Question: Where can I obtain Transposable elements of Zebra fish (Danio)
gravatar for jaqx008
3 months ago by
jaqx00840 wrote:

Hello All, Can anyone recommend a link Where I can get a file with Transposable elements for zebrafish? Thanks

zebrafish transposones genome • 170 views
ADD COMMENTlink written 3 months ago by jaqx00840

There are some article links from NCBI and other sources:

Genome Analysis of Pseudoloma neurophilia: A Microsporidian Parasite of Zebrafish (Danio rerio).

Ndikumana S et al. J Eukaryot Microbiol. (2017)

Gal4 Driver Transgenic Zebrafish: Powerful Tools to Study Developmental Biology, Organogenesis, and Neuroscience.

Kawakami K et al. Adv Genet. (2016)

Excision of the tol2 transposable element of the medaka fish, Oryzias latipes, in zebrafish, Danio rerio.

Kawakami K et al. Gene. (1998)

Transposon tools and methods in zebrafish(2005)

ADD REPLYlink modified 3 months ago • written 3 months ago by natasha.sernova3.4k

Download link for Danio rerio.

ADD REPLYlink modified 3 months ago • written 3 months ago by genomax65k

Thanks. However, this is a fasta file. I am looking for a file with all TE classes specified. example is shown below

Bf_V2_1 1   797 -   bf_rep_71   Unknown        
Bf_V2_1     848 936 +   (TA)n               Simple_repeat  
Bf_V2_1     1236    1369    -   CR1-11_BF           LINE/CR1       
Bf_V2_1     2151    2171    +   (TA)n               Simple_repeat  
Bf_V2_1     2351    3238    -   bf_rep_71           Unknown        
Bf_V2_1     3229    3413    +   DNA-X-4_BF          DNA/Unknown    
Bf_V2_1     3400    3506    +   Harbinger-N11_BF    DNA/Harbinger  
Bf_V2_1     3507    3549    -   Harbinger-N11_BF    DNA/Harbinger  
Bf_V2_1     3605    4790    -   bf_rep_71           Unknown        
Bf_V2_1     4781    4965    +   DNA-X-4_BF          DNA/Unknown    
Bf_V2_1     4952    5056    +   Harbinger-N11_BF    DNA/Harbinger
ADD REPLYlink written 3 months ago by jaqx00840

Here is the page for Danio TE classes. Not in the format you want though.

ADD REPLYlink written 3 months ago by genomax65k
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