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mmu_circPsmd1_723
Basic information of circular RNA
PanCircBase ID:
mmu_circPsmd1_723
mm39_Chr. Position ID:
chr1|86013751|86022062|+
Gene name:
Psmd1
Transcript:
ENSMUST00000139715.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
10,11,12,13,14,15
Exon/intron offsets:
0,545,2779,3964,5973,8246
Genomic length:
8311
Exon/intron sizes in nt:
79,174,112,197,96,65
Flanking exon/introns:
chr1:86012992-86013751|chr1:86022062-86044296
Splice length:
723
Other database IDs:
CIRCpedia: MMU_CIRCpedia_32275, circAtlas: mmu-Psmd1_0001
circBase: hsa_circ_0058635, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_93852
Human Ortholog IDs:
Mature spliced Sequence:
AGATAACTTGGAATGGTTGGCCAGAGCCACCAACTGGGCCAAATTTACTGCAACGGCCAGCTTGGGTGTAATCCATAAGGGCCATGAGAAGGAAGCACTACAGTTAATGGCAACATACCTTCCTAAGGACACTTCTCCAGGATCAGCCTATCAGGAAGGGGGCGGTCTCTATGCATTGGGTCTCATTCATGCCAATCATGGTGGTGACATAATTGACTATCTCCTTAATCAGCTCAAGAATGCCAGCAATGATATTGTTCGACATGGAGGCAGCCTGGGCCTTGGTTTGGCTGCAATGGGAACTGCACGTCAGGATGTGTATGATTTGCTGAAAACAAACCTGTATCAGGATGATGCTGTGACAGGGGAGGCAGCTGGCCTAGCCTTAGGTTTGGTTATGTTAGGTTCTAAAAATGCCCAGGCGATTGAGGATATGGTTGGCTATGCACAAGAGACTCAACACGAGAAGATTCTGCGCGGTCTGGCAGTTGGCATTGCGTTAGTGATGTACGGGAGGATGGAGGAGGCTGATGCTCTCATTGAGTCTCTCTGTCGTGACAAGGACCCAATTCTTAGAAGATCTGGAATGTATACTGTAGCCATGGCTTATTGTGGCTCTGGTAACAACAAAGCCATTCGGCGCCTGCTACATGTTGCTGTAAGTGATGTCAATGATGATGTCAGAAGAGCAGCAGTGGAGTCACTTGGCTTCATTTTGTTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCAGAAGAGCAGCAGTGG
59.97
GCTTCCTTCTCATGGCCCTT
60.03
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCAGAAGAGCAGCAGTGG
59.97
AGTGCTTCCTTCTCATGGCC
60.03
144
PCR template sequence:
ACAACAAAGCCATTCGGCGCCTGCTACATGTTGCTGTAAGTGATGTCAATGATGATGTCAGAAGAGCAGCAGTGGAGTCACTTGGCTTCATTTTGTTCAGAGATAACTTGGAATGGTTGGCCAGAGCCACCAACTGGGCCAAATTTACTGCAACGGCCAGCTTGGGTGTAATCCATAAGGGCCATGAGAAGGAAGCACTA
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-let-7b-5p(1), mmu-miR-135a-5p(1), mmu-miR-139-5p(1), mmu-miR-153-3p(1), mmu-miR-98-5p(1), mmu-miR-690(1), mmu-miR-673-5p(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
TCATTTTGTTCAGAGATAACTTGGAA
siRNA sets
TTCCAAGTTATCTCTGAAC, TTATCTCTGAACAAAATGA, GTTATCTCTGAACAAAATG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPSMD1_723_ORF_1
1.0853
0.20112706
0.999268102
1338
ORF sequence:
ATGGCAACATACCTTCCTAAGGACACTTCTCCAGGATCAGCCTATCAGGAAGGGGGCGGTCTCTATGCATTGGGTCTCATTCATGCCAATCATGGTGGTGACATAATTGACTATCTCCTTAATCAGCTCAAGAATGCCAGCAATGATATTGTTCGACATGGAGGCAGCCTGGGCCTTGGTTTGGCTGCAATGGGAACTGCACGTCAGGATGTGTATGATTTGCTGAAAACAAACCTGTATCAGGATGATGCTGTGACAGGGGAGGCAGCTGGCCTAGCCTTAGGTTTGGTTATGTTAGGTTCTAAAAATGCCCAGGCGATTGAGGATATGGTTGGCTATGCACAAGAGACTCAACACGAGAAGATTCTGCGCGGTCTGGCAGTTGGCATTGCGTTAGTGATGTACGGGAGGATGGAGGAGGCTGATGCTCTCATTGAGTCTCTCTGTCGTGACAAGGACCCAATTCTTAGAAGATCTGGAATGTATACTGTAGCCATGGCTTATTGTGGCTCTGGTAACAACAAAGCCATTCGGCGCCTGCTACATGTTGCTGTAAGTGATGTCAATGATGATGTCAGAAGAGCAGCAGTGGAGTCACTTGGCTTCATTTTGTTCAGAGATAACTTGGAATGGTTGGCCAGAGCCACCAACTGGGCCAAATTTACTGCAACGGCCAGCTTGGGTGTAATCCATAAGGGCCATGAGAAGGAAGCACTACAGTTAATGGCAACATACCTTCCTAAGGACACTTCTCCAGGATCAGCCTATCAGGAAGGGGGCGGTCTCTATGCATTGGGTCTCATTCATGCCAATCATGGTGGTGACATAATTGACTATCTCCTTAATCAGCTCAAGAATGCCAGCAATGATATTGTTCGACATGGAGGCAGCCTGGGCCTTGGTTTGGCTGCAATGGGAACTGCACGTCAGGATGTGTATGATTTGCTGAAAACAAACCTGTATCAGGATGATGCTGTGACAGGGGAGGCAGCTGGCCTAGCCTTAGGTTTGGTTATGTTAGGTTCTAAAAATGCCCAGGCGATTGAGGATATGGTTGGCTATGCACAAGAGACTCAACACGAGAAGATTCTGCGCGGTCTGGCAGTTGGCATTGCGTTAGTGATGTACGGGAGGATGGAGGAGGCTGATGCTCTCATTGAGTCTCTCTGTCGTGACAAGGACCCAATTCTTAGAAGATCTGGAATGTATACTGTAGCCATGGCTTATTGTGGCTCTGGTAACAACAAAGCCATTCGGCGCCTGCTACATGTTGCTGTAAGTGATGTCAATGATGATGTCAGAAGAGCAGCAGTGGAGTCACTTGGCTTCATTTTGTTC
Peptide sequence:
MATYLPKDTSPGSAYQEGGGLYALGLIHANHGGDIIDYLLNQLKNASNDIVRHGGSLGLGLAAMGTARQDVYDLLKTNLYQDDAVTGEAAGLALGLVMLGSKNAQAIEDMVGYAQETQHEKILRGLAVGIALVMYGRMEEADALIESLCRDKDPILRRSGMYTVAMAYCGSGNNKAIRRLLHVAVSDVNDDVRRAAVESLGFILFRDNLEWLARATNWAKFTATASLGVIHKGHEKEALQLMATYLPKDTSPGSAYQEGGGLYALGLIHANHGGDIIDYLLNQLKNASNDIVRHGGSLGLGLAAMGTARQDVYDLLKTNLYQDDAVTGEAAGLALGLVMLGSKNAQAIEDMVGYAQETQHEKILRGLAVGIALVMYGRMEEADALIESLCRDKDPILRRSGMYTVAMAYCGSGNNKAIRRLLHVAVSDVNDDVRRAAVESLGFILF
IRESfinder result
IRESfinder score
0.362860509
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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