Question: The sequence changes with the refseq version
1
gravatar for jinkuozhang
21 months ago by
jinkuozhang30
jinkuozhang30 wrote:

I want to know why and how NCBI update the version of accession number. Like this one: from NM_004764.3 to NM_004764.4: three bases were changed.

Thanks!

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ADD COMMENTlink modified 21 months ago • written 21 months ago by jinkuozhang30

finswimmer, Thank you!

I have NM_004764 amplified from different cDNA libraries, there sequence are the same as NM_004764.3. Now I know NCBI make minor correction to update the refeseq. However what is its Criterion that version 3 is "wrong" and version 4 is "correct"?

ADD REPLYlink written 21 months ago by jinkuozhang30
2

It is difficult to know for sure what evidence NCBI used to make the correction but here is what the notes for that record say:

REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DB072454.1, BC028581.2,
            AF104260.2 and DB527532.1.
            On Jul 8, 2010 this sequence version replaced NM_004764.3.

So the sequence has been there since 2010. I don't think either version is wrong. The latest version represents the current information NCBI (someone who looked at the evidence) has about this sequence.

Note: Please use ADD COMMENT/ADD REPLY buttons when responding to existing posts to keep threads logically organized.

ADD REPLYlink modified 21 months ago • written 21 months ago by genomax78k

genomax, Very nice information. Can I look the difference between NM_004764.3 and NM_004764.4 as SNPs?

ADD REPLYlink written 21 months ago by jinkuozhang30

I am not sure what to tell you. You have experimental evidence that seems to support the older version of the sequence (so that is hard to refute) but at the same time RefSeq sequence seems to be unchallenged/unchanged since 2010.

Take a look at the gene record for PIWIL1 and see if you are able to glean any additional information.

Are those three differences randomly scattered across the length?

ADD REPLYlink modified 21 months ago • written 21 months ago by genomax78k
1
gravatar for finswimmer
21 months ago by
finswimmer13k
Germany
finswimmer13k wrote:

Hello,

NCBI describes this in their FAQ.

fin swimmer

ADD COMMENTlink modified 21 months ago • written 21 months ago by finswimmer13k
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