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-106b-5p(1), mmu-miR-335-5p(1), mmu-miR-217-5p(1), mmu-miR-23a-3p(1), mmu-miR-483-5p(1), mmu-miR-129-5p(1), mmu-miR-540-3p(1)

siRNAs for circular RNA silencing
Junction sequence

CCTTCTCATCAGAGTAAATTGTCTTT

siRNA sets

AAAGACAATTTACTCTGAT, AAGACAATTTACTCTGATG, AGACAATTTACTCTGATGA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CICSDE1_698_ORF_1

1.0893

-0.315028235

0.022784013

108

ORF sequence:

ATGAGAAATCTCCAGCTAAAATCGTTTTTCCTTCTCATCAGAGTAAATTGTCTTTATCAGCAATGTCTTCTTCTGACCAATCAGTACAATATTATGATGATACACTAA

Peptide sequence:

MRNLQLKSFFLLIRVNCLYQQCLLLTNQYNIMMIH

IRESfinder result

IRESfinder score

0.853739104

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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