Description

The NCBI RefSeq Genes composite track shows mouse protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). All subtracks use coordinates provided by RefSeq, except for the UCSC RefSeq track, which UCSC produces by realigning the RefSeq RNAs to the genome. This realignment may result in occasional differences between the annotation coordinates provided by UCSC and NCBI. See the Methods section for more details about how the different tracks were created.

Please visit NCBI's Feedback for Gene and Reference Sequences (RefSeq) page to make suggestions, submit additions and corrections, or ask for help concerning RefSeq records.

For more information on the different gene tracks, see our Genes FAQ.

Display Conventions and Configuration

This track is a composite track that contains differing data sets. To show only a selected set of subtracks, uncheck the boxes next to the tracks that you wish to hide. Note: Not all subtracks are available on all assemblies.

RefSeq aligned annotations and UCSC alignment of RefSeq annotations

• RefSeq All – all curated and predicted annotations provided by RefSeq.
• RefSeq Curated – subset of RefSeq All that includes only those annotations whose accessions begin with NM, NR, NP or YP. (NP and YP are used only for protein-coding genes on the mitochondrion; YP is used for human only.)
• RefSeq Predicted – subset of RefSeq All that includes those annotations whose accessions begin with XM or XR.
• RefSeq Other – all other annotations produced by the RefSeq group that do not fit the requirements for inclusion in the RefSeq Curated or the RefSeq Predicted tracks.
• RefSeq Alignments – alignments of RefSeq RNAs to the mouse genome provided by the RefSeq group, following the display conventions for PSL tracks.
• RefSeq Diffs – alignment differences between the mouse reference genome(s) and RefSeq transcripts. (Track not currently available for every assembly.)
• UCSC RefSeq – annotations generated from UCSC's realignment of RNAs with NM and NR accessions to the mouse genome. This track was previously known as the "RefSeq Genes" track.
• RefSeq Select – Subset of RefSeq Curated, transcripts marked as part of the RefSeq Select dataset. A single Select transcript is chosen as representative for each protein-coding gene. See NCBI RefSeq Select.
• NCBI Orthologs – Orthologous genes were identified by NCBI's Eukaryotic Genome Annotation Pipeline for the NCBI Gene dataset using a combination of protein sequence similarity and local synteny analysis. Orthology is determined between the genome being annotated and a reference genome, such as human or zebrafish, and pairs of orthologs are grouped together. Transitive relationships are inferred within each group, for example, zebrafish <-> human <-> mouse. For more information on how NCBI calculates orthologs, see the details provided here. This track is available for the following assemblies: hg38, mm39, danRer11, canFam6, and bosTau9.

The RefSeq All, RefSeq Curated, RefSeq Predicted, RefSeq Select and UCSC RefSeq tracks follow the display conventions for gene prediction tracks. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), or reviewed (dark), as defined by RefSeq.

The item labels and codon display properties for features within this track can be configured through the check-box controls at the top of the track description page. To adjust the settings for an individual subtrack, click the wrench icon next to the track name in the subtrack list .

• Label: By default, items are labeled by gene name. Click the appropriate Label option to display the accession name or OMIM identifier instead of the gene name, show all or a subset of these labels including the gene name, OMIM identifier and accession names, or turn off the label completely.
• Codon coloring: This track has an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page.

The RefSeq Diffs track contains five different types of inconsistency between the reference genome sequence and the RefSeq transcript sequences. The five types of differences are as follows:

• mismatch – aligned but mismatching bases, plus HGVS g. to show the genomic change required to match the transcript and HGVS c./n. to show the transcript change required to match the genome.
• short gap – genomic gaps that are too small to be introns (arbitrary cutoff of < 45 bp), most likely insertions/deletion variants or errors, with HGVS g. and c./n. showing differences.
• shift gap – shortGap items whose placement could be shifted left and/or right on the genome due to repetitive sequence, with HGVS c./n. position range of ambiguous region in transcript. Here, thin and thick lines are used -- the thin line shows the span of the repetitive sequence, and the thick line shows the rightmost shifted gap.
• double gap – genomic gaps that are long enough to be introns but that skip over transcript sequence (invisible in default setting), with HGVS c./n. deletion.
• skipped – sequence at the beginning or end of a transcript that is not aligned to the genome (invisible in default setting), with HGVS c./n. deletion

When reporting HGVS with RefSeq sequences, to make sure that results from research articles can be mapped to the genome unambiguously, please specify the RefSeq annotation release displayed on the transcript's Genome Browser details page and also the RefSeq transcript ID with version (e.g. NM_012309.4 not NM_012309).

Methods

Tracks contained in the RefSeq annotation and RefSeq RNA alignment tracks were created at UCSC using data from the NCBI RefSeq project. Data files were downloaded from RefSeq in GFF file format and converted to the genePred and PSL table formats for display in the Genome Browser. Information about the NCBI annotation pipeline can be found here.

The RefSeq Diffs track is generated by UCSC using NCBI's RefSeq RNA alignments.

The UCSC RefSeq Genes track is constructed using the same methods as previous RefSeq Genes tracks. RefSeq RNAs were aligned against the mouse genome using BLAT. Those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.1% of the best and at least 96% base identity with the genomic sequence were kept.

The NCBI Orthologs track was generated using the latest NCBI files (gene2accession and gene_orthologs). NCBI chromosome identifiers were mapped to UCSC-compatible IDs using species-specific chromosome alias files, and genes were filtered to include only those located on valid NCBI chromosomes. A custom Python script processed the ortholog relationships and created bed files for each species. The bed files were then converted to BigBed format, with indexing for search functionality. The procedure is documented in the makeDoc from our GitHub repository.

Data Access

The raw data for these tracks can be accessed in multiple ways. It can be explored interactively using the Table Browser or Data Integrator. The tables can also be accessed programmatically through our public MySQL server or downloaded from our downloads server for local processing. The previous track versions are available in the archives of our downloads server. You can also access any RefSeq table entries in JSON format through our JSON API.

The data in the RefSeq Other, RefSeq Diffs, and NCBI Orthologs tracks are organized in bigBed file format; more information about accessing the information in this bigBed file can be found below. The other subtracks are associated with database tables as follows:

genePred format:

• RefSeq All - ncbiRefSeq
• RefSeq Curated - ncbiRefSeqCurated
• RefSeq Predicted - ncbiRefSeqPredicted
• RefSeq Select - ncbiRefSeqSelect
• UCSC RefSeq - refGene

PSL format:

• RefSeq Alignments - ncbiRefSeqPsl

The first column of each of these tables is "bin". This column is designed to speed up access for display in the Genome Browser, but can be safely ignored in downstream analysis. You can read more about the bin indexing system here.

The annotations in the RefSeqOther, RefSeqDiffs, and NCBI Orthologs tracks are stored in bigBed files, which can be obtained from our downloads server here, ncbiRefSeqOther.bb, ncbiRefSeqDiffs.bb, and ncbiOrtho.bb. Individual regions or the whole set of genome-wide annotations can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system from the utilities directory linked below. For example, to extract only annotations in a given region, you could use the following command:

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/mm39/ncbiRefSeq/ncbiRefSeqOther.bb -chrom=chr16 -start=34990190 -end=36727467 stdout

You can download a GTF format version of the RefSeq All table from the GTF downloads directory. The genePred format tracks can also be converted to GTF format using the genePredToGtf utility, available from the utilities directory on the UCSC downloads server. The utility can be run from the command line like so:

Note that using genePredToGtf in this manner accesses our public MySQL server, and you therefore must set up your hg.conf as described on the MySQL page linked near the beginning of the Data Access section.

A file containing the RNA sequences in FASTA format for all items in the RefSeq All, RefSeq Curated, and RefSeq Predicted tracks can be found on our downloads server here.

Please refer to our mailing list archives for questions.

Credits

This track was produced at UCSC from data generated by scientists worldwide and curated by the NCBI RefSeq project.

References

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518

Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. PMID: 24259432; PMC: PMC3965018

Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4. PMID: 15608248; PMC: PMC539979