top of page
mmu_circSlc49a4_618
Basic information of circular RNA
PanCircBase ID:
mmu_circSlc49a4_618
mm39_Chr. Position ID:
chr16|35525123|35554436|-
Gene name:
Slc49a4
Transcript:
ENSMUST00000023554.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
8,7,6,5,4
Exon/intron offsets:
0,14558,17999,25532,29183
Genomic length:
29313
Exon/intron sizes in nt:
1,83,12,86,81,09,130
Flanking exon/introns:
chr16:35518390-35525123|chr16:35554436-35555755
Splice length:
618
Other database IDs:
circAtlas: mmu-Dirc2_0006
circBase: hsa_circ_0121649, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_151083
Human Ortholog IDs:
Mature spliced Sequence:
AATTTGGAGTTGTCTGCCTAATATTCTCTGCCACGCTAGCTTATTTTCCGCCCCGGCCTCCTCTTCCTCCCAGTGTCGCTGCTGCGAGCCAGCGGCTGAGTTACCGGCGGAGCTTTTGTAGGTTACTAAGCAATTTGAGGTTTTTGATGATTGCTTTAGCATACGCAATACCACTTGGTGTGTTTGCTGGCTGGTCTGGAGTTCTGGACTTAATTTTAACACCAGTGCATGTCAGTCAAGTAGACGCTGGCTGGATTGGATTCTGGTCCATAGTTGGAGGCTGTGTTGTTGGGATAGCTATGGCAAGGTTTGCGGATTTTATCCGGGGCATGCTGAAACTGATCCTGCTCCTCCTGTTTTCTGGGGCTACCCTGTCGTCCACGTGGTTCACCCTGACCTGCCTAAACAGCATCACCCACTTGCCTTTGACAACAGTGACATTGTATGCCTCCTGCATCCTCCTGGGAGTGTTCCTGAACAGCAGCGTCCCCATATTCTTTGAGCTTTTTGTGGAAACGGTCTACCCCGTTCCAGAAGGGATCACCTGTGGAGTTGTCACCTTTTTAAGTAATATGTTCATGGGAGTGCTTTTATTTTTTGTCACATTTTATCATACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCACCTGTGGAGTTGTCACC
59.53
ACACTGGGAGGAAGAGGAGG
60.25
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CACCTGTGGAGTTGTCACCT
59.53
ACACTGGGAGGAAGAGGAGG
60.25
153
PCR template sequence:
GTCTACCCCGTTCCAGAAGGGATCACCTGTGGAGTTGTCACCTTTTTAAGTAATATGTTCATGGGAGTGCTTTTATTTTTTGTCACATTTTATCATACAGAATTTGGAGTTGTCTGCCTAATATTCTCTGCCACGCTAGCTTATTTTCCGCCCCGGCCTCCTCTTCCTCCCAGTGTCGCTGCTGCGAGCCAGCGGCTGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-137-3p(1), mmu-miR-138-5p(1), mmu-miR-149-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTTATCATACAGAATTTGGAGTTGT
siRNA sets
AACTCCAAATTCTGTATGA, CAACTCCAAATTCTGTATG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSLC49A4_618_ORF_1
1.0709
0.000637208
0.989856153
1089
ORF sequence:
ATGATTGCTTTAGCATACGCAATACCACTTGGTGTGTTTGCTGGCTGGTCTGGAGTTCTGGACTTAATTTTAACACCAGTGCATGTCAGTCAAGTAGACGCTGGCTGGATTGGATTCTGGTCCATAGTTGGAGGCTGTGTTGTTGGGATAGCTATGGCAAGGTTTGCGGATTTTATCCGGGGCATGCTGAAACTGATCCTGCTCCTCCTGTTTTCTGGGGCTACCCTGTCGTCCACGTGGTTCACCCTGACCTGCCTAAACAGCATCACCCACTTGCCTTTGACAACAGTGACATTGTATGCCTCCTGCATCCTCCTGGGAGTGTTCCTGAACAGCAGCGTCCCCATATTCTTTGAGCTTTTTGTGGAAACGGTCTACCCCGTTCCAGAAGGGATCACCTGTGGAGTTGTCACCTTTTTAAGTAATATGTTCATGGGAGTGCTTTTATTTTTTGTCACATTTTATCATACAGAATTTGGAGTTGTCTGCCTAATATTCTCTGCCACGCTAGCTTATTTTCCGCCCCGGCCTCCTCTTCCTCCCAGTGTCGCTGCTGCGAGCCAGCGGCTGAGTTACCGGCGGAGCTTTTGTAGGTTACTAAGCAATTTGAGGTTTTTGATGATTGCTTTAGCATACGCAATACCACTTGGTGTGTTTGCTGGCTGGTCTGGAGTTCTGGACTTAATTTTAACACCAGTGCATGTCAGTCAAGTAGACGCTGGCTGGATTGGATTCTGGTCCATAGTTGGAGGCTGTGTTGTTGGGATAGCTATGGCAAGGTTTGCGGATTTTATCCGGGGCATGCTGAAACTGATCCTGCTCCTCCTGTTTTCTGGGGCTACCCTGTCGTCCACGTGGTTCACCCTGACCTGCCTAAACAGCATCACCCACTTGCCTTTGACAACAGTGACATTGTATGCCTCCTGCATCCTCCTGGGAGTGTTCCTGAACAGCAGCGTCCCCATATTCTTTGAGCTTTTTGTGGAAACGGTCTACCCCGTTCCAGAAGGGATCACCTGTGGAGTTGTCACCTTTTTAAGTAATATGTTCATGGGAGTGCTTTTATTTTTTGTCACATTTTATCATACA
Peptide sequence:
MIALAYAIPLGVFAGWSGVLDLILTPVHVSQVDAGWIGFWSIVGGCVVGIAMARFADFIRGMLKLILLLLFSGATLSSTWFTLTCLNSITHLPLTTVTLYASCILLGVFLNSSVPIFFELFVETVYPVPEGITCGVVTFLSNMFMGVLLFFVTFYHTEFGVVCLIFSATLAYFPPRPPLPPSVAAASQRLSYRRSFCRLLSNLRFLMIALAYAIPLGVFAGWSGVLDLILTPVHVSQVDAGWIGFWSIVGGCVVGIAMARFADFIRGMLKLILLLLFSGATLSSTWFTLTCLNSITHLPLTTVTLYASCILLGVFLNSSVPIFFELFVETVYPVPEGITCGVVTFLSNMFMGVLLFFVTFYHT
IRESfinder result
IRESfinder score
0.715724114
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page