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mmu_circSptan1_480
Basic information of circular RNA
PanCircBase ID:
mmu_circSptan1_480
mm39_Chr. Position ID:
chr2|29898085|29901119|+
Gene name:
Sptan1
Transcript:
ENSMUST00000113719.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
30,31,32
Exon/intron offsets:
0,2625,2836
Genomic length:
3034
Exon/intron sizes in nt:
18,21,00,198
Flanking exon/introns:
chr2:29897999-29898085|chr2:29901119-29901197
Splice length:
480
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGAATTCCCTTGGGGAAACAGCCCAAAGGCTGATCCAGTCCCACCCTGAATCTGCAGAGGACTTAAAGGAAAAGTGCACAGAGTTAAACCAGGCCTGGACCAGCCTAGGGAAGCGTGCAGACCAGCGCAAGGCCAAATTGGGTGACTCCCATGATCTGCAGCGCTTCCTTAGCGATTTCCGGGACCTCATGTCTTGGATCAATGGAATACGAGGGTTGGTATCTTCAGATGAACTAGCCAAGGACGTCACTGGAGCTGAGGCTTTGCTGGAGCGACACCAGGAACACCGGACAGAAATTGATGCCAGGGCTGGCACTTTCCAGGCATTTGAGCAGTTTGGGCAGCAGCTGTTAGCTCACGGGCACTATGCCAGCCCGGAGATCAAAGAGAAACTTGATATTCTTGACCAGGAGCGCACAGACCTGGAGAAGGCCTGGGTCCAGCGCAGGATGATGCTGGACCACTGCCTGGAGTTGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATTCTTGACCAGGAGCGCAC
60.67
CTCTGCAGATTCAGGGTGGG
60.11
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATTCTTGACCAGGAGCGCAC
60.67
CCTCTGCAGATTCAGGGTGG
60.11
142
PCR template sequence:
GATCAAAGAGAAACTTGATATTCTTGACCAGGAGCGCACAGACCTGGAGAAGGCCTGGGTCCAGCGCAGGATGATGCTGGACCACTGCCTGGAGTTGCAGGTGAATTCCCTTGGGGAAACAGCCCAAAGGCTGATCCAGTCCCACCCTGAATCTGCAGAGGACTTAAAGGAAAAGTGCACAGAGTTAAACCAGGCCTGGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-34a-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-207(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCTGGAGTTGCAGGTGAATTCCCTTG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSPTAN1_480_ORF_1
1.1727
0.408606827
0.984474993
771
ORF sequence:
ATGTCTTGGATCAATGGAATACGAGGGTTGGTATCTTCAGATGAACTAGCCAAGGACGTCACTGGAGCTGAGGCTTTGCTGGAGCGACACCAGGAACACCGGACAGAAATTGATGCCAGGGCTGGCACTTTCCAGGCATTTGAGCAGTTTGGGCAGCAGCTGTTAGCTCACGGGCACTATGCCAGCCCGGAGATCAAAGAGAAACTTGATATTCTTGACCAGGAGCGCACAGACCTGGAGAAGGCCTGGGTCCAGCGCAGGATGATGCTGGACCACTGCCTGGAGTTGCAGGTGAATTCCCTTGGGGAAACAGCCCAAAGGCTGATCCAGTCCCACCCTGAATCTGCAGAGGACTTAAAGGAAAAGTGCACAGAGTTAAACCAGGCCTGGACCAGCCTAGGGAAGCGTGCAGACCAGCGCAAGGCCAAATTGGGTGACTCCCATGATCTGCAGCGCTTCCTTAGCGATTTCCGGGACCTCATGTCTTGGATCAATGGAATACGAGGGTTGGTATCTTCAGATGAACTAGCCAAGGACGTCACTGGAGCTGAGGCTTTGCTGGAGCGACACCAGGAACACCGGACAGAAATTGATGCCAGGGCTGGCACTTTCCAGGCATTTGAGCAGTTTGGGCAGCAGCTGTTAGCTCACGGGCACTATGCCAGCCCGGAGATCAAAGAGAAACTTGATATTCTTGACCAGGAGCGCACAGACCTGGAGAAGGCCTGGGTCCAGCGCAGGATGATGCTGGACCACTGCCTGGAGTTGCAG
Peptide sequence:
MSWINGIRGLVSSDELAKDVTGAEALLERHQEHRTEIDARAGTFQAFEQFGQQLLAHGHYASPEIKEKLDILDQERTDLEKAWVQRRMMLDHCLELQVNSLGETAQRLIQSHPESAEDLKEKCTELNQAWTSLGKRADQRKAKLGDSHDLQRFLSDFRDLMSWINGIRGLVSSDELAKDVTGAEALLERHQEHRTEIDARAGTFQAFEQFGQQLLAHGHYASPEIKEKLDILDQERTDLEKAWVQRRMMLDHCLELQ
IRESfinder result
IRESfinder score
0.292474507
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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