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mmu_circPsmd1_832
Basic information of circular RNA
PanCircBase ID:
mmu_circPsmd1_832
mm39_Chr. Position ID:
chr1|86044296|86061506|+
Gene name:
Psmd1
Transcript:
ENSMUST00000027432.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
17,18,19,20,21,22,23
Exon/intron offsets:
0,1935,9881,11561,14062,16139,17063
Genomic length:
17210
Exon/intron sizes in nt:
11,51,17,10,31,70,93,80,000
Flanking exon/introns:
chr1:86022062-86044296|chr1:86061506-86064684
Splice length:
832
Other database IDs:
circAtlas: mmu-Psmd1_0036
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_93854
Human Ortholog IDs:
Mature spliced Sequence:
GACGCCTGAACAGTGTCCAAGTGTGGTTTCTTTGTTGTCAGAGAGTTATAACCCTCACGTGCGCTATGGAGCTGCAATGGCCCTGGGAATCTGCTGTGCTGGTACAGGAAACAAGGAAGCAATTAATTTACTAGAGCCAATGACCAACGACCCTGTGAACTACGTGAGGCAAGGGGCTCTGATAGCTTCAGCTCTCATCATGATCCAACAGACTGAGATCACGTGTCCAAAGGTGAATCAGTTCCGGCAGCTGTATTCCAAAGTCATCAATGACAAACATGATGATGTCATGGCCAAATTTGGCGCTATTCTGGCCCAAGGCATACTGGATGCAGGTGGTCATAATGTCACAATCTCCTTACAGTCCAGGACTGGGCACACTCATATGCCGTCTGTGGTTGGCGTCCTTGTCTTCACCCAGTTCTGGTTCTGGTTTCCCCTTTCACACTTCCTGTCATTGGCTTATACTCCTACCTGTGTCATTGGCCTTAACAAGGATTTAAAGATGCCGAAAGTTCAATATAAATCAAATTGTAAACCATCCACATTCGCATATCCTGCCCCTCTGGAAGTACCAAAAGAAAAAGAAAAGGAAAAGGTTTCCACCGCTGTGTTGTCTATTACTGCCAAAGCTAAAAAAAAAGAAAAAGAAAAAGAAAAAAAGGAGGAGGAGAAGATGGAAGTGGATGAAGCAGAGAAGAAGGAAGAGAAAGAGAAGAAAAAAGAACCTGAACCAAACTTCCAGCTGTTGGATAATCCAGCACGAGTTATGCCTGCCCAGCTGAAGGTCTTAAGTATGACAGAGACCTGCAGATACCAGCCTTTTAAACCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCAGCACGAGTTATGCCTG
60.11
CATAGCGCACGTGAGGGTTA
60.18
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCAGCACGAGTTATGCCTG
60.11
AGCGCACGTGAGGGTTATAA
59.47
141
PCR template sequence:
ACCAAACTTCCAGCTGTTGGATAATCCAGCACGAGTTATGCCTGCCCAGCTGAAGGTCTTAAGTATGACAGAGACCTGCAGATACCAGCCTTTTAAACCAGACGCCTGAACAGTGTCCAAGTGTGGTTTCTTTGTTGTCAGAGAGTTATAACCCTCACGTGCGCTATGGAGCTGCAATGGCCCTGGGAATCTGCTGTGCT
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-433-3p(1), mmu-miR-22-3p(1), mmu-miR-127-5p(1), mmu-miR-183-5p(1), mmu-miR-758-3p(1), mmu-miR-207(1), mmu-miR-532-5p(1), mmu-miR-3065-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCCTTTTAAACCAGACGCCTGAACAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPSMD1_832_ORF_1
0.9551
0.224716767
0.949472817
765
ORF sequence:
ATGGCCCTGGGAATCTGCTGTGCTGGTACAGGAAACAAGGAAGCAATTAATTTACTAGAGCCAATGACCAACGACCCTGTGAACTACGTGAGGCAAGGGGCTCTGATAGCTTCAGCTCTCATCATGATCCAACAGACTGAGATCACGTGTCCAAAGGTGAATCAGTTCCGGCAGCTGTATTCCAAAGTCATCAATGACAAACATGATGATGTCATGGCCAAATTTGGCGCTATTCTGGCCCAAGGCATACTGGATGCAGGTGGTCATAATGTCACAATCTCCTTACAGTCCAGGACTGGGCACACTCATATGCCGTCTGTGGTTGGCGTCCTTGTCTTCACCCAGTTCTGGTTCTGGTTTCCCCTTTCACACTTCCTGTCATTGGCTTATACTCCTACCTGTGTCATTGGCCTTAACAAGGATTTAAAGATGCCGAAAGTTCAATATAAATCAAATTGTAAACCATCCACATTCGCATATCCTGCCCCTCTGGAAGTACCAAAAGAAAAAGAAAAGGAAAAGGTTTCCACCGCTGTGTTGTCTATTACTGCCAAAGCTAAAAAAAAAGAAAAAGAAAAAGAAAAAAAGGAGGAGGAGAAGATGGAAGTGGATGAAGCAGAGAAGAAGGAAGAGAAAGAGAAGAAAAAAGAACCTGAACCAAACTTCCAGCTGTTGGATAATCCAGCACGAGTTATGCCTGCCCAGCTGAAGGTCTTAAGTATGACAGAGACCTGCAGATACCAGCCTTTTAAACCAGACGCCTGA
Peptide sequence:
MALGICCAGTGNKEAINLLEPMTNDPVNYVRQGALIASALIMIQQTEITCPKVNQFRQLYSKVINDKHDDVMAKFGAILAQGILDAGGHNVTISLQSRTGHTHMPSVVGVLVFTQFWFWFPLSHFLSLAYTPTCVIGLNKDLKMPKVQYKSNCKPSTFAYPAPLEVPKEKEKEKVSTAVLSITAKAKKKEKEKEKKEEEKMEVDEAEKKEEKEKKKEPEPNFQLLDNPARVMPAQLKVLSMTETCRYQPFKPDA
IRESfinder result
IRESfinder score
0.430270711
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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