Human Chromosome 19 and Related Regions in Mouse: Conservative and Lineage-Specific Evolution Paramvir Dehal, Paul Predki, Anne S. Olsen, Art Kobayashi, Peg Folta, Susan Lucas, Miriam Land, Astrid Terry, Carol L. Ecale Zhou, Sam Rash, Qing Zhang, Laurie Gordon, Joomyeong Kim, Christopher Elkin, Martin J. Pollard, Paul Richardson, Dan Rokhsar, Ed Uberbacher, Trevor Hawkins, Albert Branscomb, and Lisa Stubbs

Genes identified or predicted in the assembled HSA19 sequence are listed in order, from the HSA19p centromere to the HSA19q telomere. "PS" in column 1 indicates that the gene in the corresponding row is a known pseudogene. Pseudogenes are listed only if they are known to be non-coding members of specific gene families or if they correspond to loci included in reference gene sets. Entries in column 2 identify genes that correspond to Refseq [R] or human locus link [LL] entries; locus link entries that have been assigned to HSA19 [LL-19], or genes corresponding to mouse locus link entries only [LL-MX, where X is the mouse chromosome location] are also indicated. Sequenced HSA19 clones that contain each gene are listed in column 3 with corresponding Genbank accession numbers listed in column 4. Gene names, listed in column 5, correspond to officially assigned RefSeq, Locus link, or unigene cluster names where available; alternative names are shown in parentheses in some cases. Genes with significant identities to named mouse, but not human genes are listed with "Mus" before the gene name. The suffix "-like" (e.g. HSTPCR86-like) refers to genes that are highly similar to, but not identical to, named sequence entries in public databases. "No identity" refers to loci without official ID or significant similarities, but with at least one high probability EST match. "Unknown" in column 5 identifies genes predicted on the basis of clustered mouse conserved sequence elements without significant matches to sequence entries in public cDNA databases. Unnamed genes that are members of clustered gene families, including zinc finger genes (ZNF), olfactory receptor (OR), Cytochrome p450 (Cyp2), pregnancy specific glycoprotein/ carcinoembryonic antigen (PSG, CEACAM), sialic acid glycoprotein (SIGLEC) are listed in column 5 by these family identifiers only; family symbols are also included in parentheses next to genes with names that do not clearly define the gene's affiliation. Plate-row-well address of mouse BAC clones that contain related genes are listed in columns 7 and 8; clone names in italics indicate that, presumably due to evolutionary rearrangements (e.g. inversions, transpositions, gene duplications), mouse clones listed are derived from a different mouse chromosomal location than expected from known syntenic homology relationships . Names and accession numbers of mouse clones that have been sequenced by other sequencing groups are underlined; these clone names are included specifically if their sequence fills gaps in our coverage or provides finished sequence to complement JGI draft sequence. Unless otherwise noted mouse clone numbers refer to plate-row-well addresses from the RPCI-23 BAC Library; plate-row-well addresses of mouse clones from other libraries are preceded by an identifying prefix (RG-MBAC, Caltech/Research Genetics 129/Sv BAC library ; RP21, Roswell Park 129/Sv PAC library ). Genbank accession number for each mouse BAC is shown in column 7. "NC" in column 7 indicates that the corresponding mouse region has not been cloned or sequenced. Boxes in column 6 mark positions of ZNF and OR clusters, as summarized in Table 2 of the text. Detailed information about genes in each family and mouse counterparts are given in WebTables C, and D (ZNF genes) and G (OR genes). Since orthologous relationships do not exist within most of these clustered families, mouse clones that contain syntenically homologous genes are boxed in columns 7 and 8. A more detailed version of this table, with direct links to DNA sequence, regional displays, supportive evidence for predicted genes and other information, is available on the project website (http://bahama.jgi-psf.org/pub/ch19). This web-based catalog will be updated regularly as HSA19 and mouse sequence is completed and assemblies are revised.

Web Table B: Summary of repeat content in human chromosome 19 and related mouse sequence

Human Chromosome 19 Complex Repeats					Homologous Mouse BACs Complex Repeats
	No. of elements	Coverage (bp)	Coverage %			No. of elements	Coverage (bp)	Coverage %
SINEs	59704	14915086	27.55%		SINEs	54252	6762861	12.49%
SINE/Alu	52975	14045810	25.94%		SINE/Alu	--	--	--
SINE/B1	--	--	--		SINE/B1	27655	3167517	5.85%
SINE/B2	--	--	--		SINE/B2-B4	21782	3224010	5.96%
SINE/IDs	--	--	--		SINE/IDs	3576	250445	0.46%
SINE/MIR	6729	869276	1.61%		SINE/MIR	1229	120889	0.22%
LINEs	13440	6595805	12.18%		LINEs	7476	5076739	9.38%
LINE/L1	8338	5372965	9.92%		LINE/L1	6713	4971036	9.18%
LINE/L2	4961	1203798	2.22%		LINE/L2	747	104031	0.19%
LINE/L3/CR1	141	19042	0.04%		LINE/L3/CR1	16	1672	0.00%
LTR Elements	8448	434233	8.02%		LTR Elements	10932	4477330	8.27%
LTR/MaLR	3459	1156612	2.17%		LTR/MaLR	5714	1567833	2.89%
LTR/ERVL	1216	473654	0.87%		LTR/ERVL	337	260800	0.48%
LTR/ERV class I	3282	2127332	3.93%		LTR/ERV class I	614	468623	0.87%
LTR/ERV class II	465	574218	1.06%		LTR/ERV class II	1901	1393471	2.57%
DNA Elements	4691	1003397	1.85%		DNA Elements	1292	203481	0.38%
DNA/MER1_type	3102	585935	1.08%		DNA/MER1_type	898	140681	0.25%
DNA/MER2_type	845	293177	0.54%		DNA/MER2_type	342	56538	0.10%
Total Interspersed	86412	29011485	49.89%		Total Interspersed	74269	16617500	30.69%
Unclassified	129	154864	0.29%		Unclassified	317	97089	0.18%
Small RNA	208	23733	0.04%		Small RNA	349	28010	0.05%
Simple Repeats	9022	669877	1.24%		Simple Repeats	19657	1143393	2.11%
Satellites	1089	811688	1.50%		Satellites	930	101298	0.19%
Low Complexity	5853	403984	0.75%		Low Complexity	6670	433910	0.80%
Total Repeats	--	28897110	53.37%		Total Repeats	--	18322362	38.55%
Percent GC	--	--	47.86%		Percent GC	--	--	46.41%

Web table C.

Web table D.

Web table E.

Web table F.

Web table G.

Web table H.

Supplemental Figure 1. Web fig. A. Gene duplication at the breakpoint of homology segments VII and VIII. A. Map at bottom of the figure represents genes located at the border of homology segments VII and VIII in HSA19p13.1; top line represents order of genes in human chromosome 21q22.3. Human genes are represented by gene names below or above the human maps, arrows indicate transcriptional direction of each gene. Between the two human chromosome maps are figures that show the order of related genes, with names above each map, in mouse BAC clones located at the ends of homology segment VIII (Mmu10; red line) and VIII (Mmu17, blue line), respectively. Mouse clone maps are arranged to illustrate homologies to the two human chromosomes. Plate-row-well address of the mouse clones is given below each line by boxed numbers. Both mouse BACs were selected for homology to HSA19p13.1 sequences but cross over the region of HSA19 homology into mouse DNA that is related to adjacent segments of H21q22.3. Shaded region highlights the position of gene duplications identified at breakpoint sites on both mouse chromosomes. Shaded boxes are placed over pseudogene copies or gene fragments. The position of single VR2 pseudogene, the counterpart of which is not found in HSA19 or H21 DNA, is represented by the family symbol in a shaded box.

Medium version | Full size version