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mmu_circGcfc2_439
Basic information of circular RNA
PanCircBase ID:
mmu_circGcfc2_439
mm39_Chr. Position ID:
chr6|81907648|81913002|+
Gene name:
Gcfc2
Transcript:
ENSMUST00000043195.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
3,4,5
Exon/intron offsets:
0,2146,5238
Genomic length:
5354
Exon/intron sizes in nt:
225,98,116
Flanking exon/introns:
chr6:81902875-81907648|chr6:81913002-81916360
Splice length:
439
Other database IDs:
circAtlas: mmu-Gcfc2_0001
Human Ortholog IDs:
Mature spliced Sequence:
TTGAGATCCCCGATGCAGCTTTTATTCAGGCAGCCCGCAGAAAACGGGAGTTGGCCAGGACCCCAGGGGACTACATTTCATTGGATGTAAACCACTCCTGCTCCACTTCTGACTGTAAGAGAAGCAATGAAGAGGACCCAGAGAGCGATCCTGATGACCACGAAAAGAGAATACTGTTTACCCCAAAGCCTCAAACACTCCGGCAAAGAATGGCTGAAGAAACGTCAATCAGGAGTGAGGAATCAAGTGAAGAGAGTCAGGAAGATGAAAACCAAGACATCTGGGAGCAGCAGCAGATGAGGAAAGCAGTCAGGATCCCGGCGGGACAAAATACAGACCTTTCCCACAGCAGTAAGTCTCAAACCCTGAAGAAGTTTGATACTTCCATTTCATTTCCACCGGTAAATTTGGAAATTATAAAGAAACAGTTAAATAATAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCCACAGCAGTAAGTCTCA
57.99
CTGGCCAACTCCCGTTTTCT
60.54
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCCACAGCAGTAAGTCTCA
57.99
AATGTAGTCCCCTGGGGTCC
60.62
175
PCR template sequence:
TTTCCCACAGCAGTAAGTCTCAAACCCTGAAGAAGTTTGATACTTCCATTTCATTTCCACCGGTAAATTTGGAAATTATAAAGAAACAGTTAAATAATAGTTGAGATCCCCGATGCAGCTTTTATTCAGGCAGCCCGCAGAAAACGGGAGTTGGCCAGGACCCCAGGGGACTACATTTCATTGGATGTAAACCACTCCTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-140-5p(1), mmu-miR-320-3p(1), mmu-miR-326-3p(1), mmu-miR-335-3p(1), mmu-miR-542-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGTTAAATAATAGTTGAGATCCCCGA
siRNA sets
TCTCAACTATTATTTAACT, ATCTCAACTATTATTTAAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGCFC2_439_ORF_1
0.9439
0.10092546
0.196697789
234
ORF sequence:
ATGGCTGAAGAAACGTCAATCAGGAGTGAGGAATCAAGTGAAGAGAGTCAGGAAGATGAAAACCAAGACATCTGGGAGCAGCAGCAGATGAGGAAAGCAGTCAGGATCCCGGCGGGACAAAATACAGACCTTTCCCACAGCAGTAAGTCTCAAACCCTGAAGAAGTTTGATACTTCCATTTCATTTCCACCGGTAAATTTGGAAATTATAAAGAAACAGTTAAATAATAGTTGA
Peptide sequence:
MAEETSIRSEESSEESQEDENQDIWEQQQMRKAVRIPAGQNTDLSHSSKSQTLKKFDTSISFPPVNLEIIKKQLNNS
IRESfinder result
IRESfinder score
0.484166652
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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