LINE FUSION GENES: a database of LINE expression in human genes.
BACKGROUND
Long Interspersed Nuclear Elements (LINEs) are the most abundant retrotransposons in humans. About 79% of human genes are estimated to contain at least one segment of LINE per transcription unit. Recent studies have shown that LINE elements can affect protein sequences, splicing patterns and expression of human genes.


METHODS
We have developed a database, LINE FUSION GENES, for elucidating LINE expression throughout the human gene database. We searched the 28,171 genes listed in the NCBI database for LINE elements and analyzed their structures and expression patterns. The results show that the mRNA sequences of 1,329 genes were affected by LINE expression. The LINE expression types were classified on the basis of LINEs in the 5' UTR, exon or 3' UTR sequences of the mRNAs. Our database provides further information, such as the tissue distribution and chromosomal location of the genes, and the domain structure that is changed by LINE integration. We have linked all the accession numbers to the NCBI data bank to provide mRNA sequences for subsequent users.


CONCLUSIONS
We believe that our work will interest genome scientists and might help them to gain insight into the implications of LINE expression for human evolution and disease.


BACKGROUND
http://www.primate.or.kr/line.
Kim
Dae-Soo
DS
PBBRC, Interdisciplinary Research Program of Bioinformatics, Pusan National University, Busan 609-735, Korea. kds2465@pusan.ac.kr
Kim
Tae-Hyung
TH
Huh
Jae-Won
JW
Kim
Il-Chul
IC
Kim
Seok-Won
SW
Park
Hong-Seog
HS
Kim
Heui-Soo
HS
D002874:Chromosome Mapping; D030541:Databases, Genetic; D005091:Exons; D015870:Gene Expression; D005796:Genes; D015894:Genome, Human; D006801:Humans; D020084:Long Interspersed Nucleotide Elements; D026723:Polyadenylation; D011401:Promoter Regions, Genetic; D017434:Protein Structure, Tertiary; D012333:RNA, Messenger / Q000737:chemistry*; D014018:Tissue Distribution; D020506:Untranslated Regions / Q000737:chemistry
D012333:RNA, Messenger; D020506:Untranslated Regions