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mmu_circSamhd1_745
Basic information of circular RNA
PanCircBase ID:
mmu_circSamhd1_745
mm39_Chr. Position ID:
chr2|156956141|156971836|-
Gene name:
Samhd1
Transcript:
ENSMUST00000057725.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
8,7,6,5,4,3,2
Exon/intron offsets:
0,2130,6260,7609,9067,12550,15628
Genomic length:
15695
Exon/intron sizes in nt:
101,156,71,116,161,73,67
Flanking exon/introns:
chr2:156954861-156956141|chr2:156971836-156976798
Splice length:
745
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ACAATAAAATCGCCGGCTCGTTTCTGCCCTTTTTGGATGAGGATCGTCTGGAAGATCTGGGAGTAAGTTCCTTGGAGGAGAGGAAGAAGATGATAGAATGTATCCAGCAGCTGAGTCAGTCTCGGATTGATCTAATGAAGGTATTTAATGATCCCATTCATGGCCACATTGAGTTCCACCCTCTCCTTATCAGAATCATCGACACACCTCAGTTCCAGCGACTTCGCTATATCAAGCAGCTGGGGGGCGGCTACTATGTTTTCCCTGGAGCGTCCCACAATCGCTTCGAACACAGTCTCGGAGTGGGGTACCTAGCAGGCTGCCTGGTGCGAGCACTTGCCGAAAAACAGCCAGAGCTACAGATCAGTGAGCGAGATATACTCTGTGTTCAGATTGCGGGGCTCTGCCACGACCTAGGTCATGGGCCATTTTCTCATATGTTTGATGGAAGGTTTATCCCACGGGCTCGCCCAGAGAAAAAGTGGAAGCACGAACAGGGCTCCATTGAGATGTTTGAGCATCTGGTCAATTCTAATGAACTCAAACTTGTCATGAAGAACTATGGTCTCGTCCCTGAAGAAGACATTACCTTTATCAAGGAACAAATTATGGGACCACCTATAACACCAGTCAAAGATTCCTTGTGGCCGTATAAAGGCCGCCCTGCCACGAAGAGCTTCCTTTACGAGATAGTGTCTAACAAGAGGAATGGCATCGACGTAGACAAATGGGATTATTTTGCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCCACGAAGAGCTTCCTTT
59.89
ACTCCCAGATCTTCCAGACGA
59.99
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGCCACGAAGAGCTTCCTT
60.32
ACTCCCAGATCTTCCAGACGA
59.99
146
PCR template sequence:
GGCCGTATAAAGGCCGCCCTGCCACGAAGAGCTTCCTTTACGAGATAGTGTCTAACAAGAGGAATGGCATCGACGTAGACAAATGGGATTATTTTGCCAGACAATAAAATCGCCGGCTCGTTTCTGCCCTTTTTGGATGAGGATCGTCTGGAAGATCTGGGAGTAAGTTCCTTGGAGGAGAGGAAGAAGATGATAGAATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-192-5p(1), mmu-miR-215-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTATTTTGCCAGACAATAAAATCGC
siRNA sets
ATTTTATTGTCTGGCAAAA,TTTTATTGTCTGGCAAAAT,TTTATTGTCTGGCAAAATA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSAMHD1_745_ORF_1
1.1825
0.224244878
0.932287421
663
ORF sequence:
ATGATAGAATGTATCCAGCAGCTGAGTCAGTCTCGGATTGATCTAATGAAGGTATTTAATGATCCCATTCATGGCCACATTGAGTTCCACCCTCTCCTTATCAGAATCATCGACACACCTCAGTTCCAGCGACTTCGCTATATCAAGCAGCTGGGGGGCGGCTACTATGTTTTCCCTGGAGCGTCCCACAATCGCTTCGAACACAGTCTCGGAGTGGGGTACCTAGCAGGCTGCCTGGTGCGAGCACTTGCCGAAAAACAGCCAGAGCTACAGATCAGTGAGCGAGATATACTCTGTGTTCAGATTGCGGGGCTCTGCCACGACCTAGGTCATGGGCCATTTTCTCATATGTTTGATGGAAGGTTTATCCCACGGGCTCGCCCAGAGAAAAAGTGGAAGCACGAACAGGGCTCCATTGAGATGTTTGAGCATCTGGTCAATTCTAATGAACTCAAACTTGTCATGAAGAACTATGGTCTCGTCCCTGAAGAAGACATTACCTTTATCAAGGAACAAATTATGGGACCACCTATAACACCAGTCAAAGATTCCTTGTGGCCGTATAAAGGCCGCCCTGCCACGAAGAGCTTCCTTTACGAGATAGTGTCTAACAAGAGGAATGGCATCGACGTAGACAAATGGGATTATTTTGCCAGACAATAA
Peptide sequence:
MIECIQQLSQSRIDLMKVFNDPIHGHIEFHPLLIRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVRALAEKQPELQISERDILCVQIAGLCHDLGHGPFSHMFDGRFIPRARPEKKWKHEQGSIEMFEHLVNSNELKLVMKNYGLVPEEDITFIKEQIMGPPITPVKDSLWPYKGRPATKSFLYEIVSNKRNGIDVDKWDYFARQ
IRESfinder result
IRESfinder score
0.575757242
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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