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mmu_circSamhd1_1095
Basic information of circular RNA
PanCircBase ID:
mmu_circSamhd1_1095
mm39_Chr. Position ID:
chr2|156951336|156971836|-
Gene name:
Samhd1
Transcript:
ENSMUST00000057725.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
11,10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,1131,3383,4805,6935,11065,12414,13872,17355,20433
Genomic length:
20500
Exon/intron sizes in nt:
116,92,142,101,156,71,116,161,73,67
Flanking exon/introns:
chr2:156949485-156951336|chr2:156971836-156976798
Splice length:
1095
Other database IDs:
circAtlas: mmu-Samhd1_0014
Human Ortholog IDs:
Mature spliced Sequence:
ACAATAAAATCGCCGGCTCGTTTCTGCCCTTTTTGGATGAGGATCGTCTGGAAGATCTGGGAGTAAGTTCCTTGGAGGAGAGGAAGAAGATGATAGAATGTATCCAGCAGCTGAGTCAGTCTCGGATTGATCTAATGAAGGTATTTAATGATCCCATTCATGGCCACATTGAGTTCCACCCTCTCCTTATCAGAATCATCGACACACCTCAGTTCCAGCGACTTCGCTATATCAAGCAGCTGGGGGGCGGCTACTATGTTTTCCCTGGAGCGTCCCACAATCGCTTCGAACACAGTCTCGGAGTGGGGTACCTAGCAGGCTGCCTGGTGCGAGCACTTGCCGAAAAACAGCCAGAGCTACAGATCAGTGAGCGAGATATACTCTGTGTTCAGATTGCGGGGCTCTGCCACGACCTAGGTCATGGGCCATTTTCTCATATGTTTGATGGAAGGTTTATCCCACGGGCTCGCCCAGAGAAAAAGTGGAAGCACGAACAGGGCTCCATTGAGATGTTTGAGCATCTGGTCAATTCTAATGAACTCAAACTTGTCATGAAGAACTATGGTCTCGTCCCTGAAGAAGACATTACCTTTATCAAGGAACAAATTATGGGACCACCTATAACACCAGTCAAAGATTCCTTGTGGCCGTATAAAGGCCGCCCTGCCACGAAGAGCTTCCTTTACGAGATAGTGTCTAACAAGAGGAATGGCATCGACGTAGACAAATGGGATTATTTTGCCAGAGACTGTCACCATCTTGGAATCCAAAATAATTTTGATTACAAGCGCTTCATTAAGTTTGCCCGTATCTGTGAAGTGGAGTACAAGGTCAAGGAGGACAAGACCTACATCCGTAAGGTGAAGCACATTTGTTCGAGAGAAAAGGAGGTTGGAAATCTGTATGACATGTTCCACACTCGCAACTGCTTACACCGAAGAGCTTACCAACACAAGATCAGCAACCTCATCGACATAATGATTACAGATGCCTTCCTCAAAGCAGACCCCTACGTGGAGATTACAGGGACTGCCGGGAAGAAGTTCCGCATTTCCACAGCCATTGATGACATGGAAGCCTTCACTAAGTTGACGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCAAAGCAGACCCCTACGTG
59.68
ACTCCCAGATCTTCCAGACGA
59.99
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTCAAAGCAGACCCCTACGT
59.39
ACTCCCAGATCTTCCAGACGA
59.99
164
PCR template sequence:
CTCAAAGCAGACCCCTACGTGGAGATTACAGGGACTGCCGGGAAGAAGTTCCGCATTTCCACAGCCATTGATGACATGGAAGCCTTCACTAAGTTGACGGACAATAAAATCGCCGGCTCGTTTCTGCCCTTTTTGGATGAGGATCGTCTGGAAGATCTGGGAGTAAGTTCCTTGGAGGAGAGGAAGAAGATGATAGAATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-218-5p(1), mmu-miR-192-5p(1), mmu-miR-215-5p(1), mmu-miR-680(1), mmu-miR-452-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTAAGTTGACGGACAATAAAATCGC
siRNA sets
ATTTTATTGTCCGTCAACT, TTATTGTCCGTCAACTTAG, TTTTATTGTCCGTCAACTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSAMHD1_1095_ORF_1
1.2329
0.320450538
0.999998577
2100
ORF sequence:
ATGATAGAATGTATCCAGCAGCTGAGTCAGTCTCGGATTGATCTAATGAAGGTATTTAATGATCCCATTCATGGCCACATTGAGTTCCACCCTCTCCTTATCAGAATCATCGACACACCTCAGTTCCAGCGACTTCGCTATATCAAGCAGCTGGGGGGCGGCTACTATGTTTTCCCTGGAGCGTCCCACAATCGCTTCGAACACAGTCTCGGAGTGGGGTACCTAGCAGGCTGCCTGGTGCGAGCACTTGCCGAAAAACAGCCAGAGCTACAGATCAGTGAGCGAGATATACTCTGTGTTCAGATTGCGGGGCTCTGCCACGACCTAGGTCATGGGCCATTTTCTCATATGTTTGATGGAAGGTTTATCCCACGGGCTCGCCCAGAGAAAAAGTGGAAGCACGAACAGGGCTCCATTGAGATGTTTGAGCATCTGGTCAATTCTAATGAACTCAAACTTGTCATGAAGAACTATGGTCTCGTCCCTGAAGAAGACATTACCTTTATCAAGGAACAAATTATGGGACCACCTATAACACCAGTCAAAGATTCCTTGTGGCCGTATAAAGGCCGCCCTGCCACGAAGAGCTTCCTTTACGAGATAGTGTCTAACAAGAGGAATGGCATCGACGTAGACAAATGGGATTATTTTGCCAGAGACTGTCACCATCTTGGAATCCAAAATAATTTTGATTACAAGCGCTTCATTAAGTTTGCCCGTATCTGTGAAGTGGAGTACAAGGTCAAGGAGGACAAGACCTACATCCGTAAGGTGAAGCACATTTGTTCGAGAGAAAAGGAGGTTGGAAATCTGTATGACATGTTCCACACTCGCAACTGCTTACACCGAAGAGCTTACCAACACAAGATCAGCAACCTCATCGACATAATGATTACAGATGCCTTCCTCAAAGCAGACCCCTACGTGGAGATTACAGGGACTGCCGGGAAGAAGTTCCGCATTTCCACAGCCATTGATGACATGGAAGCCTTCACTAAGTTGACGGACAATAAAATCGCCGGCTCGTTTCTGCCCTTTTTGGATGAGGATCGTCTGGAAGATCTGGGAGTAAGTTCCTTGGAGGAGAGGAAGAAGATGATAGAATGTATCCAGCAGCTGAGTCAGTCTCGGATTGATCTAATGAAGGTATTTAATGATCCCATTCATGGCCACATTGAGTTCCACCCTCTCCTTATCAGAATCATCGACACACCTCAGTTCCAGCGACTTCGCTATATCAAGCAGCTGGGGGGCGGCTACTATGTTTTCCCTGGAGCGTCCCACAATCGCTTCGAACACAGTCTCGGAGTGGGGTACCTAGCAGGCTGCCTGGTGCGAGCACTTGCCGAAAAACAGCCAGAGCTACAGATCAGTGAGCGAGATATACTCTGTGTTCAGATTGCGGGGCTCTGCCACGACCTAGGTCATGGGCCATTTTCTCATATGTTTGATGGAAGGTTTATCCCACGGGCTCGCCCAGAGAAAAAGTGGAAGCACGAACAGGGCTCCATTGAGATGTTTGAGCATCTGGTCAATTCTAATGAACTCAAACTTGTCATGAAGAACTATGGTCTCGTCCCTGAAGAAGACATTACCTTTATCAAGGAACAAATTATGGGACCACCTATAACACCAGTCAAAGATTCCTTGTGGCCGTATAAAGGCCGCCCTGCCACGAAGAGCTTCCTTTACGAGATAGTGTCTAACAAGAGGAATGGCATCGACGTAGACAAATGGGATTATTTTGCCAGAGACTGTCACCATCTTGGAATCCAAAATAATTTTGATTACAAGCGCTTCATTAAGTTTGCCCGTATCTGTGAAGTGGAGTACAAGGTCAAGGAGGACAAGACCTACATCCGTAAGGTGAAGCACATTTGTTCGAGAGAAAAGGAGGTTGGAAATCTGTATGACATGTTCCACACTCGCAACTGCTTACACCGAAGAGCTTACCAACACAAGATCAGCAACCTCATCGACATAATGATTACAGATGCCTTCCTCAAAGCAGACCCCTACGTGGAGATTACAGGGACTGCCGGGAAGAAGTTCCGCATTTCCACAGCCATTGATGACATGGAAGCCTTCACTAAGTTGACG
Peptide sequence:
MIECIQQLSQSRIDLMKVFNDPIHGHIEFHPLLIRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVRALAEKQPELQISERDILCVQIAGLCHDLGHGPFSHMFDGRFIPRARPEKKWKHEQGSIEMFEHLVNSNELKLVMKNYGLVPEEDITFIKEQIMGPPITPVKDSLWPYKGRPATKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARICEVEYKVKEDKTYIRKVKHICSREKEVGNLYDMFHTRNCLHRRAYQHKISNLIDIMITDAFLKADPYVEITGTAGKKFRISTAIDDMEAFTKLTDNKIAGSFLPFLDEDRLEDLGVSSLEERKKMIECIQQLSQSRIDLMKVFNDPIHGHIEFHPLLIRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVRALAEKQPELQISERDILCVQIAGLCHDLGHGPFSHMFDGRFIPRARPEKKWKHEQGSIEMFEHLVNSNELKLVMKNYGLVPEEDITFIKEQIMGPPITPVKDSLWPYKGRPATKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARICEVEYKVKEDKTYIRKVKHICSREKEVGNLYDMFHTRNCLHRRAYQHKISNLIDIMITDAFLKADPYVEITGTAGKKFRISTAIDDMEAFTKLT
IRESfinder result
IRESfinder score
0.560997384
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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