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mmu_circScfd1_552
Basic information of circular RNA
PanCircBase ID:
mmu_circScfd1_552
mm39_Chr. Position ID:
chr12|51430887|51440693|+
Gene name:
Scfd1
Transcript:
ENSMUST00000219434.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
2,3,4,5,6,7
Exon/intron offsets:
0,2945,5177,6201,8078,9716
Genomic length:
9806
Exon/intron sizes in nt:
71,89,91,123,88,90
Flanking exon/introns:
chr12:51424419-51430887|chr12:51440693-51443462
Splice length:
552
Other database IDs:
circAtlas: mmu-Scfd1_0006
circBase: hsa_circ_0101537, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_11819
Human Ortholog IDs:
Mature spliced Sequence:
TGGCTCTGAAGCGGATGTTGAATTTCAATGTGCCTCATGTTAAAAACAGTACTGGAGAACCAGTATGGAAGGTACTCATTTATGACAGATTTGGCCAAGATATCATCTCTCCTCTGCTGTCTGTGAAGGAACTGAGAGACATGGGCATCACTCTGCATCTCCTTTTGCACTCAGACCGAGATCCGATTCCAGATGTTCCTGCAGTGTACTTTGTGATGCCAACCGAAGAAAATATTGACAGACTGTGCCAGGATCTTCGAAATCAGCTCTATGAATCCTATTATTTAAATTTTATTTCTGCGATTTCAAGAAGTAAACTGGAAGACATTGCGAATGCAGCATTGGCCGCTAGTGCAGTCACACAAGTTGCCAAGGTTTTTGACCAGTATCTCAATTTTATTACTTTGGAAGATGACATGTTTGTATTATGTAATCAAAATAAGGAACTTGTTTCATATCGTGCCATTAACAGGCCAGACATCACAGACACAGAGATGGAAACTGTTATGGACACTATTGTGGACAGCCTCTTCTGCTTTTTTGTTACATTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCCAGACATCACAGACACA
59.96
ACCTTCCATACTGGTTCTCCA
58.08
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGGCCAGACATCACAGACA
59.68
ACCTTCCATACTGGTTCTCCA
58.08
156
PCR template sequence:
TCATATCGTGCCATTAACAGGCCAGACATCACAGACACAGAGATGGAAACTGTTATGGACACTATTGTGGACAGCCTCTTCTGCTTTTTTGTTACATTAGTGGCTCTGAAGCGGATGTTGAATTTCAATGTGCCTCATGTTAAAAACAGTACTGGAGAACCAGTATGGAAGGTACTCATTTATGACAGATTTGGCCAAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-298-5p(2), mmu-miR-182-5p(1), mmu-miR-183-5p(1), mmu-miR-301a-3p(1), mmu-miR-369-3p(1), mmu-miR-669d-5p(1), mmu-miR-350-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTGTTACATTAGTGGCTCTGAAGCG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSCFD1_552_ORF_1
1.0467
0.11225115
0.993274532
1089
ORF sequence:
ATGTTGAATTTCAATGTGCCTCATGTTAAAAACAGTACTGGAGAACCAGTATGGAAGGTACTCATTTATGACAGATTTGGCCAAGATATCATCTCTCCTCTGCTGTCTGTGAAGGAACTGAGAGACATGGGCATCACTCTGCATCTCCTTTTGCACTCAGACCGAGATCCGATTCCAGATGTTCCTGCAGTGTACTTTGTGATGCCAACCGAAGAAAATATTGACAGACTGTGCCAGGATCTTCGAAATCAGCTCTATGAATCCTATTATTTAAATTTTATTTCTGCGATTTCAAGAAGTAAACTGGAAGACATTGCGAATGCAGCATTGGCCGCTAGTGCAGTCACACAAGTTGCCAAGGTTTTTGACCAGTATCTCAATTTTATTACTTTGGAAGATGACATGTTTGTATTATGTAATCAAAATAAGGAACTTGTTTCATATCGTGCCATTAACAGGCCAGACATCACAGACACAGAGATGGAAACTGTTATGGACACTATTGTGGACAGCCTCTTCTGCTTTTTTGTTACATTAGTGGCTCTGAAGCGGATGTTGAATTTCAATGTGCCTCATGTTAAAAACAGTACTGGAGAACCAGTATGGAAGGTACTCATTTATGACAGATTTGGCCAAGATATCATCTCTCCTCTGCTGTCTGTGAAGGAACTGAGAGACATGGGCATCACTCTGCATCTCCTTTTGCACTCAGACCGAGATCCGATTCCAGATGTTCCTGCAGTGTACTTTGTGATGCCAACCGAAGAAAATATTGACAGACTGTGCCAGGATCTTCGAAATCAGCTCTATGAATCCTATTATTTAAATTTTATTTCTGCGATTTCAAGAAGTAAACTGGAAGACATTGCGAATGCAGCATTGGCCGCTAGTGCAGTCACACAAGTTGCCAAGGTTTTTGACCAGTATCTCAATTTTATTACTTTGGAAGATGACATGTTTGTATTATGTAATCAAAATAAGGAACTTGTTTCATATCGTGCCATTAACAGGCCAGACATCACAGACACAGAGATGGAAACTGTTATGGACACTATTGTGGACAGCCTCTTCTGCTTTTTTGTTACATTA
Peptide sequence:
MLNFNVPHVKNSTGEPVWKVLIYDRFGQDIISPLLSVKELRDMGITLHLLLHSDRDPIPDVPAVYFVMPTEENIDRLCQDLRNQLYESYYLNFISAISRSKLEDIANAALAASAVTQVAKVFDQYLNFITLEDDMFVLCNQNKELVSYRAINRPDITDTEMETVMDTIVDSLFCFFVTLVALKRMLNFNVPHVKNSTGEPVWKVLIYDRFGQDIISPLLSVKELRDMGITLHLLLHSDRDPIPDVPAVYFVMPTEENIDRLCQDLRNQLYESYYLNFISAISRSKLEDIANAALAASAVTQVAKVFDQYLNFITLEDDMFVLCNQNKELVSYRAINRPDITDTEMETVMDTIVDSLFCFFVTL
IRESfinder result
IRESfinder score
0.750879065
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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