1. Endogenous Retroviral promoter of the Human gene Kim Tae Hyung http://www.primate.or.kr Oct 02,2004 MPL

2. Origin of a substantial fraction of human regulatory sequences from transposable elements King Jordan 1, Igor B. Rogozin 1, Galina V. Glazko 2 and Eugene V. Koonin 1 1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A/Room N511M,1 2 1 8600 Rockville Pike, Bethesda, MD 20894, USA 2 Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Lab, University Park, PA 16802, USA Generally, we are interested in understanding the evolution of life. Specifically, to obtain glimpses of such understanding, we employ existing and new methods of computational biology to perform research in three main directions. i) Empirical comparative and evolutionary genomics - comparison of prokaryotic and eukaryotic genomes with the aim of predicting gene functions, constructing evolutionary scenarios for particular gene families and functional categories, and deciphering general evolutionary trends. One of the evolutionary phenomena we are particularly interested in is horizontal gene transfer between diverse organisms. One of the products of this research direction is the database of Clusters of Orthologous Groups of proteins (COGs). ii) Exploitation of genome comparisons, particularly those between relatively close genomes, for addressing fundmanetal issue of evolutionary biology such as the nature of adaptation and selection in different categories of genes. iii) Classification and evolutionary analysis of protein domains and domain architectures. An important dimension in this type of research is discovery of "new" domains that are shared by many diverse proteins but have not been defined previously. Principal Research Interests

3. Types of alternative splicing events

4. Transposable element (TE)-derived sequences in human regulatory regions The Human Promoter Database (HPD; http://zlab.bu.edu/~mfrith/HPD.html)http://zlab.bu.edu/~mfrith/HPD.html

5. Transposable elements (TEs) in human regulatory sequences

6. Transposable element (TE)-derived cis-regulatory elements

7. Sequence alignment of the -globin locus and a mammalian apparent long terminal repeat (LTR)-retrotransposon (MaLR)

9. The types and consequences of alternative promoters

10. Proposed mechanisms that could lead to creation of alternative promoters

11. Selected human and rodent genes with alternative promoters

14. Promoter activity of the ENDRB LTR

16. Tissue specific 97 kb

17. MID1

18. Functional analysis of alternative MID1 promoters

19. Antisense and RNAi

20. Experimental analysis of alternative splicing

21. Analysis of expressed pattern by providing ERV-derived promoter in the HESAS

22. Total : 135 Internal : 38 LTR : 97 Known Gene : 48 LTR-derived : 37 Internal : 11 Unknown Gene: 87 (LOCXXX, FLJXXXX, MGCXXXX,….) The statistic about ERV-derived promoter in the HESAS

23. CHR.ACC.GENELTRERVTissueTYPE 1 NT_004487.16NCF2LTR27TSS_GT NT_004487.16PLAC3MER41TSS NT_004686.16GBP5LTR12HERV9TSS NT_004836.15SMYD3LTR8TSS_GT NT_019273.16CHIALTR66HERVLTSS_GT NT_037485.3MAN1C1MER52TSS 3 NT_005612.14SIAT1MER21TSS_GT NT_005612.14ZNF80pTR5TSS NT_022517.16CCBP2MER39TSS_GT 5 NT_006713.13ARSBLTR37TSS NT_023148.12FISLTR12HERV9TSS NT_078018.1BIRC1MER21TSS_GT 6NT_007592.13ZNF323LTR18HERVLTSS_GT 7 NT_007819.14NUDT1LTR1TSS_GT NT_030008.6ABCA13LTR12HERV9TSS_GT NT_079596.1NOS3LTR10HERVITSS 8 NT_008046.14HHLA1LTR7HERVHTSS NT_008127.15HSJ001348LTR43TSS NT_008183.17RPESPMER9TSS NT_078037.2CA1MER74TSS_GT 9NT_008470.16BAATMER11TSS 11 NT_009237.16NOV1LTR18HERVLTSS_GT NT_033899.6PRDM10LTR52TSS 12 NT_009759.15GALNT8LTR14HERVKTSS NT_029419.10CPMMER39TSS_GT 13NT_009952.14G30MER57TSS_GT NT_026437.10TCL6MER4TSS 15 NT_010194.16CYP19A1MER21TSS_GT NT_010274.15SV2BMER39TSS_GT 16 NT_010393.14OTOALTR45TSS_GT NT_037887.3MSLNMER54TSS_GT 17 NT_010755.14GSDMLLTR7HERVHTSS NT_010799.14CCL15MER50TSS 19NT_011109.15FPRL2LTR54TSS 20 NT_011387.8HSPC072MLT2TSS_GT NT_011387.8NSFL1CLTR10HERVITSS 21NT_011512.9DSCR8LTR9TSS The consequences of LTR-derived promoters in the HESAS