Schema for NCBI RefSeq - RefSeq gene predictions from NCBI
  Database: hub_567047_hs1    Primary Table: hub_567047_ncbiRefSeq Data last updated: 2022-09-08
Big Bed File Download: /gbdb/hs1/ncbiRefSeq/ncbiRefSeq.bb
Item Count: 108,944
The data is stored in the binary BigBed format.

Format description: bigGenePred gene models
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart165511900Start position in chromosome
chromEnd165686948End position in chromosome
nameXR_007070820.1Name or ID of item, ideally both human readable and unique
score0Score (0-1000)
strand++ or - for strand
thickStart165686948Start of where display should be thick (start codon)
thickEnd165686948End of where display should be thick (stop codon)
reserved0RGB value (use R,G,B string in input file)
blockCount3Number of blocks
blockSizes183,138,2001,Comma separated list of block sizes
chromStarts0,169475,173047,Start positions relative to chromStart
name2LOC112268276Alternative/human readable name
cdsStartStatnoneStatus of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStatnoneStatus of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames-1,-1,-1,Exon frame {0,1,2}, or -1 if no frame for exon
typeTranscript type
geneNameXR_007070820.1Primary identifier for gene
geneName2LOC112268276Alternative/human readable gene name
geneTypeGene type

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsname2cdsStartStatcdsEndStatexonFramestypegeneNamegeneName2geneType
chr1165511900165686948XR_007070820.10+16568694816568694803183,138,2001,0,169475,173047,LOC112268276nonenone-1,-1,-1,XR_007070820.1LOC112268276
chr1165821740165836006NR_146890.10-16583600616583600603433,89,179,0,1109,14087,LINC01675nonenone-1,-1,-1,NR_146890.1LINC01675
chr1165949824165971136NR_002925.20+1659711361659711360769,98,144,189,163,143,558,0,843,8533,16872,17943,19717,20754,FMO9Pnonenone-1,-1,-1,-1,-1,-1,-1,NR_002925.2FMO9P
chr1166185311166202191NM_001314014.20+16618691816619624304130,134,1486,3773,0,1477,9460,13107,POGKcmplcmpl-1,0,1,-1,NM_001314014.2POGK
chr1166185311166202191NM_017542.50+16618679016619624306130,134,127,99,1486,3773,0,1477,7134,8016,9460,13107,POGKcmplcmpl-1,0,0,1,1,-1,NM_017542.5POGK
chr1166202342166222098NM_053053.40-166203399166222067081210,163,152,210,98,66,92,105,0,1609,3674,5691,7313,12936,13254,19651,TADA1cmplcmpl0,2,0,0,1,1,2,0,NM_053053.4TADA1
chr1166254011166321373NM_199351.30-16626518316632110101011208,673,217,114,177,147,57,120,333,318,0,12524,14410,18886,27120,28410,31333,48555,49591,67044,ILDR2cmplcmpl0,2,1,1,1,1,1,1,1,0,NM_199351.3ILDR2
chr1166273001166279443XR_007070825.10+16627944316627944303437,234,86,0,4721,6356,LOC124904449nonenone-1,-1,-1,XR_007070825.1LOC124904449
chr1166273001166318584XR_007070826.10+16631858416631858403437,79,477,0,43620,45106,LOC124904449nonenone-1,-1,-1,XR_007070826.1LOC124904449
chr1166293584166318885XR_007070827.10+1663188851663188850588,205,79,200,63,0,200,23037,24523,25238,LOC124904449nonenone-1,-1,-1,-1,-1,XR_007070827.1LOC124904449

RefSeq All (hub_567047_ncbiRefSeq) Track Description
 

Description

The NCBI RefSeq Genes composite track shows 24 Jan 2022 Homo sapiens/GCF_009914755.1_T2T-CHM13v2.0 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.

Display Conventions and Configuration

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

The tracks available here can include (not all may be present):
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 2022 Homo sapiens/GCF_009914755.1_T2T-CHM13v2.0 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 RefSeq Alignments track follows the display conventions for PSL tracks.

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_009914755.1_T2T-CHM13v2.0_genomic.gff.gz delivered with the NCBI RefSeq genome assemblies at the FTP location:
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/ 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: 3,117,292,070 bases

Curated and Predicted Gene count: 108,944
Bases in these genes: 1,612,562,606
Percent genome coverage: % 51.730

Curated gene count: 82,572
Bases in curated genes: 1,377,848,543
Percent genome coverage: % 44.200

Predicted gene count: 26,372
Bases in genes: 287,621,756
Percent genome coverage: % 9.227

Other annotation count: 16,326
Bases in other annotations: 32,222,985
Percent genome coverage: % 1.034

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