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mmu_circFocad_1140
Basic information of circular RNA
PanCircBase ID:
mmu_circFocad_1140
mm39_Chr. Position ID:
chr4|88042824|88104319|+
Gene name:
Focad
Transcript:
ENSMUST00000097992.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
3,4,5,6,7,8,9,10
Exon/intron offsets:
0,4310,30049,45319,50025,53494,57996,61292
Genomic length:
61495
Exon/intron sizes in nt:
75,155,105,102,205,207,88,203
Flanking exon/introns:
chr4:88039595-88042824|chr4:88104319-88114995
Splice length:
1140
Other database IDs:
circAtlas: mmu-Focad_0034
circAtlas: hsa-FOCAD_0238
Human Ortholog IDs:
Mature spliced Sequence:
GCTGTAGGTCATCTTATTGCTGCTGTCTTAAAAGAACATGGTGTTTCAGAAAAGATACACCAATCCACAAACCAGACGGCTGCCTTGAACTTGCTGTGGGAGAAGTGCTGCAGTGACCATGTGGTTGTGCGGACAGCCTGCAGCGAGGGACTGGTGGCACTTGTCGCCCAGGGTCATGCAGAGTTCAGCTATGTTCTCAATGGGATACTCAACCTGACTCCTTCTGCCAGGAATATGTCTGGTTTGATAAAAGCCCTTATGAAATTATTACAGATGCAAGCACTGAGAGAAGGACAAAGCGGGGAAAAGGACATTCAGGATATATATTCTATCAGAAATCCTCCTCAGCCTTTGATCACCGTGCTTGAGCACAGGCCTGATTGCTGGCCACTACTCCTGCAGCAGCTGACAGCTTTTTTCCAGCAATGCCCTGAAAGGTCAGAAGCTTCATGTGTCCAAATAATGGCGCCATTTCTGTGGTATCTCTACTGTGAACCATCTCAGCTAGAGGAATATGCCAAGCTTCGACTGTCGCTGCTCAAAGTCTTACTTCAGCCCAGAGGTGTCTGTGAGGAAGCGCAGCTGTCAGTACGGGAGCAGAGCACCCTTCAGCTGTGCTGTAGCATGCTTCCATGCTTGCAGATGAAAGATCTGATGCAGACAACAGAAATGATGCTGTTCGTCGAGGAAGTATATCTAAGCCTTCTGCGGCATCCTGGCTTCTGGAAAAGTCAGCTTACCCAGCTGACCCTTCAGCTGCTGTGCATCTGTGAAGTCAGCTTAAAGATAACTGGGGAGTGCTCATCTTTAATTCACCTTTTAGAGCGCAGTGTTGAACTTCTTGGGGAGGATTTTCCTGTCGAATTGGTCATTATTGGAATTGCTTTACTACTTCTACAGATGCCAGCAAGTCAACAGAAGCCACTATTAAACCTAGCTTTGAAGCTCCTCTCGCTTACTGAGGGTCAGAAAATCCCGAAGGCATCCCTGCTGCTCCTGGTGCCTCTTCTGCAGATACTATCTTCCACTGCCCTGGAAGACTGTCTGGCCATGGGTGAGGAAGGCCCCTCCAGGCAGCAGTTAGCTCTCAGTCTTGTGGAAGTGCTACAGAAAGAGCGTCACGGAGACGACAGCCACACG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGCCATGGGTGAGGAAG
60.08
AGCCGTCTGGTTTGTGGATT
59.89
177
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGCCATGGGTGAGGAAG
60.08
GCCGTCTGGTTTGTGGATTG
59.76
176
PCR template sequence:
CTGTCTGGCCATGGGTGAGGAAGGCCCCTCCAGGCAGCAGTTAGCTCTCAGTCTTGTGGAAGTGCTACAGAAAGAGCGTCACGGAGACGACAGCCACACGGCTGTAGGTCATCTTATTGCTGCTGTCTTAAAAGAACATGGTGTTTCAGAAAAGATACACCAATCCACAAACCAGACGGCTGCCTTGAACTTGCTGTGGG
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-miR-15a-5p(1), mmu-miR-141-3p(1), mmu-miR-34c-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-320-3p(1), mmu-miR-34b-5p(1), mmu-miR-499-5p(1), mmu-miR-680(1), mmu-miR-532-5p(1), mmu-miR-188-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CGACAGCCACACGGCTGTAGGTCATC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFOCAD_1140_ORF_1
1.139
0.10134702
0.99999386
2046
ORF sequence:
ATGTCTGGTTTGATAAAAGCCCTTATGAAATTATTACAGATGCAAGCACTGAGAGAAGGACAAAGCGGGGAAAAGGACATTCAGGATATATATTCTATCAGAAATCCTCCTCAGCCTTTGATCACCGTGCTTGAGCACAGGCCTGATTGCTGGCCACTACTCCTGCAGCAGCTGACAGCTTTTTTCCAGCAATGCCCTGAAAGGTCAGAAGCTTCATGTGTCCAAATAATGGCGCCATTTCTGTGGTATCTCTACTGTGAACCATCTCAGCTAGAGGAATATGCCAAGCTTCGACTGTCGCTGCTCAAAGTCTTACTTCAGCCCAGAGGTGTCTGTGAGGAAGCGCAGCTGTCAGTACGGGAGCAGAGCACCCTTCAGCTGTGCTGTAGCATGCTTCCATGCTTGCAGATGAAAGATCTGATGCAGACAACAGAAATGATGCTGTTCGTCGAGGAAGTATATCTAAGCCTTCTGCGGCATCCTGGCTTCTGGAAAAGTCAGCTTACCCAGCTGACCCTTCAGCTGCTGTGCATCTGTGAAGTCAGCTTAAAGATAACTGGGGAGTGCTCATCTTTAATTCACCTTTTAGAGCGCAGTGTTGAACTTCTTGGGGAGGATTTTCCTGTCGAATTGGTCATTATTGGAATTGCTTTACTACTTCTACAGATGCCAGCAAGTCAACAGAAGCCACTATTAAACCTAGCTTTGAAGCTCCTCTCGCTTACTGAGGGTCAGAAAATCCCGAAGGCATCCCTGCTGCTCCTGGTGCCTCTTCTGCAGATACTATCTTCCACTGCCCTGGAAGACTGTCTGGCCATGGGTGAGGAAGGCCCCTCCAGGCAGCAGTTAGCTCTCAGTCTTGTGGAAGTGCTACAGAAAGAGCGTCACGGAGACGACAGCCACACGGCTGTAGGTCATCTTATTGCTGCTGTCTTAAAAGAACATGGTGTTTCAGAAAAGATACACCAATCCACAAACCAGACGGCTGCCTTGAACTTGCTGTGGGAGAAGTGCTGCAGTGACCATGTGGTTGTGCGGACAGCCTGCAGCGAGGGACTGGTGGCACTTGTCGCCCAGGGTCATGCAGAGTTCAGCTATGTTCTCAATGGGATACTCAACCTGACTCCTTCTGCCAGGAATATGTCTGGTTTGATAAAAGCCCTTATGAAATTATTACAGATGCAAGCACTGAGAGAAGGACAAAGCGGGGAAAAGGACATTCAGGATATATATTCTATCAGAAATCCTCCTCAGCCTTTGATCACCGTGCTTGAGCACAGGCCTGATTGCTGGCCACTACTCCTGCAGCAGCTGACAGCTTTTTTCCAGCAATGCCCTGAAAGGTCAGAAGCTTCATGTGTCCAAATAATGGCGCCATTTCTGTGGTATCTCTACTGTGAACCATCTCAGCTAGAGGAATATGCCAAGCTTCGACTGTCGCTGCTCAAAGTCTTACTTCAGCCCAGAGGTGTCTGTGAGGAAGCGCAGCTGTCAGTACGGGAGCAGAGCACCCTTCAGCTGTGCTGTAGCATGCTTCCATGCTTGCAGATGAAAGATCTGATGCAGACAACAGAAATGATGCTGTTCGTCGAGGAAGTATATCTAAGCCTTCTGCGGCATCCTGGCTTCTGGAAAAGTCAGCTTACCCAGCTGACCCTTCAGCTGCTGTGCATCTGTGAAGTCAGCTTAAAGATAACTGGGGAGTGCTCATCTTTAATTCACCTTTTAGAGCGCAGTGTTGAACTTCTTGGGGAGGATTTTCCTGTCGAATTGGTCATTATTGGAATTGCTTTACTACTTCTACAGATGCCAGCAAGTCAACAGAAGCCACTATTAAACCTAGCTTTGAAGCTCCTCTCGCTTACTGAGGGTCAGAAAATCCCGAAGGCATCCCTGCTGCTCCTGGTGCCTCTTCTGCAGATACTATCTTCCACTGCCCTGGAAGACTGTCTGGCCATGGGTGAGGAAGGCCCCTCCAGGCAGCAGTTAGCTCTCAGTCTTGTGGAAGTGCTACAGAAAGAGCGTCACGGAGACGACAGCCACACG
Peptide sequence:
MSGLIKALMKLLQMQALREGQSGEKDIQDIYSIRNPPQPLITVLEHRPDCWPLLLQQLTAFFQQCPERSEASCVQIMAPFLWYLYCEPSQLEEYAKLRLSLLKVLLQPRGVCEEAQLSVREQSTLQLCCSMLPCLQMKDLMQTTEMMLFVEEVYLSLLRHPGFWKSQLTQLTLQLLCICEVSLKITGECSSLIHLLERSVELLGEDFPVELVIIGIALLLLQMPASQQKPLLNLALKLLSLTEGQKIPKASLLLLVPLLQILSSTALEDCLAMGEEGPSRQQLALSLVEVLQKERHGDDSHTAVGHLIAAVLKEHGVSEKIHQSTNQTAALNLLWEKCCSDHVVVRTACSEGLVALVAQGHAEFSYVLNGILNLTPSARNMSGLIKALMKLLQMQALREGQSGEKDIQDIYSIRNPPQPLITVLEHRPDCWPLLLQQLTAFFQQCPERSEASCVQIMAPFLWYLYCEPSQLEEYAKLRLSLLKVLLQPRGVCEEAQLSVREQSTLQLCCSMLPCLQMKDLMQTTEMMLFVEEVYLSLLRHPGFWKSQLTQLTLQLLCICEVSLKITGECSSLIHLLERSVELLGEDFPVELVIIGIALLLLQMPASQQKPLLNLALKLLSLTEGQKIPKASLLLLVPLLQILSSTALEDCLAMGEEGPSRQQLALSLVEVLQKERHGDDSHT
IRESfinder result
IRESfinder score
0.581752543
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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