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mmu_ciSft2d1_1441
Basic information of circular RNA
PanCircBase ID:
mmu_ciSft2d1_1441
mm39_Chr. Position ID:
chr17|8540667|8542108|+
Gene name:
Sft2d1
Transcript:
ENSMUST00000154553.2
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
5
Exon/intron offsets:
0
Genomic length:
1441
Exon/intron sizes in nt:
1441
Flanking exon/introns:
chr17:8540667-8542108
Splice length:
1441
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTTATATCAGCCAGTCTGGCTATCTGCTCACTGTCCCTACTCCACCATTGTCCTAGAACAAAACTGAGGCCAGTTTCATGAAGCCCTCAAGAGAGTCAGTGTCCCATAAACAGACGTAAGGTGGGTCTGCGGTCTCTAACCTACCCAGAGGTTGTTAAGCATAGGTCCCTGTGAGCACACTCATGCTGAGACTGGTTGCTACTCTAACAGCGTCCTAGACTGGGCCTGGGTCCTCTGCTTTGCCTGCTGCAGACTCTGTGTGCTTTGGGGGAAGCGACAGTGTGAAAAGCTCCCAGAGAAGGTAGGTCCAGAGAACAAGCAGATCAACAAATAGGATTAAAAAGAATTTCCATCAGGACCACATGTGGTGGTGATATCTTTAATCAGCATCCTAGAGGCAGAGAAAGACAGCTCTCTTGAGTTTGAGGTCAGCCTGCTCTACATAGTAACTTCCAGATCAGCTGAGGGCTCCTTGTGTGTGTGGTTGTGCCATAAGGAAGTCAGAGGATAACTTGCAAGAGCCAGTTCTCTTCTTCCACAATGTGGGTGCCGGGTTGTCAGACTTGGCAAACAATTGCTTTTACCCACTAATCCATCTTGTCTCCTCCTCTCAACTTTAAGGGCAGGGGCTAGTTGTGTAGCTTAGTGGTAGAGAGCATTTGTCCAGCTGGAGACAAGTCCTTAGCACCTGCCCACCTTCTTCCCCCCAATGATTAGGAATTCTCAAGTCAGTTATCTTAGAACATTGTAGGAACTTCATATTATCCCAGAAGACTGCAGTAGTATAATTGCCCTTTTAAAAAACAAACAAACAAAAACAAATAAAACAAACTCTCTGGGTGATGGTTGGATGCACCTCTAATCCCAGCACCAAGGAGGCAGAGGCAGGAGGACCTTTGGGAGTTTGATGCCAAAATGAGTTCCAGGACAGCCAGGACTACACAGAGAAACCCTGTCTCACAAAAAGAAGCAAAACCAAAAACCTCAAGAAGCCAGGCATGATAGTGCATGCTGTAATCCCAGTGCGTGGGAGATTGAGGCAGGATTGCTGTAGGTTCAAGGCCAGTCAGGGCTGTGTATCAAAACATCTCCAAAGAACAAAATATTGAGGGTAAGTAATTCCATGGAGTTTTACGGGGTTTTAAATGCTGATTGTAGGAAGGGTTACATCACTTTGTAGCATCAGGGTCACATCAAGCTATAACCTTGAAGCGTTCTATTTCCAGCCTTTGCATACAGTCACTTATGCTGTGTATTTTATAGTATTTAAGATAATAGGGATGGCATTGGAAAGGAAATTACTTTCATGGGCAATATTTAAAGTTTTGAAATATATAAGGATAAAAACAAACAAACAGGATATCCATTTTAAAGCGAAGAATTGAACCTGATTTATAATGCTACTTTTTAAAACTTGAATGTGTTGTTTGTTGCTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCGAAGAATTGAACCTGA
55.28
GGGCTTCATGAAACTGGCCT
60.61
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCGAAGAATTGAACCTGA
55.28
AGGGCTTCATGAAACTGGCC
60.61
157
PCR template sequence:
AGGATAAAAACAAACAAACAGGATATCCATTTTAAAGCGAAGAATTGAACCTGATTTATAATGCTACTTTTTAAAACTTGAATGTGTTGTTTGTTGCTAGGTAAGTTATATCAGCCAGTCTGGCTATCTGCTCACTGTCCCTACTCCACCATTGTCCTAGAACAAAACTGAGGCCAGTTTCATGAAGCCCTCAAGAGAGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-5101(3), mmu-miR-134-5p(1), mmu-miR-298-5p(1), mmu-miR-326-3p(1), mmu-miR-495-3p(1), mmu-miR-214-3p(1), mmu-miR-411-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGTTTGTTGCTAGGTAAGTTATATCA
siRNA sets
ATATAACTTACCTAGCAAC, TATAACTTACCTAGCAACA, TGATATAACTTACCTAGCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CISFT2D1_1441_ORF_5
0.5994
-0.338153552
0.007182539
90
ORF sequence:
ATGTGTTGTTTGTTGCTAGGTAAGTTATATCAGCCAGTCTGGCTATCTGCTCACTGTCCCTACTCCACCATTGTCCTAGAACAAAACTGA
Peptide sequence:
MCCLLLGKLYQPVWLSAHCPYSTIVLEQN
IRESfinder result
IRESfinder score
0.754106992
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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