Welcome to the LongMan lncRNA database

According to the GENCODE-annotated 13562 human lncRNAs (the GENCODE v7 catalogue), we have identified the orthologues of these lncRNAs in 16 mammalian genomes by a large-scale genome search using the Infernal program, and have organized all the lncRNAs into LongMan, which is the first orthologous lncRNA database. The current version (v1.0) of LongMan contains the sequences of 13562 human lncRNAs and their 133646 orthologues, certain important secondary information of these lncRNAs (including transposable elements and DNA binding motifs in lncRNAs and DNA binding sites in some genomic regions), and the whole genome sequences of human and the 16 mammals. Moreover, LongTarget, the program we developed for predicting lncRNA/DNA binding analysis, has been integrated into LongMan.

The versions of the whole genome sequences we used are: human (GRC37/hg19), chimpanzee (CSAC 2.1.4/panTro4), macaque (BGI CR_1.0/rheMac3), marmoset (WUGSC 3.2/calJac3), tarsier (Broad/tarSyr1), Mouse lemur (Broad/micMur1), Tree shrew (Broad/tupBel1), Mouse (GRCm38/mm10), Rat (Baylor3.4/rn4), Guinea pig (Broad/cavPor3), Rabbit (Broad/oryCun2), Dog (Broad CanFam3.1/canFam3), Cow (Baylor Btau_4.6.1/bosTau7), Elephant (Broad/loxAfr3), Hedgehog (EriEur2.0/eriEur2), Opossum (Broad/monDom5), and Platypus (WUGSC 5.0.1/ornAna1).

Currently, users can
  • -search and browse the human lncRNAs (identified and annotated by GENCODE consortium) in the database;
  • -search and browse the orthologues of human lncRNAs in 16 mammals in the database;
  • -predict DNA binding motifs and binding sites of the a searched lncRNA in the database;
  • -predict DNA binding motifs and binding sites of a batch of lncRNAs in the database (all of the lncRNAs in a search result) in a genomic region;
  • -predict DNA binding motifs and binding sites of any given lncRNAs (available at the lncRNA:DNA triplex page of this web site);
  • -download the sequences of a lncRNA and its orthologues in 16 mammals in the database;
  • -browse the record in the www.lncRNAdb.org database.
All the functions of this website are tested to work with Google Chrome and Mozilla Firefox, so we recommend the user the two browsers. And, for details on the use of LongMan and LongTarget, please refer to the user manuals (which can be downloaded at the “Download” page of this web site).
Feedback:Please send feedbacks and bug reports to  zhuhao@smu.edu.cn