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.
-This track is a multi-view composite track that contains differing data set views. -Instructions for configuring multi-view tracks are -here. +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.
-The views available for this track include: +The subtracks available for this track include:The RefSeq All, RefSeq Curated, RefSeq Predicted, RefSeq Clinical 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.
@@ -91,38 +85,34 @@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. Click the view name -(NCBI RefSeq or UCSC RefSeq) to globally modify the settings for all subtracks in -the view. To adjust the settings for an individual subtrack, click the wrench icon next to the -track name in the subtrack list (available only for views containing more than one track).
+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 .The RefSeq Diffs track contains five different types of inconsistency between the @@ -148,65 +138,67 @@ transcript sequence (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 unambigously, +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).
-Tracks contained in the RefSeq annotation and RefSeq RNA alignment views were created at UCSC using +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 $organism genome using BLAT. Those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.1% of the best and at least 96% base identity with the genomic sequence were kept.
The raw data for these tracks can be accessed in multiple ways. It can be explored interactively using the Table Browser or Data Integrator. The tables can also be accessed programmatically through our public MySQL server or downloaded from our downloads server for local processing.
+target="_blank">downloads server for local processing. You can also access any RefSeq table +entries in JSON format through our +JSON API.The data in the RefSeq Other and RefSeq Diffs tracks are organized in bigBed file format; more information about accessing the information in this bigBed file can be found below. The other subtracks are associated with database tables as follows:
The annotations in the RefSeqOther and RefSeqDiffs tracks are stored in bigBed files, which can be obtained from our downloads server here, ncbiRefSeqOther.bb and ncbiRefSeqDiffs.bb. Individual regions or the whole set of genome-wide annotations can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system from the utilities directory linked below. For example, to extract only annotations in a given region, you could use the following command:
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/$db/ncbiRefSeq/ncbiRefSeqOther.bb -chrom=chr16 -start=34990190 -end=36727467 stdout
-The genePred format tracks can also be downloaded in GTF format using the +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:
genePredToGtf $db ncbiRefSeqPredicted ncbiRefSeqPredicted.gtfNote 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.