text: user82: What are the actual differences between different annotation databases? 
  My lab, for reasons still unknown to me, prefers Ensembl annotations (we're working with transcript/exon expression estimation), while some software ship with RefSeq annotations. Are there significant differences between them today, or are they, for all intents and purposes, interchangeable (e.g., are exon coordinates between RefSeq and Ensembl annotations interchangeable)?
  
  user1579: While annotations between RefSeq and Gencode are not so different is the coding regions (genes), Gencode is much more rich in the intergenic regions. This could be very advantagous for epigenetic studies, where regulation is of interest.   
  
  user5024: The UCSC Genome Browser Genes FAQ discusses this question in detail:
  https://genome.ucsc.edu/FAQ/FAQgenes.html#ens
  
  Officially, the Ensembl and GENCODE gene models are the same. On the
    latest human and mouse genome assemblies (hg38 and mm10), the
    identifiers, transcript sequences, and exon coordinates are almost
    identical between equivalent Ensembl and GENCODE versions (excluding
    alternative sequences or fix sequences).
  GENCODE uses the UCSC convention of prefixing chromosome names with
    "chr", e.g. "chr1" and "chrM", but Ensembl calls these "1" or "MT". At
    the time of writing (Ensembl 89), a few transcripts differ due to
    conversion issues. In addition, around 160 PAR genes are duplicated in
    GENCODE but only once in Ensembl. The differences affect fewer than 1%
    of the transcripts. Apart from gene annotation itself, the links to
    external databases differ.
  The GENCODE Release History shows the release dates and can be linked
    to corresponding Ensembl releases. You can download the gene
    transcript models from the website https://gencodegenes.org or from
    http://ensembl.org. For most applications, the files distributed on
    the GENCODE website should be easier to use, as the third party
    database links are easier to parse and the sequence identifiers match
    the UCSC genome files, at least for the primary chromosomes.
  Additional information on this question can be found on the GENCODE
    FAQ page.
  
  
  user235: To add practical advice to what others have said:
  In a practical sense, I think the biggest difference between RefSeq and Ensembl/GENCODE is in the sensitivity/specificity trade off. 
  Ensembl aims more towards the inclusive end, including a far larger number of transcript variants, many of which are only weakly supported.
  RefSeq trades some of this sensitivity for specificity - you can be more confident that a RefSeq transcript exists, but less confident that the ReqSeq annotation includes all of the real transcripts for a gene. 
  
  user161: Ensembl vs Gencode
  https://www.gencodegenes.org/faq.html
  
  The GENCODE annotation is made by merging the Havana manual gene annotation and the Ensembl automated gene annotation. [...] In practical terms, the GENCODE annotation is identical to the Ensembl annotation.
  
  Further, for the GTF file differences:
  
  The only exception is that the genes which are common to the human chromosome X and Y PAR regions can be found twice in the GENCODE GTF, while they are shown only for chromosome X in the Ensembl file.
  
  Gencode(Ensembl) vs RefSeq
  Gencode is in almost all cases more comprehensive. For example, this is NCBI RefSeq vs Ensembl (v24, release 83) for BRCA gene:
  
  RefSeq and Gencode are not interchangeable in most cases, though RefSeq annotations will often be a subset of the Gencode ones.
  
  user203: To add to rightskewed answer:
  While it is true that:
  Gencode is an additive set of annotation (the manual one done by Havana and an automated one done by Ensembl),
  the annotation (GTF) files are quite similar for a few exceptions involving the X chromosome and Y par and additional remarks in the Gencode file (see more at FAQ - Gencode).
  
  What are the actual differences between different annotation databases?
  
  They are a few differences, but the main one  for me (and it could be stupid) is
  that Refseq is developed by the American NCBI and
  the ENSEMBL is mainly developed by the European EMBL-EBI.
  Often, labs or people will just start using what is the best known to them (because of a course or workshop) or because they start working with one of the databases with one specific tool and keep with it later.
  
  My lab, for reasons still unknown to me, prefers Ensembl annotations (we're working with transcript/exon expression estimation), while some software ship with RefSeq annotations.
  
  Your lab might be mostly European based people or they might also have read papers like the one from Frankish et al.  Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction. BMC Genomics 2015; 16(Suppl 8):S2 - DOI: 10.1186/1471-2164-16-S8-S2
  From the Frankish et al. paper paper:
  
  The GENCODE Comprehensive transcripts contain more exons, have greater genomic coverage and capture many more variants than RefSeq in both genome and exome datasets, while the GENCODE Basic set shows a higher degree of concordance with RefSeq and has fewer unique features.
  
  As for:
  
  Are there significant differences between them today, or are they, for all intents and purposes, interchangeable (e.g., are exon coordinates between RefSeq and Ensembl annotations interchangeable)?
  
  No. I don't think they are great differences between them as that the global picture should stay the same (although you will see different results if you are interested in a small set of genes). However, they are not directly interchangeable. Particularly as there are many versions of Ensembl and Refseq based on different genome annotations (and those won't be interchangeable between themselves either in most cases).
  However, you can easily translate most[1] of your Refseq IDs to ENSEMBL IDs and vice-versa with tools as http://www.ensembl.org/biomart/martview for example (there are devoted libraries/API as well like Biocondutor: biomaRt
  [1] Most as sometimes, they might be annotated in one of the database but haven't (yet) an equivalent in the other.
  EDIT
  In fine, even if people tends to keep to what they are used to (and that the annotations are constantly expanded and corrected) depending on the research subject one might be interested in using one database over another:
  From Zhao S, Zhang B. A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification. BMC Genomics. 2015;16: 97. paper:
  
  When choosing an annotation database, researchers should keep in mind that no database is perfect and some gene annotations might be inaccurate or entirely wrong. [..] Wu et al. [27] suggested that when conducting research that emphasizes reproducible and robust gene expression estimates, a less complex genome annotation, such as RefGene, might be preferred. When conducting more exploratory research, a more complex genome annotation, such as Ensembl, should be chosen.
  [..]
  [27] Wu P-Y, Phan JH, Wang MD. Assessing the impact of human genome annotation choice on RNA-seq expression estimates. BMC Bioinformatics. 2013;14(Suppl 11):S8. doi: 10.1186/1471-2105-14-S11-S8.
  
  
original_text: 82: <p>What are the actual differences between different annotation databases? </p>
  
  <p>My lab, for reasons still unknown to me, prefers Ensembl annotations (we're working with transcript/exon expression estimation), while some software ship with RefSeq annotations. Are there significant differences between them today, or are they, for all intents and purposes, interchangeable (e.g., are exon coordinates between RefSeq and Ensembl annotations interchangeable)?</p>
   1579: <p>While annotations between RefSeq and Gencode are not so different is the coding regions (genes), Gencode is much more rich in the intergenic regions. This could be very advantagous for epigenetic studies, where regulation is of interest.   </p>
   5024: <p>The UCSC Genome Browser Genes FAQ discusses this question in detail:
  <a href="https://genome.ucsc.edu/FAQ/FAQgenes.html#ens" rel="nofollow noreferrer">https://genome.ucsc.edu/FAQ/FAQgenes.html#ens</a></p>
  
  <blockquote>
    <p>Officially, the Ensembl and GENCODE gene models are the same. On the
    latest human and mouse genome assemblies (hg38 and mm10), the
    identifiers, transcript sequences, and exon coordinates are almost
    identical between equivalent Ensembl and GENCODE versions (excluding
    alternative sequences or fix sequences).</p>
    
    <p>GENCODE uses the UCSC convention of prefixing chromosome names with
    "chr", e.g. "chr1" and "chrM", but Ensembl calls these "1" or "MT". At
    the time of writing (Ensembl 89), a few transcripts differ due to
    conversion issues. In addition, around 160 PAR genes are duplicated in
    GENCODE but only once in Ensembl. The differences affect fewer than 1%
    of the transcripts. Apart from gene annotation itself, the links to
    external databases differ.</p>
    
    <p>The GENCODE Release History shows the release dates and can be linked
    to corresponding Ensembl releases. You can download the gene
    transcript models from the website <a href="https://gencodegenes.org" rel="nofollow noreferrer">https://gencodegenes.org</a> or from
    <a href="http://ensembl.org" rel="nofollow noreferrer">http://ensembl.org</a>. For most applications, the files distributed on
    the GENCODE website should be easier to use, as the third party
    database links are easier to parse and the sequence identifiers match
    the UCSC genome files, at least for the primary chromosomes.</p>
    
    <p>Additional information on this question can be found on the GENCODE
    FAQ page.</p>
  </blockquote>
   235: <p>To add practical advice to what others have said:</p>
  
  <p>In a practical sense, I think the biggest difference between RefSeq and Ensembl/GENCODE is in the sensitivity/specificity trade off. </p>
  
  <p>Ensembl aims more towards the inclusive end, including a far larger number of transcript variants, many of which are only weakly supported.</p>
  
  <p>RefSeq trades some of this sensitivity for specificity - you can be more confident that a RefSeq transcript exists, but less confident that the ReqSeq annotation includes all of the real transcripts for a gene. </p>
   161: <h2>Ensembl vs Gencode</h2>
  
  <p><a href="https://www.gencodegenes.org/faq.html" rel="noreferrer">https://www.gencodegenes.org/faq.html</a></p>
  
  <blockquote>
    <p>The GENCODE annotation is made by merging the Havana manual gene annotation and the Ensembl automated gene annotation. [...] In practical terms, the GENCODE annotation is identical to the Ensembl annotation.</p>
  </blockquote>
  
  <p>Further, for the GTF file differences:</p>
  
  <blockquote>
    <p>The only exception is that the genes which are common to the human chromosome X and Y PAR regions can be found twice in the GENCODE GTF, while they are shown only for chromosome X in the Ensembl file.</p>
  </blockquote>
  
  <h2>Gencode(Ensembl) vs RefSeq</h2>
  
  <p>Gencode is in almost all cases <a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-16-S8-S2" rel="noreferrer">more comprehensive</a>. For example, this is NCBI RefSeq vs Ensembl (v24, release 83) for BRCA gene:
  <a href="https://i.stack.imgur.com/MO5Gb.png" rel="noreferrer"><img src="https://i.stack.imgur.com/MO5Gb.png" alt="enter image description here"></a></p>
  
  <p>RefSeq and Gencode are not interchangeable in most cases, though RefSeq annotations will often be a subset of the Gencode ones.</p>
   203: <p>To add to <a href="https://bioinformatics.stackexchange.com/a/38/203">rightskewed answer</a>:
  While it is true that:</p>
  <p>Gencode is an additive set of annotation (the manual one done by Havana and an automated one done by Ensembl),</p>
  <p>the annotation (GTF) files are quite similar for a few exceptions involving the X chromosome and Y par and additional remarks in the Gencode file (see more at <a href="https://www.gencodegenes.org/faq.html" rel="noreferrer">FAQ - Gencode</a>).</p>
  <blockquote>
  <p>What are the actual differences between different annotation databases?</p>
  </blockquote>
  <p>They are a few differences, but the main one  <strong>for me (and it could be stupid)</strong> is</p>
  <p>that <strong>Refseq is developed by the American NCBI</strong> and</p>
  <p>the <strong>ENSEMBL is mainly developed by the European EMBL-EBI.</strong></p>
  <p>Often, labs or people will just start using what is the best known to them (because of a course or workshop) or because they start working with one of the databases with one specific tool and keep with it later.</p>
  <blockquote>
  <p>My lab, for reasons still unknown to me, prefers Ensembl annotations (we're working with transcript/exon expression estimation), while some software ship with RefSeq annotations.</p>
  </blockquote>
  <p>Your lab might be mostly European based people or they might also have read papers like the one from Frankish et al.  Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction. BMC Genomics 2015; 16(Suppl 8):S2 - DOI: 10.1186/1471-2164-16-S8-S2</p>
  <p>From the <a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-16-S8-S2" rel="noreferrer">Frankish et al. paper</a> paper:</p>
  <blockquote>
  <p>The GENCODE Comprehensive transcripts contain more exons, have greater genomic coverage and capture many more variants than RefSeq in both genome and exome datasets, while the GENCODE Basic set shows a higher degree of concordance with RefSeq and has fewer unique features.</p>
  </blockquote>
  <p>As for:</p>
  <blockquote>
  <p>Are there significant differences between them today, or are they, for all intents and purposes, interchangeable (e.g., are exon coordinates between RefSeq and Ensembl annotations interchangeable)?</p>
  </blockquote>
  <p>No. I don't think they are great differences between them as that the global picture should stay the same (although you will see different results if you are interested in a small set of genes). However, <strong>they are not directly interchangeable</strong>. Particularly as there are many versions of Ensembl and Refseq based on different genome annotations (and those won't be interchangeable between themselves either in most cases).</p>
  <p><strong>However, you can easily translate</strong> most[1] of your Refseq IDs to ENSEMBL IDs and vice-versa with tools as <a href="http://www.ensembl.org/biomart/martview" rel="noreferrer">http://www.ensembl.org/biomart/martview</a> for example (there are devoted libraries/API as well like <a href="https://bioconductor.org/packages/release/bioc/html/biomaRt.html" rel="noreferrer">Biocondutor: biomaRt</a></p>
  <p>[1] Most as sometimes, they might be annotated in one of the database but haven't (yet) an equivalent in the other.</p>
  <p><strong>EDIT</strong></p>
  <p>In fine, even if people tends to keep to what they are used to (and that the annotations are constantly expanded and corrected) depending on the research subject one might be interested in using one database over another:</p>
  <p>From <a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1308-8" rel="noreferrer">Zhao S, Zhang B. A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification. BMC Genomics. 2015;16: 97.</a> paper:</p>
  <blockquote>
  <p>When choosing an annotation database, researchers should keep in mind that no database is perfect and some gene annotations might be inaccurate or entirely wrong. [..] Wu et al. [27] suggested that when conducting research that emphasizes reproducible and robust gene expression estimates, a less complex genome annotation, such as RefGene, might be preferred. When conducting more exploratory research, a more complex genome annotation, such as Ensembl, should be chosen.</p>
  <p>[..]</p>
  <p>[27] Wu P-Y, Phan JH, Wang MD. Assessing the impact of human genome annotation choice on RNA-seq expression estimates. BMC Bioinformatics. 2013;14(Suppl 11):S8. doi: 10.1186/1471-2105-14-S11-S8.</p>
  </blockquote>
  