Schema for lincRNA TUCP - lincRNA and TUCP transcripts
  Database: hg38    Primary Table: lincRNAsTranscripts    Row Count: 21,482   Data last updated: 2015-04-09
Format description: A gene prediction.
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
name TCONS_l2_00002359varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 16606int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 29370int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 16606int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 16606int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 8int(10) unsigned range Number of exons
exonStarts 16606,16853,17232,17605,179...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 16765,17055,17368,17742,180...longblob   Exon end positions (or start positions for minus strand item)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
585TCONS_l2_00002359chr1-16606293701660616606816606,16853,17232,17605,17914,18267,24737,29320,16765,17055,17368,17742,18061,18379,24891,29370,
585TCONS_l2_00002363chr1-16857299611685716857716857,17232,17605,17914,18267,24737,29823,17055,17368,17742,18061,18379,24891,29961,
585TCONS_l2_00002362chr1-16857293701685716857816857,17232,17605,17914,18267,18912,24737,29320,17055,17368,17742,18061,18366,19139,24891,29370,
585TCONS_l2_00002361chr1-16857197591685716857616857,17232,17605,17914,18267,18912,17055,17368,17742,18061,18379,19759,
585TCONS_l2_00002360chr1-16857177511685716857216857,17232,17055,17751,
585TCONS_l2_00002364chr1-17232293701723217232417232,17914,18267,29320,17742,18061,18366,29370,
585TCONS_l2_00002365chr1-17605293701760517605717605,17914,18267,18496,18912,24737,29320,17742,18061,18362,18554,19139,24891,29370,
73TCONS_l2_00002368chr1-892942681268929489294289294,266863,90404,268126,
585TCONS_l2_00002367chr1-892941209328929489294489294,92090,112699,120774,91629,92240,112804,120932,
585TCONS_l2_00002369chr1-89550911058955089550289550,90286,90050,91105,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

lincRNA TUCP (lincRNAsTranscripts) Track Description
 

Description

This track displays the Human Body Map lincRNAs (large intergenic non coding RNAs) and TUCPs (transcripts of uncertain coding potential), as well as their expression levels across 22 human tissues and cell lines. The Human Body Map catalog was generated by integrating previously existing annotation sources with transcripts that were de-novo assembled from RNA-Seq data. These transcripts were collected from ~4 billion RNA-Seq reads across 24 tissues and cell types.

Expression abundance was estimated by Cufflinks (Trapnell et al., 2010) based on RNA-Seq. Expression abundances were estimated on the gene locus level, rather than for each transcript separately and are given as raw FPKM. The prefixes tcons_ and tcons_l2_ are used to describe lincRNAs and TUCP transcripts, respectively. Specific details about the catalog generation and data sets used for this study can be found in Cabili et al (2011). Extended characterization of each transcript in the human body map catalog can be found at the Human lincRNA Catalog website.

Expression abundance scores range from 0 to 1000, and are displayed from light blue to dark blue respectively:

01000

Credits

The body map RNA-Seq data was kindly provided by the Gene Expression Applications research group at Illumina.

References

Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011 Sep 15;25(18):1915-27. PMID: 21890647; PMC: PMC3185964

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010 May;28(5):511-5. PMID: 20436464; PMC: PMC3146043