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mmu_circTlk2_958
Basic information of circular RNA
PanCircBase ID:
mmu_circTlk2_958
mm39_Chr. Position ID:
chr11|105144116|105170051|+
Gene name:
Tlk2
Transcript:
ENSMUST00000106939.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
13,14,15,16,17,18,19,20,21
Exon/intron offsets:
0,1675,3579,6970,13862,16335,17808,22546,25827
Genomic length:
25935
Exon/intron sizes in nt:
6,79,88,29,29,01,70,13,00,00,000
Flanking exon/introns:
chr11:105140463-105144116|chr11:105170051-105171910
Splice length:
958
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GTTAACGTTAGCCGAGTACCATGAACAAGAGGAAATCTTCAAACTTAGATTAGGTCATCTTAAGAAAGAGGAAGCAGAAATCCAGGCAGAGCTGGAAAGGCTGGAAAGGGTTAGGAATCTACACATCAGGGAATTAAAAAGGATACATAATGAAGACAATTCGCAGTTTAAAGACCATCCAACACTAAATGACAGATATTTGTTGTTACATCTTTTGGGTAGAGGAGGTTTCAGTGAAGTTTACAAGGCATTTGATCTAACGGAGCAAAGATATGTAGCTGTGAAAATTCACCAGTTAAATAAAAACTGGAGAGATGAGAAAAAGGAGAATTACCACAAGCATGCGTGTAGGGAATACCGGATTCACAAGGAGCTGGACCACCCCAGGATAGTGAAGCTGTATGATTACTTTTCACTGGACACTGACTCGTTTTGTACAGTATTAGAATACTGTGAAGGGAATGACCTGGACTTCTACCTAAAACAGCACAAATTAATGTCGGAGAAAGAAGCCCGATCCATTATTATGCAGATTGTGAATGCTTTAAAGTACTTAAATGAAATAAAACCTCCCATCATACACTATGACCTCAAACCAGGTAATATCCTTTTAGTAAATGGTACAGCATGTGGAGAGATAAAAATTACAGATTTTGGTCTTTCCAAGATCATGGATGATGATAGCTACAATTCAGTGGATGGCATGGAGCTGACGTCACAAGGAGCTGGTACTTATTGGTATTTACCACCAGAGTGTTTTGTGGTTGGGAAAGAGCCACCAAAGATCTCAAATAAAGTCGATGTTTGGTCAGTGGGTGTGATCTTCTACCAGTGTCTTTATGGGAGGAAGCCTTTTGGCCATAACCAGTCCCAGCAAGATATTCTACAAGAGAATACTATTCTTAAGGCTACTGAAGTACAGTTCCCGCCAAAGCCAGTAGTAACACCTGAAGCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGAAGTACAGTTCCCGCCA
59.68
AGCTCTGCCTGGATTTCTGC
60.39
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGAAGTACAGTTCCCGCCAA
60.27
AGCTCTGCCTGGATTTCTGC
60.39
140
PCR template sequence:
CCATAACCAGTCCCAGCAAGATATTCTACAAGAGAATACTATTCTTAAGGCTACTGAAGTACAGTTCCCGCCAAAGCCAGTAGTAACACCTGAAGCAAAGGTTAACGTTAGCCGAGTACCATGAACAAGAGGAAATCTTCAAACTTAGATTAGGTCATCTTAAGAAAGAGGAAGCAGAAATCCAGGCAGAGCTGGAAAGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(1), mmu-miR-429-3p(1), mmu-miR-221-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-758-3p(1), mmu-miR-215-5p(1), mmu-miR-673-5p(1), mmu-miR-335-3p(1), mmu-miR-3065-5p(1), mmu-miR-670-5p(1), mmu-miR-1904(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACCTGAAGCAAAGGTTAACGTTAGCC
siRNA sets
TAACGTTAACCTTTGCTTC, AACGTTAACCTTTGCTTCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTLK2_958_ORF_1
0.9473
0.087703527
0.584060648
486
ORF sequence:
ATGTCGGAGAAAGAAGCCCGATCCATTATTATGCAGATTGTGAATGCTTTAAAGTACTTAAATGAAATAAAACCTCCCATCATACACTATGACCTCAAACCAGGTAATATCCTTTTAGTAAATGGTACAGCATGTGGAGAGATAAAAATTACAGATTTTGGTCTTTCCAAGATCATGGATGATGATAGCTACAATTCAGTGGATGGCATGGAGCTGACGTCACAAGGAGCTGGTACTTATTGGTATTTACCACCAGAGTGTTTTGTGGTTGGGAAAGAGCCACCAAAGATCTCAAATAAAGTCGATGTTTGGTCAGTGGGTGTGATCTTCTACCAGTGTCTTTATGGGAGGAAGCCTTTTGGCCATAACCAGTCCCAGCAAGATATTCTACAAGAGAATACTATTCTTAAGGCTACTGAAGTACAGTTCCCGCCAAAGCCAGTAGTAACACCTGAAGCAAAGGTTAACGTTAGCCGAGTACCATGA
Peptide sequence:
MSEKEARSIIMQIVNALKYLNEIKPPIIHYDLKPGNILLVNGTACGEIKITDFGLSKIMDDDSYNSVDGMELTSQGAGTYWYLPPECFVVGKEPPKISNKVDVWSVGVIFYQCLYGRKPFGHNQSQQDILQENTILKATEVQFPPKPVVTPEAKVNVSRVP
IRESfinder result
IRESfinder score
0.639222075
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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