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mmu_circTlk1_910
Basic information of circular RNA
PanCircBase ID:
mmu_circTlk1_910
mm39_Chr. Position ID:
chr2|70575846|70617339|-
Gene name:
Tlk1
Transcript:
ENSMUST00000135128.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
11,10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,431,3732,4932,6732,8937,11971,23359,24501,41374
Genomic length:
41493
Exon/intron sizes in nt:
13,71,11,93,90,96,47,70,00,00,000
Flanking exon/introns:
chr2:70572586-70575846|chr2:70617339-70655536
Splice length:
910
Other database IDs:
CIRCpedia: MMU_CIRCpedia_27587, circAtlas: mmu-Tlk1_0002
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_153229
Human Ortholog IDs:
Mature spliced Sequence:
GTGCAATGGATGAGCTTCACAGTCTGGACCCAAGAAGGCAAGAATTATTGGAAGCAAGATTTACTGGAGTTGCTACTGGGAGTACTGGGAGTACTGGGAGTTGCAGTGTTGGAGCAAAAGCTTCAACAAATAATGAAAGTTCTAATCACAGTTTTGGAAGCTTAGGATCTCTAAGTGACAAAGAATCAGAGAGACAACTGGCAGGCAGCTGAAAGGACTGTGCAAGTGACGGGACTTTATCTGCAGTAGGTTCCCTTGAGACACCAGAGAAGAAACAATCAGAGTCATCCAGGGGAAGAAAGAGAAAAGCAGAAAGTCAGAATGAAAGTAGTCAGGGAAAAAGTATCGGGGGACGTGGCCATAAGATCAGCGACTATTTTGAATACCAAGGTGGAAATGGCTCGAGTCCAGTAAGAGGCATCCCTCCAGCAATCCGTTCTCCGCAGAACTCACACTCACATTCCACTCCTTCCTCATCTGTTCGACCGAATAGCCCTTCTCCTACTGCATTAGCTTTCGGGGACCACCCTGTTGTACAACCAAAGCAGTTATCCTTTAAGATCACTCAAACTGATCTTACAATGCTGAAATTGGCAGCATTAGAAAGTACTAAAAATCAAGACCTGGAGAAGAAGGAAGGCCGGATTGATGATCTGCTCAGGGCCAACTGTGATCTCAGGCGGCAAATAGATGATCAACAGAAATTACTTGAAAAATACAAAGAACGATTAAATAAGTGCATATCTATGAGCAAGAAACTACTTATTGAAAAGAGTACACAAGAAAAATTGTCTAGCAGAGAAAAGAGTATGCAAGATCGGTTGCGCCTTGGGCACTTTACCACAGTTAGACACGGCGCTTCCTTTACAGAACAGTGGACAGATGGTTTTGCATTTCAGAATCTTGTGAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACGGCGCTTCCTTTACAGAA
59.97
TCCCAGTACTCCCAGTAGCA
59.29
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTAGACACGGCGCTTCCTTT
59.97
TCCCAGTACTCCCAGTAGCA
59.29
154
PCR template sequence:
TGCAAGATCGGTTGCGCCTTGGGCACTTTACCACAGTTAGACACGGCGCTTCCTTTACAGAACAGTGGACAGATGGTTTTGCATTTCAGAATCTTGTGAAGTGCAATGGATGAGCTTCACAGTCTGGACCCAAGAAGGCAAGAATTATTGGAAGCAAGATTTACTGGAGTTGCTACTGGGAGTACTGGGAGTACTGGGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
17
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-206-3p(1), mmu-miR-26a-5p(1), mmu-miR-106b-5p(1), mmu-miR-196a-5p(1), mmu-miR-203-3p(1), mmu-miR-351-5p(1), mmu-miR-26b-5p(1), mmu-miR-127-5p(1), mmu-miR-207(1), mmu-miR-669d-5p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAATCTTGTGAAGTGCAATGGATGA
siRNA sets
TTGCACTTCACAAGATTCT, TCATCCATTGCACTTCACA, ATTGCACTTCACAAGATTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTLK1_910_ORF_1
0.7788
0.075280173
0.25700356
342
ORF sequence:
ATGCTGAAATTGGCAGCATTAGAAAGTACTAAAAATCAAGACCTGGAGAAGAAGGAAGGCCGGATTGATGATCTGCTCAGGGCCAACTGTGATCTCAGGCGGCAAATAGATGATCAACAGAAATTACTTGAAAAATACAAAGAACGATTAAATAAGTGCATATCTATGAGCAAGAAACTACTTATTGAAAAGAGTACACAAGAAAAATTGTCTAGCAGAGAAAAGAGTATGCAAGATCGGTTGCGCCTTGGGCACTTTACCACAGTTAGACACGGCGCTTCCTTTACAGAACAGTGGACAGATGGTTTTGCATTTCAGAATCTTGTGAAGTGCAATGGATGA
Peptide sequence:
MLKLAALESTKNQDLEKKEGRIDDLLRANCDLRRQIDDQQKLLEKYKERLNKCISMSKKLLIEKSTQEKLSSREKSMQDRLRLGHFTTVRHGASFTEQWTDGFAFQNLVKCNG
IRESfinder result
IRESfinder score
0.62352311
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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