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mmu_circSlc30a9_503

Basic information of circular RNA
PanCircBase ID:

mmu_circSlc30a9_503

mm39_Chr. Position ID:

chr5|67473020|67487294|+

Gene name:

Slc30a9

Transcript:

ENSMUST00000113676.6

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

5

Exon/intron indexes:

2,3,4,5,6

Exon/intron offsets:

0,11175,12020,12764,14215

Genomic length:

14274

Exon/intron sizes in nt:

168,100,93,83,59

Flanking exon/introns:

chr5:67464540-67473020|chr5:67487294-67490396

Splice length:

503

Other database IDs:

circAtlas: mmu-Slc30a9_0019

circAtlas: hsa-SCAF8_0001

Human Ortholog IDs:
Mature spliced Sequence:

GATGGAAGAATGTAATGACATTTGAAAGCTTTACATATGTGGTTCCCGACATTCACCCACATTTATCTATTATAAATCAAGTCAAGTTGTACTCTACGAATGTCCAGAAAGGAGGGCAGGGCTCACAGACTCCAAAAGCTGACAAAGTCCCATCACTTACACAAACAGTCAAAGCAGTCCTTAAGAAAAGGGATTATGGATCAAAATACACTAAGAATAATTTCATCACTGGAGTGAGAGCAATAAACGAGTTCTGCCTTAAGTCCAGTGATTTAGAACAACTTCGAAAAATCAGGCGGCGAAGTCCCCACGATGACACCGAGTCCTTTACTGTGTTCTTGAGGTCAGATGTGGAAGCAAAAGCTTTGGAAGTTTGGGGAAGCCTTGAAGCTCTTGCCAGAGAGAAAAAATTGCGTAAAGAAGCAGAAATAGAATACAGAGAACGGCTATTTAGAAACCAAAGAATATTAAGAGAATATGGTGATTTCTTGGGAAACACAAAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

GCAGAAATAGAATACAGAGAACGGC

60.05

TGTGGGTGAATGTCGGGAAC

60.25

142

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GCAGAAATAGAATACAGAGAACGGC

60.05

ATGTGGGTGAATGTCGGGAA

59.3

143

PCR template sequence:

GAAAAAATTGCGTAAAGAAGCAGAAATAGAATACAGAGAACGGCTATTTAGAAACCAAAGAATATTAAGAGAATATGGTGATTTCTTGGGAAACACAAAGGATGGAAGAATGTAATGACATTTGAAAGCTTTACATATGTGGTTCCCGACATTCACCCACATTTATCTATTATAAATCAAGTCAAGTTGTACTCTACGAA

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

7

Interacting miRNAs (#binding sites)

mmu-miR-9-5p(1), mmu-miR-382-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-5101(1), mmu-miR-539-5p(1), mmu-miR-1904(1), mmu-miR-376a-3p(1)

siRNAs for circular RNA silencing
Junction sequence

GGGAAACACAAAGGATGGAAGAATGT

siRNA sets

TCCATCCTTTGTGTTTCCC, ACATTCTTCCATCCTTTGT, TTCCATCCTTTGTGTTTCC

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCSLC30A9_503_ORF_1

0.6205

-0.019807864

0.364311122

504

ORF sequence:

ATGACATTTGAAAGCTTTACATATGTGGTTCCCGACATTCACCCACATTTATCTATTATAAATCAAGTCAAGTTGTACTCTACGAATGTCCAGAAAGGAGGGCAGGGCTCACAGACTCCAAAAGCTGACAAAGTCCCATCACTTACACAAACAGTCAAAGCAGTCCTTAAGAAAAGGGATTATGGATCAAAATACACTAAGAATAATTTCATCACTGGAGTGAGAGCAATAAACGAGTTCTGCCTTAAGTCCAGTGATTTAGAACAACTTCGAAAAATCAGGCGGCGAAGTCCCCACGATGACACCGAGTCCTTTACTGTGTTCTTGAGGTCAGATGTGGAAGCAAAAGCTTTGGAAGTTTGGGGAAGCCTTGAAGCTCTTGCCAGAGAGAAAAAATTGCGTAAAGAAGCAGAAATAGAATACAGAGAACGGCTATTTAGAAACCAAAGAATATTAAGAGAATATGGTGATTTCTTGGGAAACACAAAGGATGGAAGAATGTAA

Peptide sequence:

MTFESFTYVVPDIHPHLSIINQVKLYSTNVQKGGQGSQTPKADKVPSLTQTVKAVLKKRDYGSKYTKNNFITGVRAINEFCLKSSDLEQLRKIRRRSPHDDTESFTVFLRSDVEAKALEVWGSLEALAREKKLRKEAEIEYRERLFRNQRILREYGDFLGNTKDGRM

IRESfinder result

IRESfinder score

0.598298544

IRES/non IRES

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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