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mmu_circSamhd1_887
Basic information of circular RNA
PanCircBase ID:
mmu_circSamhd1_887
mm39_Chr. Position ID:
chr2|156954719|156971836|-
Gene name:
Samhd1
Transcript:
ENSMUST00000057725.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
9,8,7,6,5,4,3,2
Exon/intron offsets:
0,1422,3552,7682,9031,10489,13972,17050
Genomic length:
17117
Exon/intron sizes in nt:
142,101,156,71,116,161,73,67
Flanking exon/introns:
chr2:156952559-156954719|chr2:156971836-156976798
Splice length:
887
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
ACAATAAAATCGCCGGCTCGTTTCTGCCCTTTTTGGATGAGGATCGTCTGGAAGATCTGGGAGTAAGTTCCTTGGAGGAGAGGAAGAAGATGATAGAATGTATCCAGCAGCTGAGTCAGTCTCGGATTGATCTAATGAAGGTATTTAATGATCCCATTCATGGCCACATTGAGTTCCACCCTCTCCTTATCAGAATCATCGACACACCTCAGTTCCAGCGACTTCGCTATATCAAGCAGCTGGGGGGCGGCTACTATGTTTTCCCTGGAGCGTCCCACAATCGCTTCGAACACAGTCTCGGAGTGGGGTACCTAGCAGGCTGCCTGGTGCGAGCACTTGCCGAAAAACAGCCAGAGCTACAGATCAGTGAGCGAGATATACTCTGTGTTCAGATTGCGGGGCTCTGCCACGACCTAGGTCATGGGCCATTTTCTCATATGTTTGATGGAAGGTTTATCCCACGGGCTCGCCCAGAGAAAAAGTGGAAGCACGAACAGGGCTCCATTGAGATGTTTGAGCATCTGGTCAATTCTAATGAACTCAAACTTGTCATGAAGAACTATGGTCTCGTCCCTGAAGAAGACATTACCTTTATCAAGGAACAAATTATGGGACCACCTATAACACCAGTCAAAGATTCCTTGTGGCCGTATAAAGGCCGCCCTGCCACGAAGAGCTTCCTTTACGAGATAGTGTCTAACAAGAGGAATGGCATCGACGTAGACAAATGGGATTATTTTGCCAGAGACTGTCACCATCTTGGAATCCAAAATAATTTTGATTACAAGCGCTTCATTAAGTTTGCCCGTATCTGTGAAGTGGAGTACAAGGTCAAGGAGGACAAGACCTACATCCGTAAGGTGAAGCACATTTGTTCGAGAGAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCCCGTATCTGTGAAGTGG
59.75
ACTCCCAGATCTTCCAGACGA
59.99
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCCCGTATCTGTGAAGTGGA
59.46
ACTCCCAGATCTTCCAGACGA
59.99
148
PCR template sequence:
GCGCTTCATTAAGTTTGCCCGTATCTGTGAAGTGGAGTACAAGGTCAAGGAGGACAAGACCTACATCCGTAAGGTGAAGCACATTTGTTCGAGAGAAAAGACAATAAAATCGCCGGCTCGTTTCTGCCCTTTTTGGATGAGGATCGTCTGGAAGATCTGGGAGTAAGTTCCTTGGAGGAGAGGAAGAAGATGATAGAATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-218-5p(1), mmu-miR-192-5p(1), mmu-miR-215-5p(1), mmu-miR-452-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTCGAGAGAAAAGACAATAAAATCGC
siRNA sets
TTTATTGTCTTTTCTCTCG, TTTTATTGTCTTTTCTCTC, ATTTTATTGTCTTTTCTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSAMHD1_887_ORF_1
0.9951
0.242003546
0.977910344
864
ORF sequence:
ATGATAGAATGTATCCAGCAGCTGAGTCAGTCTCGGATTGATCTAATGAAGGTATTTAATGATCCCATTCATGGCCACATTGAGTTCCACCCTCTCCTTATCAGAATCATCGACACACCTCAGTTCCAGCGACTTCGCTATATCAAGCAGCTGGGGGGCGGCTACTATGTTTTCCCTGGAGCGTCCCACAATCGCTTCGAACACAGTCTCGGAGTGGGGTACCTAGCAGGCTGCCTGGTGCGAGCACTTGCCGAAAAACAGCCAGAGCTACAGATCAGTGAGCGAGATATACTCTGTGTTCAGATTGCGGGGCTCTGCCACGACCTAGGTCATGGGCCATTTTCTCATATGTTTGATGGAAGGTTTATCCCACGGGCTCGCCCAGAGAAAAAGTGGAAGCACGAACAGGGCTCCATTGAGATGTTTGAGCATCTGGTCAATTCTAATGAACTCAAACTTGTCATGAAGAACTATGGTCTCGTCCCTGAAGAAGACATTACCTTTATCAAGGAACAAATTATGGGACCACCTATAACACCAGTCAAAGATTCCTTGTGGCCGTATAAAGGCCGCCCTGCCACGAAGAGCTTCCTTTACGAGATAGTGTCTAACAAGAGGAATGGCATCGACGTAGACAAATGGGATTATTTTGCCAGAGACTGTCACCATCTTGGAATCCAAAATAATTTTGATTACAAGCGCTTCATTAAGTTTGCCCGTATCTGTGAAGTGGAGTACAAGGTCAAGGAGGACAAGACCTACATCCGTAAGGTGAAGCACATTTGTTCGAGAGAAAAGACAATAAAATCGCCGGCTCGTTTCTGCCCTTTTTGGATGAGGATCGTCTGGAAGATCTGGGAGTAA
Peptide sequence:
MIECIQQLSQSRIDLMKVFNDPIHGHIEFHPLLIRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVRALAEKQPELQISERDILCVQIAGLCHDLGHGPFSHMFDGRFIPRARPEKKWKHEQGSIEMFEHLVNSNELKLVMKNYGLVPEEDITFIKEQIMGPPITPVKDSLWPYKGRPATKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARICEVEYKVKEDKTYIRKVKHICSREKTIKSPARFCPFWMRIVWKIWE
IRESfinder result
IRESfinder score
0.596437674
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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