We are analyzing https://link.springer.com/article/10.1007/s00335-015-9583-x.

Title:
Creating reference gene annotation for the mouse C57BL6/J genome assembly | Mammalian Genome
Description:
Annotation on the reference genome of the C57BL6/J mouse has been an ongoing project ever since the draft genome was first published. Initially, the principle focus was on the identification of all protein-coding genes, although today the importance of describing long non-coding RNAs, small RNAs, and pseudogenes is recognized. Here, we describe the progress of the GENCODE mouse annotation project, which combines manual annotation from the HAVANA group with Ensembl computational annotation, alongside experimental and in silico validation pipelines from other members of the consortium. We discuss the more recent incorporation of next-generation sequencing datasets into this workflow, including the usage of mass-spectrometry data to potentially identify novel protein-coding genes. Finally, we will outline how the C57BL6/J genebuild can be used to gain insights into the variant sites that distinguish different mouse strains and species.
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Keywords {🔍}

annotation, pubmed, mouse, genome, article, google, scholar, gencode, gene, cas, transcript, central, data, models, human, havana, genes, rnaseq, proteincoding, transcripts, harrow, manual, ensembl, sequencing, sequence, based, project, analysis, reference, rna, expression, res, process, model, loci, sequences, nat, computational, nature, genomes, alternative, cds, evidence, fig, annotated, mammalian, mudge, noncoding, functional, regions,

Topics {✒️}

crispr/cas-mediated genome engineering single-molecule long-read survey transcript-level classifications—termed ‘biotypes article download pdf single-gene laboratory studies gov/projects/genome/assembly/grc/ candidate insulin-dependent diabetes protein-coding gene naaladl2 fixed-vocabulary ‘attributes’ attached carrillo-de santa pau single-locus laboratory studies combining rt-pcr-seq genome-sequencing era began upstream protein-coding genes crispr/cas assays identical intron/exon boundaries crispr/cas system existing protein-coding genes wild-derived inbred mice aid phenotype-based investigations nanopore-based rna sequencing sanger-sequenced transcriptomics data large protein-coding gene full-length rna-seq mouse protein-coding genes full-length coding transcripts missing protein-coding genes split read-supported introns creating gene ottmus00000051138 data sources—chiefly transcriptomics related subjects perez-riverol mass-spectrometry-based draft sequence-specific control strain c57bl/6j separate end-sequencing protocols sanger-sequenced cdnas/ests privacy choices/manage cookies large-scale proteome analysis griffiths-jones full size image large-scale structural variation genome reference consortium article mudge mammalian reference sequences rna-guided platform mouse reference assembly long noncoding rnas encode project consortium protein-coding gene

Questions {❓}

Experiments done in Black-6 mice: what does it mean?
Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M (2007) What is a gene, post-ENCODE?

Schema {🗺️}

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      headline:Creating reference gene annotation for the mouse C57BL6/J genome assembly
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