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mmu_circAgpat4_258

Basic information of circular RNA
PanCircBase ID:

mmu_circAgpat4_258

mm39_Chr. Position ID:

chr17|12370578|12370836|+

Gene name:

Agpat4

Transcript:

ENSMUST00000164143.8

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

1

Exon/intron indexes:

2

Exon/intron offsets:

0

Genomic length:

258

Exon/intron sizes in nt:

258

Flanking exon/introns:

chr17:12337727-12370578|chr17:12370836-12417638

Splice length:

258

Other database IDs:

CIRCpedia: MMU_CIRCpedia_5503, circAtlas: mmu-Agpat4_0001

circBase: hsa_circ_0078626, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_54280

Human Ortholog IDs:
Mature spliced Sequence:

ACACTTTCCTGAGCCCCGGATCTTTCCCCCTTCTGGAACTATCCCACCATACGGATTTATCTCTTGAGAATCCCCACACCATGGACCTCATCGGGCTGCTGAAGTCCCAGTTTCTATGTCACCTGGTCTTCTGCTACGTGTTCATCGCCTCGGGGCTCATTGTCAACGCCATCCAGCTGTGCACGCTGGTCATCTGGCCCATCAACAAGCAGCTGTTCCGCAAGATCAATGCCAGACTCTGCTACTGCGTCTCCAGCC

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

GGTCATCTGGCCCATCAACA

60.03

CCGATGAGGTCCATGGTGTG

60.46

165

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TGGTCATCTGGCCCATCAAC

60.03

CCGATGAGGTCCATGGTGTG

60.46

166

PCR template sequence:

ATTGTCAACGCCATCCAGCTGTGCACGCTGGTCATCTGGCCCATCAACAAGCAGCTGTTCCGCAAGATCAATGCCAGACTCTGCTACTGCGTCTCCAGCCACACTTTCCTGAGCCCCGGATCTTTCCCCCTTCTGGAACTATCCCACCATACGGATTTATCTCTTGAGAATCCCCACACCATGGACCTCATCGGGCTGCT

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

NA

Interacting miRNAs (#binding sites)

NA

siRNAs for circular RNA silencing
Junction sequence

TGCGTCTCCAGCCACACTTTCCTGAG

siRNA sets

GAAAGTGTGGCTGGAGACG

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCAGPAT4_258_ORF_1

1.2153

0.448227077

0.878313513

435

ORF sequence:

ATGGACCTCATCGGGCTGCTGAAGTCCCAGTTTCTATGTCACCTGGTCTTCTGCTACGTGTTCATCGCCTCGGGGCTCATTGTCAACGCCATCCAGCTGTGCACGCTGGTCATCTGGCCCATCAACAAGCAGCTGTTCCGCAAGATCAATGCCAGACTCTGCTACTGCGTCTCCAGCCACACTTTCCTGAGCCCCGGATCTTTCCCCCTTCTGGAACTATCCCACCATACGGATTTATCTCTTGAGAATCCCCACACCATGGACCTCATCGGGCTGCTGAAGTCCCAGTTTCTATGTCACCTGGTCTTCTGCTACGTGTTCATCGCCTCGGGGCTCATTGTCAACGCCATCCAGCTGTGCACGCTGGTCATCTGGCCCATCAACAAGCAGCTGTTCCGCAAGATCAATGCCAGACTCTGCTACTGCGTCTCCAGC

Peptide sequence:

MDLIGLLKSQFLCHLVFCYVFIASGLIVNAIQLCTLVIWPINKQLFRKINARLCYCVSSHTFLSPGSFPLLELSHHTDLSLENPHTMDLIGLLKSQFLCHLVFCYVFIASGLIVNAIQLCTLVIWPINKQLFRKINARLCYCVSS

IRESfinder result

IRESfinder score

0.458993375

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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