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mmu_circSlc29a4_630

Basic information of circular RNA
PanCircBase ID:

mmu_circSlc29a4_630

mm39_Chr. Position ID:

chr5|142691110|142700875|+

Gene name:

Slc29a4

Transcript:

ENSMUST00000058418.8

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

5

Exon/intron indexes:

2,3,4,5,6

Exon/intron offsets:

0,6607,7531,8655,9690

Genomic length:

9765

Exon/intron sizes in nt:

180,132,114,129,75

Flanking exon/introns:

chr5:142688046-142691110|chr5:142700875-142703346

Splice length:

630

Other database IDs:

CIRCpedia: MMU_CIRCpedia_9207

circBase: hsa_circ_0079246

Human Ortholog IDs:
Mature spliced Sequence:

TGTGAACTGCCATGGGCTCTATCGGAAGCCAGCGCCTCAAGGAGCCCTGCGTGGCAGCCACATCTGACCAGAGTGTGGTGACAAGCTTTAGCTTTGACAACTTCCAGCTGGAGACGACAGCAGAGGGGGCTCAGGATCCAGGCATCAGAGTCAGGGGTGTCCCCACTTTCACAGACTCTGCGGTAGAGGAGCCTGTGCCAGATGACCGCTACCATGCCATCTACTTTGCCATGCTGCTGGCTGGCGTGGGCTTCCTACTGCCATACAACAGCTTTATCACCGATGTCGACTATCTTCACCACAAGTACCCAGGGACCTCCATCGTATTTGACATGAGCCTCACCTATATCCTGGTGGCATTGGCGGCTGTGCTCCTAAACAACGTTGTGGTGGAGAGGTTGAACCTGCACACCAGGATCACCACAGGCTACCTCCTCGCCTTGGGTCCCTTGCTCTTTATCAGCATATGCGATGTGTGGCTGCAGCTCTTCTCTCACGACCAGGCTTACGCCATCAACCTGGCCGCCGTGGGCACTGTGGCCTTTGGTTGCACAGTGCAGCAATCTAGCTTCTATGGCTACACGGGATTACTGCCCAAGAGGTACACGCAGGGTGTGATGACTGGAGAGA

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

GCACAGTGCAGCAATCTAGC

59.9

ACACTCTGGTCAGATGTGGC

59.68

157

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GCACAGTGCAGCAATCTAGC

59.9

ACTCTGGTCAGATGTGGCTG

59.39

155

PCR template sequence:

GGCACTGTGGCCTTTGGTTGCACAGTGCAGCAATCTAGCTTCTATGGCTACACGGGATTACTGCCCAAGAGGTACACGCAGGGTGTGATGACTGGAGAGATGTGAACTGCCATGGGCTCTATCGGAAGCCAGCGCCTCAAGGAGCCCTGCGTGGCAGCCACATCTGACCAGAGTGTGGTGACAAGCTTTAGCTTTGACAA

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

11

Interacting miRNAs (#binding sites)

mmu-let-7a-5p(1), mmu-miR-16-5p(1), mmu-miR-103-3p(1), mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-382-5p(1), mmu-miR-107-3p(1), mmu-miR-98-5p(1), mmu-miR-3470b(1), mmu-miR-540-3p(1), mmu-miR-670-5p(1)

siRNAs for circular RNA silencing
Junction sequence

ATGACTGGAGAGATGTGAACTGCCAT

siRNA sets

GTTCACATCTCTCCAGTCA, ATGGCAGTTCACATCTCTC, TGGCAGTTCACATCTCTCC

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCSLC29A4_630_ORF_1

1.3368

0.402729298

0.966527913

624

ORF sequence:

ATGGGCTCTATCGGAAGCCAGCGCCTCAAGGAGCCCTGCGTGGCAGCCACATCTGACCAGAGTGTGGTGACAAGCTTTAGCTTTGACAACTTCCAGCTGGAGACGACAGCAGAGGGGGCTCAGGATCCAGGCATCAGAGTCAGGGGTGTCCCCACTTTCACAGACTCTGCGGTAGAGGAGCCTGTGCCAGATGACCGCTACCATGCCATCTACTTTGCCATGCTGCTGGCTGGCGTGGGCTTCCTACTGCCATACAACAGCTTTATCACCGATGTCGACTATCTTCACCACAAGTACCCAGGGACCTCCATCGTATTTGACATGAGCCTCACCTATATCCTGGTGGCATTGGCGGCTGTGCTCCTAAACAACGTTGTGGTGGAGAGGTTGAACCTGCACACCAGGATCACCACAGGCTACCTCCTCGCCTTGGGTCCCTTGCTCTTTATCAGCATATGCGATGTGTGGCTGCAGCTCTTCTCTCACGACCAGGCTTACGCCATCAACCTGGCCGCCGTGGGCACTGTGGCCTTTGGTTGCACAGTGCAGCAATCTAGCTTCTATGGCTACACGGGATTACTGCCCAAGAGGTACACGCAGGGTGTGATGACTGGAGAGATGTGA

Peptide sequence:

MGSIGSQRLKEPCVAATSDQSVVTSFSFDNFQLETTAEGAQDPGIRVRGVPTFTDSAVEEPVPDDRYHAIYFAMLLAGVGFLLPYNSFITDVDYLHHKYPGTSIVFDMSLTYILVALAAVLLNNVVVERLNLHTRITTGYLLALGPLLFISICDVWLQLFSHDQAYAINLAAVGTVAFGCTVQQSSFYGYTGLLPKRYTQGVMTGEM

IRESfinder result

IRESfinder score

0.428192529

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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