top of page
mmu_circGabra4_669
Basic information of circular RNA
PanCircBase ID:
mmu_circGabra4_669
mm39_Chr. Position ID:
chr5|71790888|71799669|-
Gene name:
Gabra4
Transcript:
ENSMUST00000031121.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
7,6,5,4,3
Exon/intron offsets:
0,4586,7282,7517,8713
Genomic length:
8781
Exon/intron sizes in nt:
153,144,83,221,68
Flanking exon/introns:
chr5:71781457-71790888|chr5:71799669-71814513
Splice length:
669
Other database IDs:
CIRCpedia: MMU_CIRCpedia_215609, circAtlas: mmu-Gabra4_0003
Human Ortholog IDs:
Mature spliced Sequence:
GTCCTGTTACAGAAGTGAAAACTGATATATATGTCACCAGCTTTGGGCCCGTTTCTGATGTTGAAATGGAATACACTATGGATGTGTTCTTCAGACAGACATGGATTGACAAAAGACTAAAATATGACGGCCCAATTGAAATCTTGAGGCTGAATAATATGATGGTCACCAAAGTTTGGACCCCTGATACTTTCTTCAGGAATGGAAAGAAATCTGTCTCACATAACATGACAGCTCCAAATAAGCTTTTTAGAATTATGAGAAATGGCACTATTTTATACACAATGAGACTCACCATAAGTGCGGAGTGCCCCATGAGACTGGTGGATTTTCCTATGGATGGTCATGCCTGCCCTTTGAAATTTGGGAGTTATGCATATCCCAAAAGTGAGATGATCTACACCTGGACCAAAGGCCCTGAGAAGTCAGTGGAGGTGCCAAAGGAGTCTTCTAGCTTAGTTCAATATGACCTCATTGGGCAGACTGTATCAAGCGAGACTATCAAATCTATTACAGGTGAATACATTGTTATGACGGTTTACTTCCACCTCAGACGGAAGATGGGCTACTTTATGATTCAGACGTATATCCCATGCATCATGACAGTGATTCTTTCTCAAGTTTCCTTCTGGATAAACAAGGAGTCTGTTCCAGCTAGAACTGTATTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCCATGCATCATGACAGTGA
59.44
ACATCAGAAACGGGCCCAAA
60.18
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCCATGCATCATGACAGTGA
59.44
AACATCAGAAACGGGCCCAA
60.18
143
PCR template sequence:
TTTATGATTCAGACGTATATCCCATGCATCATGACAGTGATTCTTTCTCAAGTTTCCTTCTGGATAAACAAGGAGTCTGTTCCAGCTAGAACTGTATTTGGTCCTGTTACAGAAGTGAAAACTGATATATATGTCACCAGCTTTGGGCCCGTTTCTGATGTTGAAATGGAATACACTATGGATGTGTTCTTCAGACAGAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(2), mmu-miR-138-5p(1), mmu-miR-96-5p(1), mmu-miR-452-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAACTGTATTTGGTCCTGTTACAGA
siRNA sets
AACAGGACCAAATACAGTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGABRA4_669_ORF_1
0.9333
0.068229994
0.99732026
1272
ORF sequence:
ATGGAATACACTATGGATGTGTTCTTCAGACAGACATGGATTGACAAAAGACTAAAATATGACGGCCCAATTGAAATCTTGAGGCTGAATAATATGATGGTCACCAAAGTTTGGACCCCTGATACTTTCTTCAGGAATGGAAAGAAATCTGTCTCACATAACATGACAGCTCCAAATAAGCTTTTTAGAATTATGAGAAATGGCACTATTTTATACACAATGAGACTCACCATAAGTGCGGAGTGCCCCATGAGACTGGTGGATTTTCCTATGGATGGTCATGCCTGCCCTTTGAAATTTGGGAGTTATGCATATCCCAAAAGTGAGATGATCTACACCTGGACCAAAGGCCCTGAGAAGTCAGTGGAGGTGCCAAAGGAGTCTTCTAGCTTAGTTCAATATGACCTCATTGGGCAGACTGTATCAAGCGAGACTATCAAATCTATTACAGGTGAATACATTGTTATGACGGTTTACTTCCACCTCAGACGGAAGATGGGCTACTTTATGATTCAGACGTATATCCCATGCATCATGACAGTGATTCTTTCTCAAGTTTCCTTCTGGATAAACAAGGAGTCTGTTCCAGCTAGAACTGTATTTGGTCCTGTTACAGAAGTGAAAACTGATATATATGTCACCAGCTTTGGGCCCGTTTCTGATGTTGAAATGGAATACACTATGGATGTGTTCTTCAGACAGACATGGATTGACAAAAGACTAAAATATGACGGCCCAATTGAAATCTTGAGGCTGAATAATATGATGGTCACCAAAGTTTGGACCCCTGATACTTTCTTCAGGAATGGAAAGAAATCTGTCTCACATAACATGACAGCTCCAAATAAGCTTTTTAGAATTATGAGAAATGGCACTATTTTATACACAATGAGACTCACCATAAGTGCGGAGTGCCCCATGAGACTGGTGGATTTTCCTATGGATGGTCATGCCTGCCCTTTGAAATTTGGGAGTTATGCATATCCCAAAAGTGAGATGATCTACACCTGGACCAAAGGCCCTGAGAAGTCAGTGGAGGTGCCAAAGGAGTCTTCTAGCTTAGTTCAATATGACCTCATTGGGCAGACTGTATCAAGCGAGACTATCAAATCTATTACAGGTGAATACATTGTTATGACGGTTTACTTCCACCTCAGACGGAAGATGGGCTACTTTATGATTCAGACGTATATCCCATGCATCATGACAGTGATTCTTTCTCAAGTTTCCTTCTGGATAAACAAGGAGTCTGTTCCAGCTAGAACTGTATTT
Peptide sequence:
MEYTMDVFFRQTWIDKRLKYDGPIEILRLNNMMVTKVWTPDTFFRNGKKSVSHNMTAPNKLFRIMRNGTILYTMRLTISAECPMRLVDFPMDGHACPLKFGSYAYPKSEMIYTWTKGPEKSVEVPKESSSLVQYDLIGQTVSSETIKSITGEYIVMTVYFHLRRKMGYFMIQTYIPCIMTVILSQVSFWINKESVPARTVFGPVTEVKTDIYVTSFGPVSDVEMEYTMDVFFRQTWIDKRLKYDGPIEILRLNNMMVTKVWTPDTFFRNGKKSVSHNMTAPNKLFRIMRNGTILYTMRLTISAECPMRLVDFPMDGHACPLKFGSYAYPKSEMIYTWTKGPEKSVEVPKESSSLVQYDLIGQTVSSETIKSITGEYIVMTVYFHLRRKMGYFMIQTYIPCIMTVILSQVSFWINKESVPARTVF
IRESfinder result
IRESfinder score
0.57710102
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page