Description

The NCBI RefSeq Genes composite track shows 24 Jan 2018 Brachypodium distachyon/GCF_000005505.3_Brachypodium_distachyon_v3.0 protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). All subtracks use coordinates provided by RefSeq. 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.

Data Access

Download GCF_000005505.3_Brachypodium_distachyon_v3.0.ncbiRefSeq.gtf.gz GTF file.

Display Conventions and Configuration

To show only a selected set of subtracks, uncheck the boxes next to the tracks that you wish to hide.

RefSeq annotations and alignments

• 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 24 Jan 2018 Brachypodium distachyon/GCF_000005505.3_Brachypodium_distachyon_v3.0 genome provided by the RefSeq group.

The RefSeq All, RefSeq Curated and RefSeq Predicted, 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.

Color	Level of review
	Reviewed: the RefSeq record has been reviewed by NCBI staff or by a collaborator. The NCBI review process includes assessing available sequence data and the literature. Some RefSeq records may incorporate expanded sequence and annotation information.
	Provisional: the RefSeq record has not yet been subject to individual review. The initial sequence-to-gene association has been established by outside collaborators or NCBI staff.
	Predicted: the RefSeq record has not yet been subject to individual review, and some aspect of the RefSeq record is predicted.

The item labels and codon display properties for features within this track can be configured through the 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.

Methods

The RefSeq annotation and RefSeq RNA alignment tracks were created at UCSC using data from the NCBI RefSeq project. GFF format data files were downloaded from the file GCF_000005505.3_Brachypodium_distachyon_v3.0_genomic.gff.gz delivered with the NCBI RefSeq genome assemblies at the FTP location:
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/505/GCF_000005505.3_Brachypodium_distachyon_v3.0/ The GFF file was converted to the genePred and PSL table formats for display in the Genome Browser. Information about the NCBI annotation pipeline can be found here.

Track statistics summary

Total genome size: 271,298,618 bases

Curated and Predicted Gene count: 47,531
Bases in these genes: 106,549,758
Percent genome coverage: % 39.274

Curated gene count: 476
Bases in curated genes: 468,325
Percent genome coverage: % 0.173

Predicted gene count: 47,055
Bases in genes: 106,308,097
Percent genome coverage: % 39.185

Other annotation count: 1,905
Bases in other annotations: 5,548,924
Percent genome coverage: % 2.045

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