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mmu_circGtf3c5_877
Basic information of circular RNA
PanCircBase ID:
mmu_circGtf3c5_877
mm39_Chr. Position ID:
chr2|28459303|28468086|-
Gene name:
Gtf3c5
Transcript:
ENSMUST00000113889.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
9,8,7,6,5,4,3
Exon/intron offsets:
0,1127,1321,1821,2904,4085,8584
Genomic length:
8783
Exon/intron sizes in nt:
8,39,88,11,15,10,51,96,000
Flanking exon/introns:
chr2:28458639-28459303|chr2:28468086-28469529
Splice length:
877
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GAATGTCTGACTTCCAGTACTTGGCAGTGCACACAGAAGCTGGTGGCAAGCATGTTTCCATGTATGACAGAGTGCTCATGCGCAAGCCTGAGAAGGAGGAGTTCTTCCATCAGGAGCTACCACTCTACATCCCCCCACCCATCTTCTCCAGGCTGGACACCCCTGTGGACTATTTCTATCGCCCTGAGACACAGCACCGAGAAGGCTATCATAATCCCACCATCTCAGGGGAGAACCTGATTGGACTGAGTAGAGCCCGGCGCCCCCACAACGCCATCTTTGTCAACTTTGAGGACACTGAGGTTCCTGAACAGCCTTTGGAGGCTGCAGTCCAGACATGGAAGAAGGCCTGCACCAATCCCATAGATCAGAAGGTGGAAGAGGAGCTGAGGAAGCTCTTTGACATCCGTCCTGTTTGGTCACGAAATGCTGTCAAGTCTAACGTCAGTGTCCATCCTGACAAGCTTAAGATCTTGCTTCCCTATATGGCTTATTACATGATAACAGGCCCGTGGAGAAGCTTGTGGATTCGATTTGGCTATGACCCTCGAAAACACCCAGATGCCAAGATTTATCAAGTCCTTGATTTTCGAATCCGCTGTGGAATGAAATACGGTTATGGCTCCAGGGACATGCCTGTTAAAGCGAAGCGTAGCACGTACAACTACAGCCTGCCCATCACCGTCAAGAAGACATCCAACCAGCCTGGCACCATGCATGACCTGAAGCAGGGCCTGGGCCCATCAGGAACTGATGGCCCACGGAAATTGACCTACAATAAATACAAACTCAAGGATTCGGTCTACATCTTCCGGGAAGGGGCTCTGCCACCCTATCGACAGATGTTCTACCAGCTGTGTGATTTGAATGTGGAGGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCGGTCTACATCTTCCGGGA
59.74
TGGAAACATGCTTGCCACCA
60.76
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCGGTCTACATCTTCCGGG
58.89
GGAAACATGCTTGCCACCAG
60.04
140
PCR template sequence:
ATAAATACAAACTCAAGGATTCGGTCTACATCTTCCGGGAAGGGGCTCTGCCACCCTATCGACAGATGTTCTACCAGCTGTGTGATTTGAATGTGGAGGAGAATGTCTGACTTCCAGTACTTGGCAGTGCACACAGAAGCTGGTGGCAAGCATGTTTCCATGTATGACAGAGTGCTCATGCGCAAGCCTGAGAAGGAGGA
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-181a-5p(1), mmu-miR-324-3p(1), mmu-miR-207(1), mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
TGAATGTGGAGGAGAATGTCTGACTT
siRNA sets
AAGTCAGACATTCTCCTCC, ACATTCTCCTCCACATTCA, TCAGACATTCTCCTCCACA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGTF3C5_877_ORF_1
1.0667
0.376964689
0.990313282
885
ORF sequence:
ATGTGGAGGAGAATGTCTGACTTCCAGTACTTGGCAGTGCACACAGAAGCTGGTGGCAAGCATGTTTCCATGTATGACAGAGTGCTCATGCGCAAGCCTGAGAAGGAGGAGTTCTTCCATCAGGAGCTACCACTCTACATCCCCCCACCCATCTTCTCCAGGCTGGACACCCCTGTGGACTATTTCTATCGCCCTGAGACACAGCACCGAGAAGGCTATCATAATCCCACCATCTCAGGGGAGAACCTGATTGGACTGAGTAGAGCCCGGCGCCCCCACAACGCCATCTTTGTCAACTTTGAGGACACTGAGGTTCCTGAACAGCCTTTGGAGGCTGCAGTCCAGACATGGAAGAAGGCCTGCACCAATCCCATAGATCAGAAGGTGGAAGAGGAGCTGAGGAAGCTCTTTGACATCCGTCCTGTTTGGTCACGAAATGCTGTCAAGTCTAACGTCAGTGTCCATCCTGACAAGCTTAAGATCTTGCTTCCCTATATGGCTTATTACATGATAACAGGCCCGTGGAGAAGCTTGTGGATTCGATTTGGCTATGACCCTCGAAAACACCCAGATGCCAAGATTTATCAAGTCCTTGATTTTCGAATCCGCTGTGGAATGAAATACGGTTATGGCTCCAGGGACATGCCTGTTAAAGCGAAGCGTAGCACGTACAACTACAGCCTGCCCATCACCGTCAAGAAGACATCCAACCAGCCTGGCACCATGCATGACCTGAAGCAGGGCCTGGGCCCATCAGGAACTGATGGCCCACGGAAATTGACCTACAATAAATACAAACTCAAGGATTCGGTCTACATCTTCCGGGAAGGGGCTCTGCCACCCTATCGACAGATGTTCTACCAGCTGTGTGATTTGAATGTGGAG
Peptide sequence:
MWRRMSDFQYLAVHTEAGGKHVSMYDRVLMRKPEKEEFFHQELPLYIPPPIFSRLDTPVDYFYRPETQHREGYHNPTISGENLIGLSRARRPHNAIFVNFEDTEVPEQPLEAAVQTWKKACTNPIDQKVEEELRKLFDIRPVWSRNAVKSNVSVHPDKLKILLPYMAYYMITGPWRSLWIRFGYDPRKHPDAKIYQVLDFRIRCGMKYGYGSRDMPVKAKRSTYNYSLPITVKKTSNQPGTMHDLKQGLGPSGTDGPRKLTYNKYKLKDSVYIFREGALPPYRQMFYQLCDLNVE
IRESfinder result
IRESfinder score
0.396862363
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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