You can get all these from Ensembl: ftp://ftp.ensembl.org/pub/current_fasta/homo_sapiens/ncrna/
Pierre, there are several lncRNA annotations for human (of course there is overlap between them).
Annotations that have exon/intron coordinates:
- Derrien et al., 2012 - The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression;
- Cabili et al., 2011 - Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses;
- Kelley D., Rinn J., 2012 - Transposable elements reveal a stem cell specific class of long noncoding;
- NONCODEv4 (See edit 13.11.28).
- Necsulea et al., 2014 - The evolution of lncRNA repertoires and expression patterns in tetrapods;
Annotations that have only locus coordinates:
- Sigova et al., 2013 - Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells;
- Orom et al., 2010 - Long noncoding RNAs with enhancer-like function in human cells (lots of overlap with Gencode);
- Hangauer et al., 2013 - Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs;
- Laurent et al., 2013 - VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer.
Also there is:
- LNCipedia - a comprehensive compendium of long non-coding RNAs;
"210831 lncRNA from eukaryotes, eubacteria, archebacteria, and viral and viroids"
"Human lncRNA: 56018 genes & 95135 transcripts"
"Mouse lncRNA: 46475 genes & 67628 transcripts"
"Expression profile of lncRNAs for human and mouse, as well as predict functions of these lncRNA genes"