Question: Line-1 Sequence
3
gravatar for Bio_X2Y
8.3 years ago by
Bio_X2Y3.6k
Ireland
Bio_X2Y3.6k wrote:

Does anyone know where I can find the DNA sequence for human LINE-1 (L1)?

I understand that it has 2 open reading frames, so that equates in my head to maybe 2 gene symbols I should be looking for?

sequence dna • 8.5k views
ADD COMMENTlink modified 8.0 years ago by Casey Bergman17k • written 8.3 years ago by Bio_X2Y3.6k
4
gravatar for iw9oel_ad
8.3 years ago by
iw9oel_ad6.0k
iw9oel_ad6.0k wrote:

Querying the EBI ENA with the text 'human line repeat' gives 155 results. Top result is

M19503      Human Line-1 repeat mRNA with 2 open reading frames.

The accession number will fetch the relevant records from Genbank or EMBL.

PUBMED; 2454389. Skowronski J., Fanning T.G., Singer M.F.; "Unit-length line-1 transcripts in human teratocarcinoma cells"; Mol. Cell. Biol. 8(4):1385-1397(1988).

PUBMED; 1701022. Swergold G.D.; "Identification, characterization, and cell specificity of a human LINE-1 promoter"; Mol. Cell. Biol. 10(12):6718-6729(1990).

That EMBL record was last updated in 2008, but I don't know what was changed. There's no guarantee that any particular record is definitive in EMBL/Genbank.

Dropping this sequence into Ensembl blast hits ENSG00000240563 which is L1TD1 in HGNC nomenclature. From there, there are links to more recent publications.

ADD COMMENTlink modified 8.3 years ago • written 8.3 years ago by iw9oel_ad6.0k

Thanks Keith. I'm a bit concerned that that sequence (GenBank M19503.1) might be a bit ancient - it's from 1993. Do you know if there are official HUGO gene symbols or RefSeqs associated with these genes? I can't seem to find any. Thanks

ADD REPLYlink written 8.3 years ago by Bio_X2Y3.6k

NM_019079 is a RefSeq accession from 2009 (linked from Ensembl above)

ADD REPLYlink written 8.3 years ago by iw9oel_ad6.0k
4
gravatar for Treylathe
8.3 years ago by
Treylathe940
San Francisco
Treylathe940 wrote:

Since Lines are repeat elements (non-LTR retrotransposons to be more exact), there are several families with somewhat differing sequences. They encode reverse transcriptase and apurinic-apyrimidinic endonuclease but they are a bit more complex than that: http://gydb.org/index.php/Retroelements#Non-LTR_retroelements There are indeed 2 ORF, but the first encodes a gag-like region, it's the second that encode the two functions above.

That 1993 report is probably good for the sequence. You could search in dbRIP http://dbrip.brocku.ca/searchRIP.html for sequences (advanced search, choose subfamily l1hs).

l1td1 is the hugo id of the above NM_019079 I believe.

ADD COMMENTlink written 8.3 years ago by Treylathe940
2
gravatar for Casey Bergman
8.3 years ago by
Casey Bergman17k
Athens, GA, USA
Casey Bergman17k wrote:

I would recommend getting a free RepBase account (http://www.girinst.org/accountservices/register.php) and use the annotations in the EMBL formatted RepBase records to identify the appropriate L1 sub-family relevant to your problem:

http://www.girinst.org/repbase/update/browse.php?letter=L&division=Primates&customdivision=&rank=&type=L1&autonomous=1&nonautonomous=1&simple=1&format=EMBL#browse

ADD COMMENTlink written 8.3 years ago by Casey Bergman17k
1
gravatar for Fred Fleche
8.3 years ago by
Fred Fleche4.3k
Paris, France
Fred Fleche4.3k wrote:

The Entrez Gene page for this gene which gives two distinct mRNAS for you gene. So according to Refseq there are two distinct transcripts but they are encoding the same protein.[?][?] The Ensembl page gives only one transcript that is identical to one of the Refseq transcript. [?]Since a picture is worth a thousand words, find below the transcripts from Refesq and Ensembl for you gene of interest:[?] alt text [?]And if you want to keep track of it I would suggest to use his Geneid (54596) or his Ensembl ID (ENSG00000240563) cause they are more stable than the HUGO Gene Name.[?]

ADD COMMENTlink modified 8.3 years ago • written 8.3 years ago by Fred Fleche4.3k
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