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mmu_circTxnl1_637
Basic information of circular RNA
PanCircBase ID:
mmu_circTxnl1_637
mm39_Chr. Position ID:
chr18|63807119|63815378|-
Gene name:
Txnl1
Transcript:
ENSMUST00000237004.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,1395,2830,5304,8162
Genomic length:
8259
Exon/intron sizes in nt:
173,70,123,174,97
Flanking exon/introns:
chr18:63804757-63807119|chr18:63815378-63825146
Splice length:
637
Other database IDs:
circAtlas: mmu-Txnl1_0002
circBase: hsa_circ_0108670, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_88485
Human Ortholog IDs:
Mature spliced Sequence:
GTGTGGACCGTGTCTTCGGATTGCCCCGGCGTTCAGCTCTATGAGTAATAAGTACCCACAGGCAGTCTTCTTGGAAGTAGATGTGCATCAGTGCCAGGGAACAGCTGCCACCAACAACATATCAGCAACACCTACGTTTTTGTTTTTTCGAAACAAAGTGAGAATCGATCAGTATCAAGGAGCAGATGCTGTGGGACTAGAAGAGAAAATCAAGCAGCACTTAGAAAATGATCCTGGAAGCAATGAGGACGCAGACATTCCAAAGGGCTATATGGATTTAATGCCTTTTATTAACAAAGCTGGTTGTGAATGTCTTAATGAAAGTGATGAGCACGGCTTTGACAACTGTTTACGAAAAGACATGTCCTTCTTGGAGTCTGACTGTGATGAGCAGCTCCTTATTACTGTGGCATTCAATCAGCCTGTTAAGCTTTATTCCATGAAGTTTCAAGGACCAGATAACGGTCAGGGTCCTAAATATGTAAAAATTTTTATCAACCTACCCCGATCTATGGATTTTGAGGAGGCGGAAAGGAGTGAGCCAACTCAAGCTCTGGAACTGACAGAAGATGACATTAAAGAAGATGGCATTGTTCCTCTTCGTTATGTTAAATTTCAGAATGTCAACAGTGTAACT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCCAACTCAAGCTCTGGAA
59.23
ACTCATAGAGCTGAACGCCG
59.9
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCCAACTCAAGCTCTGGAA
59.23
CAAGAAGACTGCCTGTGGGT
59.89
171
PCR template sequence:
TGAGCCAACTCAAGCTCTGGAACTGACAGAAGATGACATTAAAGAAGATGGCATTGTTCCTCTTCGTTATGTTAAATTTCAGAATGTCAACAGTGTAACTGTGTGGACCGTGTCTTCGGATTGCCCCGGCGTTCAGCTCTATGAGTAATAAGTACCCACAGGCAGTCTTCTTGGAAGTAGATGTGCATCAGTGCCAGGGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-181b-5p(1), mmu-miR-382-3p(1), mmu-miR-96-5p(1), mmu-miR-467b-5p(1), mmu-miR-190b-5p(1), mmu-miR-673-5p(1), mmu-miR-5099(1)
siRNAs for circular RNA silencing
Junction sequence
CAACAGTGTAACTGTGTGGACCGTGT
siRNA sets
ACGGTCCACACAGTTACAC, ACACGGTCCACACAGTTAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTXNL1_637_ORF_1
1.149
0.183759027
0.906335827
645
ORF sequence:
ATGAGTAATAAGTACCCACAGGCAGTCTTCTTGGAAGTAGATGTGCATCAGTGCCAGGGAACAGCTGCCACCAACAACATATCAGCAACACCTACGTTTTTGTTTTTTCGAAACAAAGTGAGAATCGATCAGTATCAAGGAGCAGATGCTGTGGGACTAGAAGAGAAAATCAAGCAGCACTTAGAAAATGATCCTGGAAGCAATGAGGACGCAGACATTCCAAAGGGCTATATGGATTTAATGCCTTTTATTAACAAAGCTGGTTGTGAATGTCTTAATGAAAGTGATGAGCACGGCTTTGACAACTGTTTACGAAAAGACATGTCCTTCTTGGAGTCTGACTGTGATGAGCAGCTCCTTATTACTGTGGCATTCAATCAGCCTGTTAAGCTTTATTCCATGAAGTTTCAAGGACCAGATAACGGTCAGGGTCCTAAATATGTAAAAATTTTTATCAACCTACCCCGATCTATGGATTTTGAGGAGGCGGAAAGGAGTGAGCCAACTCAAGCTCTGGAACTGACAGAAGATGACATTAAAGAAGATGGCATTGTTCCTCTTCGTTATGTTAAATTTCAGAATGTCAACAGTGTAACTGTGTGGACCGTGTCTTCGGATTGCCCCGGCGTTCAGCTCTATGAGTAA
Peptide sequence:
MSNKYPQAVFLEVDVHQCQGTAATNNISATPTFLFFRNKVRIDQYQGADAVGLEEKIKQHLENDPGSNEDADIPKGYMDLMPFINKAGCECLNESDEHGFDNCLRKDMSFLESDCDEQLLITVAFNQPVKLYSMKFQGPDNGQGPKYVKIFINLPRSMDFEEAERSEPTQALELTEDDIKEDGIVPLRYVKFQNVNSVTVWTVSSDCPGVQLYE
IRESfinder result
IRESfinder score
0.553125925
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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