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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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