Supplementary Information for Riethman Et Al

Supplementary Information for Riethman et al.

Table I

Telomere Reagentsa / Reagent size (kb) / Evidence for Tel linkage of Reagent b / Golden Path Working Draft Sequence c / Size of Srpt in Draft Seq (kb)d / Distance from Working Draft Sequence to Telomere (kb) / half-YAC derived sequences (kb)e / Accession numbers for sequences
yRM2109 f / 290 / Srpt / ctg 15478 / none / <290 / 3
bRP11-1129o4 / 90 / Srpt / ctg18006 and ctg17658 / 90 / unk
yRM2123 / 270 / RARE, Srpt / ctg 16359 / none / 250 / 106 / AF229518-AF229607
yRM2052 / 330 / RARE, Srpt / ctg 14747 / none / 30-50 / 24 / AF282480-AF282513, AF328420-AF328428
yRM2112 / 240 / RARE, Srpt / none available / na / unk / 8 / AF282051-AF282064, AF328429-AF328441
yRM2161 / 300 / Srpt / ctg 15945 / none / 1-100 / 16 / AF283057-AF283067, AF328442-AF328456
yRM2175 / 220 / Srpt / ctg 13038 / none / 125 / 28 / AF282584-AF282593, AF328457-AF328491
yRM2038 / 200 / RARE, Srpt / ctg 14096 / 60 / 0 / 1 / AF328492, AF328493
yRM2173 / 140 / Srpt / ctg18487 / 250 / 10-15 / 14,684 / AF328494-AF328515
bRP11-811i15 / 156 / Srpt / ctg 18167 / 15 / unk
yRM2070 / 270 / Srpt / ctg 14667 / 80 / 100-140 / 28 / AF270591-AF270612
yRM2107 / 400 (chim) / Srpt / ctg 15907 / 120 / unk / 2 / AF328516-AF328519
yRM2158 / 280 / RARE, Srpt / ctg 16045 / 100 / 30-60 / 13 / AF327079-AF327095
yRM2185 / 260 / RARE, Srpt / none available / na / unk / 37 / AF240581-AF240616
yRM2000 / 230 / RARE, Srpt / ctg 17429 / 10 / 0 / 225 / AF027390
yRM2205 / 300 / RARE, Srpt / ctg 15438 / 150 / <134 / 9 / AF282580-AF282583, AF328520-AF328528
yRM2053 / 170 / RARE, Srpt / ctg 16007 / 0 / 20 / 13 / AF327096-AF327116
yRM2039 / 180 / RARE, Srpt / ctg13361 / 80 / 150 / 1 / AF328529
yRM2092 / 210 / Srpt / ctg 17342 / 40 / 5-30 / 46 / AF240617-AF240621, AF328530-AF328536
yRM2189 / 320 / Srpt / ctg 14676 / 20 / 20-100 / 9 / AF282514-AF282524
yRM2136 / 270 / Srpt / ctg19085 / 0 / 100-150 / 110 / AF283016-AF283056
yRM2209g / 125 / RARE, Srpt / ctg 18272 / 0 (A) / 45 (A) / 13 / AF261922-AF261936, AF328537
bRP11-304M2 / 185 / 125 (B) / unk (B)
yRM2072 / 65 / Srpt / ctg13517 / none / 30 / 53 / AF240622-AF240626
yRM2019 / 100 / Srpt / ctg13698 / 20 / 1-233 / 1 / AF328538
yRM2196 / 190 / RARE, Srpt / ctg18706 / 0 / 46-106 / 2 / AF328539-AF328541
yRM2067 / 100 / RARE, Srpt / ctg 16981 / 0 / 5-20 / 15 / AF270514-AF270537
yRM2006 / 200 / RARE, Srpt / ctg17003 / 2 / 5-15 / 2
yRM2183 / 190 / Srpt / ctg16687 / 35 / 20-100 / 68 / AF270634-AF270644, AF276873-AF276885, AF281978-AF281977
yRM2118h / 300 / RARE, Srpt / ctg 15544 / 36 (A) / 0 / 10 / AF327117-AF327134
100 (B) / 140_tel (B)
yA11 / 250 / Srpt / ctg17189 / 20 / < 150 / 62 / AF281900-AF281977
yRM2111 / 105 / RARE, Srpt / none available / 15 / 20 / 89 / AF240580, AF261697-AF261711
yRM2009 / 140 / RARE, Srpt / none available / na / unk / 12 / AF282554-AF282563, AF328542-AF328551
yRM2102 / 220 / RARE, Srpt / ctg 12616 / 100 / 10 / 79 / AF270538-AF270590
yRM2050 / 290 / RARE, Srpt / ctg 15058 / 0 / 20-80 / 21 / AF282525-AF282553, AF329208-AF329214
yRM2001 / 50 / RARE, Srpt / none available / 70 / 25 / 2 / U11826, U12257, AF329206, AF32907
cLLNLR-271e8 / 44 / Srpt / none available / 16 / unk
yRM2005 / 180 / Srpt / ctg 16537 / 0 / 55 / 43 / AF282564-AF282579 AF327135-AF327173, AF327175-AF327179
bRP11-476i15 / Srpt / ctg 16334 / 40 / unk
yRM2208 / 290 / RARE, Srpt / ctg21fin5 / 20 / 0 / 1
yRM2117 / 75 / Srpt / ctg22fin11 / 20 / 50 / 1 / AF327182, AF327183
cosmid ctgi / PFGE, Srpt / none available / na / <500
yRM2195 / 320 / PFGE, Srpt / ctg 15749 / 30 / 0 / 1 / AF327180, AF327181
yRM2195 / 320 / PFGE, Srpt / ctg Y8, tel part of ctg 15749 / 30 / 0 / 1 / AF327180, AF327181

aHalf-YAC clones are designated by the prefix y, BAC clones by b, and cosmid by c.

b RARE, RecA-assisted Restriction Endonuclease cleavage mapping (Riethman et al., 1997). Srpt, subtelomeric repeats adjacent to human telomere sequence in the clone

cGolden Path Working Draft Sequence contigs which overlap with the indicated subtelomeric regions can be accessed from (Oct 7, 2000 freeze). Discrepacies between clones used to derive working draft sequence and our mapping experiments are noted in Table II, supplementary information, Nature website.

dSize of subtelomeric repeat region detected in working draft sequence is based upon the length of BLAST2 homology segments of sequence from the indicated working draft sequence contig with previously characterized subtelomeric repeat sequences (Srpt).

eHalf-YAC-derived sequences were acquired from the centromeric ends of cloned inserts (V-I junction sequences), from end-sequences of half-YAC derived cosmids, and from shotgun sequencing of half-YAC-derived cosmids (either partially or fully assembled). Sequences can be accessed via the GenBank accessions (to be completed), or they can be downloaded in FASTA format from ( Additional half-YAC-derived sequences associated with the isolation of microsatellite and radiation hybrid markers have been described previously (Ning et al., 1996; Rosenberg et al., 1997; Knight et al., 2000).

fThe 1p telomere region includes both subtelomeric and other low-copy repeats. FISH of 1ptel half-YAC DNA yields signals at multiple telomeric sites as well as at 1p36, 1q42, 1q44, 4q28, and Yq11.2. Knight et al. (2000) have isolated BACs from the 1p36 region adjacent to 1p-associated subtelomeric repeats, their position relative to the 1p half-YACs is not clear at present.

gctg18272 contains, in addition to the 11ptel-derived clones, subtelomeric repeat-derived BACs derived from many separate telomeres. The cloned 11ptel allele (Allele A) is 170 kb smaller than 11ptel allele B, into which bRP11-304M2 extends

h16ptel is characterized by several alleles whose sizes vary by up to 260 kb (Wilkie et al., 1991). Allele A (the shortest allele) has been sequenced completely (Flint et al., 1997). yRM2118 extends approximately 175 kb beyond the A allele, and contains sequences from BACs in ctg15544 which are not contained in the A allele. The size and sequence content of yRM2118 are consistent with it containing the B allele of the 16p telomere.

ithe 500 kb from the Xp/Yp telomere to the SHOX gene is covered by a cosmid ctg (Gianfrancesco et al., 1998) whose sequence is not yet available.

Riethman, H., Birren, B. & Gnirke, A. Preparation, manipulation, and mapping of high molecular weight DNA. in Genome Analysis: A Laboratory Manual, Volume 1, Analyzing DNA (eds. Birren, B., Green, E., Klapholz, S., and Meyers, R., and Roskams, J.) 83-248 (Cold Spring Harbor Laboratory Press, New York, 1997).

Ning, Y., Roschke, A., Smith, A. C. M., Machal, M., Precht, K., Riethman, H., Ledbetter, D. H., Flint, J., Horsley, S., Regan, R., Kearney, L., Knight, S., Kvaloy, K. & Brown, W. R. A. A complete set of human telomeric probes and their clinical application. Nature Genet.14, 86-89 (1996).

Rosenberg, M., Hui, L., Ma, J., Nusbaum, H. C., Clark, K., Robinson, L., Dziadzio, L., Swain, P. M., Keith, T., Hudson, T. J., Biesecker, L. G. & Flint, J. Characterization of short tandem repeats from thirty-one human telomeres. Genome Res. 7, 917-923 (1997).

Knight, S. J. L., Lese, C. M., Precht, K. P., Kuc, J., Ning, Y., Lucas, S., Regan, R., Brenan, M., Nicod, A., Martin Lawrie, N., Cardy, D. L. N., Nguyen, H., Hudson, T. J., Riethman, H. C., Ledbetter, D. H. & Flint, J. An optimized set of human telomere clones for studying telomere integrity and architecture. Am. J. Hum. Genet.67, 320-332 (2000).

Wilkie, A. O. M., Higgs, D. R., Rack, K. A., Buckle, V. J., Spurr, N. K., Fischel-Ghodsian, N., Ceccherini, I., Brown, W. R. A. & Harris, P. C. Stable length polymorphism of up to 260 kb at the tip of the short arm of human chromosome 16. Cell 64, 595-606 (1991).

Flint, J., Thomas, K., Micklem, Gos, Raynham, H., Clark, K., Doggett, N. A., King, A. & Higgs, D. R. The relationship between chromosome structure and function at a human telomeric region. Nat. Genet.15, 252-257 (1997).

Gianfrancesco, F., Esposito, T., Montanini, L., Ciccodicola, A., Mumm, S., Mazzarella, R., Rao, E., Giglio, S., Rappold, G. & Forabosco, A. A novel pseudoautosomal gene encoding a putative GTP-binding protein resides in the vicinity of the Xp/Yp telomere. Hum. Mol. Genet.7(3), 407-414 (1998).

Table II

Evidence for Tel linkagec / Large-scale variationd / Reagents / Reagent size (kb) / Sequencese / Statusf / Seq origing / Comments
(see for updated half-YAC derived sequences)
Srpt / y
yRM2109 / 290 / S / HR_RKM / 290 kb half-YAC
yRM2017 / 75 / S / HR_RKM / 75 kb half-YAC
The 1p telomere region includes both subtelomeric and other low-copy repeats. FISH of yRM2109 and yRM2017 DNA yields signals at multiple telomeric sites as well as at 1p36, 1q42, 1q44, 4q28, and Yq11.2. Knight et al. (2000) have isolated BACs from the 1p36 region adjacent to 1p-associated subtelomeric repeats (ctg18006), their position relative to the 1p half-YACs is not clear at present
RP11-201D24 / 157 / AC069591 / D / WIBR / contains 2109V-I
Srpt / y / It is not clear whether ctg15478 and ctg 18006 overlap
RP11-465B22 / AL390719 / D
RP11-671c15 / AC079860 / D / WUGSC / connects ctg18006 with ctg17658
RP11-668e2 / AC027823 / D / WIBR
RP11-1129o4 / 90 / AF276983 / D / IMB
RARE, Srpt / n
yRM2123 / 270 / S / HR_RKM / 270 kb half-YAC spanning 1q telomere region
yRM2004 / 50 / S / HR_RKM / 50 kb half-YAC containing most distal segment of 1q telomere region
1qtel cosmids / S / HR_RKM
RP11-407H12 / 185 / AL358874 / D / SC / Overlaps with Cen end of RP11-438F14
RP11-438F14 / 167 / AL391534 / D / SC / Contains 2123V-I; about 250 kb of half-YAC DNA is distal to telomeric end of RP11-438F14
RARE, Srpt / n
yRM2052 / 330 / S / HR_RKM / 330 kb half-YAC spanning 2p telomere region
yRM2242 / 180 / S / HR_RKM / 180 kb half-YAC spanning distal segment of 2p telomere region
2ptel cosmids / S / HR_RKM
RP11-379N10 / 164 / AC044885 / D / WIBR / contains 2052V-I probe
RP11-356M6 / AC079779 / D / WUGSC / contains 2052V-I probe
RP11-683F4 / contains 2052V-I probe, 2242V-I probe
RP11-1N7 / 182 / AC021641 / D / WIBR / contains 2242V-I probe
RP11-292i6 / 173 / AC067919 / D / WIBR / contains 2242V-I probe
RP11-75D19 / contains 2242V-I probe
RARE, Srpt / y / No BAC draft sequence available
yRM2112 / 240 / S / HR_RKM / 240 kb half-YAC spanning 2qtel region
yRM2003 / 125 / S / HR_RKM / 125 kb half-YAC spanning distal segment of 2qtel
2qtel cosmids / S / HR_RKM
RP11-115B2 / no seq / Contains 2112V-I, 2205H, 2003V-Is, 275(1e), 275(1f) probes
RP11-341N2 / no seq / Contains 2205H, 2003V-Is, 275(1e), 275(1f) probes, * listed as a chr 8 ctg, probably due to DNA segment at 2q duplicated at 8p, extends more telomerically than overlapping RP11-115B2
Srpt / unk / ctg15945 is primarily 3ptel-derived, but includes at least one sequenced clone (RP11-157G15) that is incorrectly merged.
yB47 / 450 / 450 kb half-YAC spanning 3ptel region
yRM2161 / 300 / S / HR_RKM / 300 kb half-YAC spanning distal segment of 3ptel
3ptel cosmids / S / HR_RKM
RP11-114K9 / 185 / AC011609 / F / BCM / Contains 2161V-I
RP11-600o17 / AC046155 / D / CHGC / Contains 2161V-I, more telomeric than RP11-114K9
RP11-166F3 / 125 / AC026171 / D / Beijing / Contains 2161V-I, more telomeric than RP11-114K9
RP11-605m1 / 152 / AC068321 / D / Beijing / extends more telomerically than RP11-114K9
RP11-1120H22 / 148 / AC018810 / D / Beijing / extends more telomerically than RP11-114K9
RP11-260K16 / 146 / AC026178 / D / Beijing / extends more telomerically than RP11-114K9
RP11-306H5 / 170 / AC026187 / D / Beijing / extends more telomerically than RP11-114K9
RP11-265o10 / 92 / AC034189 / D / Beijing / extends more telomerically than RP11-114K9
RP11-731E12 / 155 / AC055763 / D / BCM / extends more telomerically than RP11-114K9
RP11-385A18 / 165 / AC066595 / D / Beijing / extends most telomerically
Srpt / unk
yB35 / 375 / 375 kb half-YAC spanning 3qtel region
yRM2175 / 220 / S / HR_RKM / 220 kb half-YAC spanning distal 3qtel
3qtel cosmids / S / HR_RKM
RP11-432D10 / 151 / AC068302 / D / BCM
RP11-114F20 / 183 / AC018707 / D / WUGSC / contains 2175V-I
RP5-1061c18 / 149 / AL121981 / F / SC / contains 2175V-I; extends more telomerically than RP5-1061c18; *listed incorrectly as a chr 1 clone
RARE, Srpt / unk / Part of ctg 14096 appears to be discontiguous with 4PTEL (Z9574) and yRM2038; possible false merg due to 4p low-copy repeat
yRM2038 / 200 / S / HR_RKM / 200 kb half-YAC spanning 4ptel region
y4PTEL / 118 / Z95704 / F / SC / 118 kb half-YAC spanning distal 4ptel region, finished sequence Z9574
Srpt / y / ctg18487 is comprised of an extensive region of low-copy repeat, and can be extended more centromerically by including sequenced BACs incorrectly merged into other contigs
yRM2173 / 140 / S / HR_RKM / 140 kb half-YAC spanning distal 4qtel region
yRM2021 / 110 / 110 kb half-YAC spanning distal 4qtel region
4qtel cosmids / S / HR_RKM
RP11-45F23 / 148 / AC020698 / D / WUGSC / overlaps with RP11-462G22, listed as chr 5 clone
RP11-14K14 / AC023760 / D
RP11-462G22 / 181 / AC018687 / D / WUGSC / overlaps with finished sequence AF250324, listed as chr 5 clone
RP11-463J17 / AF250324 / F / RPCI / RP11-463J17 and RP6-92G13RCB2 formed a ctg that was sequenced (finished sequence AF250324, 246 kb)
RP6-92G13RCB2 / AF250324 / F / RPCI / finished sequence
RP11-570J4 / 123 / AL158045 / D / SC / overlaps with finished sequence AF250324
RP11-119M6 / 162 / AL138998 / D / SC / overlaps with finished sequence AF250324
RP13-495M19 / 99 / AC069169 / D / WIBR / overlaps with finished sequence AF250324
CTD-2011o21 / AC068331 / D / WIBR / overlaps with finished sequences AF250324 and AF146191
RP3-503A8 / AF146191 / F / RPCI
PAC 226K22 / AF146191 / F / RPCI / Clone contains 2173V-I, finished sequence
c34 / AF146191 / F / RPCI / Cosmid contig, finished sequence
cT379 / U85056 / F / Hewitt / Cosmid contig, finished sequence
U74496 / F / Hewitt / 4q subtelomeric region
Srpt / unk / Working draft sequence of RP11-811i15 includes about 15 kb of Srpt sequence; other clones contain significant segments of perfect homology with ctg18167, but do not appear to be from this telomere region.
no half-YAC
CTD-2083E4 / 140 / AC021087 / D / JGI / Sequenced BAC
CTD-2231H16 / 200 / AC010443 / D / JGI / Sequenced BAC
RP11-811i15 / 156 / AC027825 / D / WIBR / Most distal 5ptel BAC, contains subtel repeats and internal (TTAGGG)n sequences
Srpt / y
yRM2070 / 270 / S / HR_RKM / 270 kb half-YAC spanning 5qtel region
yB22 / 225 / 225 kb half-YAC spanning distal 5qtel
5qtel cosmids / S / HR_RKM
CTB-14A14 / 183 / AC008620 / D / JGI / Contains 2070V-I, no subtelomeric repeats
CTC-338M12 / 121 / AC008443 / F / JGI / Contains 2070V-I, subtelomeric repeats, incorrect merg with 6qtel ctg
RP11-324K20 / 232 / AL161615 / D / SC / Contains 2070V-I, subtelomeric repeats; listed incorrectly as a chr 13 clone, most telomeric
Srpt / y / Working draft sequence contains approx 120 kb segment of Srpt, clone order listed in Golden Path working draft sequence is incorrect
yRM2107 / 400 (chim) / S / HR_RKM / yRM2107 is a chimeric half-YAC whose centromeric end maps to an interstitial segment of chromosome 9 but whose telomeric end maps to 6ptel and contains sequences identical to those in ctg15907. The exact size of the 6ptel-specific region of the half-YAC has not been determined, but the actual size of the Tel Seq Gap is likely to be much less than that indicated
RP11-233K4 / 187 / AC058816 / D / WUGSC
RP11-178E20 / 170 / AC044842 / D / WIBR
RP1-125A24 / 100 / AL133540 / D / SC
RP11-328C17 / 200 / AL365272 / D / SC
RP3-416J7 / 124 / AL035696 / F / SC / PAC containing subtelomeric repeats
RP4-609N19 / AC004842 / F / WUGSC / PAC containing subtelomeric repeats
RP1-24o22 / 165 / AL353654 / D / SC / PAC containing subtelomeric repeats, most telomeric
RARE, Srpt / y / Working draft sequence includes approx 100 kb segment of Srpt, part of ctg 16045 is incorrectly merged, probably due to Srpt-containing BACs
yRM2158 / 280 / S / HR_RKM / 280 kb half-YAC spanning 6qtel region
6qtel cosmids / S / HR_RKM
RP5-894D12 / 120 / AL078605 / F / SC
RP1-140C12 / 143 / AL008628 / F / SC / contains 2158V-I
RP1-191N21 / 114 / AL031259 / F / SC / extends more telomerically than RP1-140C12
LLNLR-226C11 / 36 / AC016626 / F / JGI / listed as chr 19 cosmid
RP11-226i21 / 190 / AC009954 / D / WUGSC / most telomeric
RARE, Srpt / y / Working draft sequence not available from 7ptel BACs; terminal 300 kb ctg not connected to rest of 7p BAC map.
yRM2185 / 260 / S / HR_RKM / 260 kb half-YAC spanning 7ptel region
7ptel cosmids / S / HR_RKM
RP11-713A20 / 185 / no seq / contains 2185V-I; about 80 kb of half-YAC is distal to end of BAC ctg
RP11-90P13 / no seq / contains 2185V-I
RP11-482G13 / 150 / no seq / contains 2185V-I
RARE, Srpt / n
yRM2000 / 230 / AF027390 / F / HR_RKM / 230 kb half-YAC spanning 7qtel region; contains 2000V-I, sequence extends to telomere
7qtel cosmids
RP5-1058P19 / 93 / AC007269 / F / WUGSC / contains 2000V-I, overlaps cen end of yRM2000
RP4-764o12 / 113 / AC006476 / F / WUGSC / telomeric to RP5-1058P19, contained within yRM2000
RARE, Srpt / y
yRM2205 / 300 / S / HR_RKM / 300 kb half-YAC spanning 8ptel region
8ptel cosmids / S / HR_RKM
RP11-338B22 / 170 / AC018881 / D / WUGSC
RP11-18D5 / 175 / AC016992 / D / WUGSC / Contains 2205V-I, overlaps with CTA-366D10
CTA-366D10 / 166 / AF166490 / D / IMB / extends more telomerically than 18D5, contains low-copy subtelomeric repeats
LLNLR-226c11 / 36 / AC016626 / F / JGI / may be in variant 8ptel allele, or mistakenly merged due to Srpt content, also at 6qtel
RP5-855D21 / 138 / AC004908 / F / WUGSC / may be in variant 8ptel allele, or mistakenly merged due to Srpt content
RP11-139L10 / 85 / AC008165 / F / WUGSC / may be in variant 8ptel allele, or mistakenly merged due to Srpt content
RARE, Srpt / n
yRM2053 / 170 / S / HR_RKM / 170 kb half-YAC spanning 8qtel region
8qtel cosmids / S / HR_RKM
KOX18-21 / 108 / AF124523 / F / IMB / contains 2053V-I
P5A4.00 (PAC) / 70 / AF146367 / F / IMB / contains 2053V-I
P2G2 (PAC) / 128 / AF118808 / F / IMB / contains 2053V-I; extends more telomerically than P5A4.00.
RP5-1056B24 / 150 / AF216665 / D / IMB / contains 2053V-I
RP5-1111B24 / 126 / AF176681 / D / IMB / contains 2053V-I
RP5-1047A19 / 113 / AF238280 / D / IMB
RP5-1124C13 / 98 / AF216670 / D / IMB
CTD-2300i18 / 90 / AF216668 / D / IMB
RP5-1109M23 / 70 / AF235103 / D / IMB / extends most telomerically, <20 kb from 8qtel
RARE, Srpt / unk
yRM2039 / 180 / S / HR_RKM / 180 kb half-YAC spanning 9ptel region
RP11-59o6 / 167 / AL158832 / F / SC
RP11-174M15 / 175 / AL356244 / D / SC / contains 2039 V-I, extends more telomerically than RP11-59o6
Srpt / y
yRM2235 / 730 / S / HR_RKM / 730 kb half-YAC spanning 9qtel region, unstable/rearranged
yRM2092 / 210 / S / HR_RKM / 210 kb half-YAC spanning 9qtel region
yRM2241 / 65 / S / HR_RKM / 65 kb half-YAC spanning distal 9qtel region
9qtel cosmids / S / HR_RKM
RP11-424e7 / 200 / AC020707 / D / WUGSC / contains 2235V-I, 2092V-I, and 2241V-I
Srpt / unk / 2189V-I falls in clone gap region of working draft sequence ctg 14676
yRM2189 / 320 / S / HR_RKM / 320 kb half-YAC spanning 10ptel region
yRM2203 / 120 / S / HR_RKM / 120 kb half-YAC spanning distal 10ptel region
10ptel cosmids / S / HR_RKM
RP11-10D13 / 157 / AC011167 / D / WIBR / contains yRM2189 sequences, not 2189V-I or 2203V-I
RP11-145i2 / 168 / AC022391 / D / GTC / contains 2203V-I, extends more telomerically than RP11-10D13
Srpt / unk
yRM2136 / 270 / S / HR_RKM / 270 kb half-YAC spanning 10qtel region
10qtel cosmids / S / HR_RKM
LA10NC01_177_C_11 / 43 / AC006177 / D / GTC
RP11-122K13 / 135 / AL360181 / D / SC / Overlaps with centromeric end of RP11-108K14
LA10NC01_15_E_11 / 44 / AC006171 / D / GTC / Cosmid clone, wholly within RP11-108K14
RP11-108K14 / 164 / AL161645 / D / SC / Contains 2136V-I, most telomeric
RARE, Srpt / y / ctg18272 contains, in addition to the 11ptel-derived clones, subtelomeric repeat-derived BACs derived from many separate telomeres.
yRM2209 / 125 / S / HR_RKM / 125 kb half-YAC spanning 11ptel region
11ptel cosmids / S / HR_RKM
95 kb cosmid ctg / 95 / AF015416 / F / UTSW / 11p15.5 finished sequence derived from 3 overlapping cosmids
RP11-304M2 / 185 / AC069287 / D / WUGSC / most telomeric, subtelomeric repeats; is part of a long variant 11ptel allele (allele B)
Srpt / unk
yRM2072 / 65 / S / HR_RKM / 65 kb half-YAC derived from 11qtel; appears to have suffered an internal deletion
11qtel cosmids / S / HR_RKM
RP11-340L13 / 170 / AC027594 / D / WIBR / contains yRM2072-derived sequences
RP11-651K21 / 200 / AC073904 / D / WUGSC
Srpt / y
yRM2019 / 100 / S / HR_RKM / 100 kb half-YAC spanning 12ptel region
RP5-1154L15 / 118 / AC006205 / F / BCM
RP11-350L7 / 143 / AC005844 / F / BCM
RP11-283i3 / 177 / AC00746 / F / BCM
RP11-467M14 / 161 / AC016741 / D / WUGSC
RP11-598F7 / 168 / AC026369 / D / BCM / contains 2019V-I, subtelomeric repeats, most telomeric
RARE, Srpt / n
yRM2196 / 190 / S / HR_RKM / 190 kb half-YAC spanning 12qtel region
12qtel cosmids / S / HR_RKM
RP11-386i8 / 164 / AC073911 / D / BCM / contains 2196V-I
RP11-360H6 / 180 / AC026338 / D / BCM / contains 2196V-I
CTD-2140B24 / 144 / AC026786 / D / JGI / * listed incorrectly as a chr 5 clone; contains 2196V-I, extends more telomerically than RP11-360H6
RARE, Srpt / n / ctg16981 contains, in addition to bona fide 13qtel BACs, several BACs with segments of high homology with 13qtel sequences, but which are derived from elsewhere
yRM2067 / 100 / S / HR_RKM / 100 kb half-YAC spanning 13qtel region
13qtel cosmids / S / HR_RKM
RP11-245B11 / AL161774 / D / SC / overlaps with centromeric end of RP11-569d9
RP11-303B11 / AC068390 / D / WIBR / very odd htgs pattern, small bits of 2225p22 and 569d9, + large segments with 7q31(?) BACs. Not from 13qtel.
RP11-569D9 / 161 / AL160396 / D / SC / contains 2002V-I, extends to within 20 kb of 13q telomere
CTD-2225P22 / 165 / AC079047 / D / WIBR / perf homol with small part of RP11-569d9, shares large homol segment with RP11-474E23 (18q11-12). Not from 13qtel.
RARE, Srpt / y
yRM2006 / 200 / S / HR_RKM / 200 kb half-YAC spanning 14qtel region
14qtel cosmids / S / HR_RKM
Honjo et al. IgGH ctg / 200 / AB019438 / F / JST / finished sequence continues a total of 957 kb towards cen
Honjo et al. IgGH ctg / 200 / AB019437 / F / JST / contains 2006V-I, sequence extends to within 15 kb of 14q telomere
Srpt / unk
yRM2183 / 190 / S / HR_RKM / 190 kb half-YAC spanning 15qtel region
15qtel cosmids / S / HR_RKM
RP11-14C10 / 208 / AC016672 / D / WUGSC
RP11-89k11 / 166 / AC027559 / D / WIBR
RP11-12e6 / contains 2183V-I
RP11-341B7 / 163 / AC025234 / D / WUGSC / contains 2183V-I
RP11-95F11 / 170 / AC055861 / D / WIBR / contains 2183V-I, extends more telomerically than RP11-341B7
RP11-509H22 / contains 2183V-I
RP11-250A3 / contains 2183V-I
RP11-304H4 / contains 2183V-I
RARE, Srpt / y
16ptel is characterized by several alleles whose sizes vary by up to 260 kb (Wilkie et al, 1991). Allele A (the shortest allele) has been sequenced completely (Flint et al., 1997). yRM2118 extends approximately 175 kb beyond the A allele, and contains sequences from BACs in ctg15544 which are not contained in the A allele. The size and sequence content (it contains the TelBam11 Srpt sequence are consistent with it containing the B allele of the 16p telomere.
yRM2118 / 300 / S / HR_RKM / 300 kb half-YAC spanning variant allele of 16ptel region, extends 175 kb beyond telomere of allele A
16ptel cosmids / S / HR_RKM
XX-310H5 / Z69705 / F / SC / NT_000655; Finished sequence NT_000655 continues a total of 356 kb towards the centromere
XX-CRJ14 / Z69890 / F / SC / NT_000655
XX-COS12 / Z69706 / F / SC / NT_000655
GG4 / Z84722 / F / SC / NT_000655
GG1 / Z84721 / F / SC / NT_000655
XX-24F8 / Z69666 / F / SC / NT_000655
X94 / Z84813 / F / SC / NT_000655
XX-CRA36 / Z69720 / F / SC / NT_000655
XX-CNFG9 / Z69719 / F / SC / NT_000655
LAW2 / Z84723 / F / SC / NT_000655
pTEL / Z84812 / F / SC / NT_000655 telomeric end of 16ptel allele A
RP11-344L6 / 203 / AC007604 / D / JGI / Sequences encompassed by half-YAC yRM2118, variant allele of 16ptel
RP11-568F1 / 200 / AC010552 / D / JGI / Sequences encompassed by half-YAC yRM2118, variant allele of 16ptel, more telomeric than RP11-344L6
Srpt / y / yA11 / 250 / 250 kb half-YAC spanning 16qtel region
16qtel cosmids / S / HR_RKM
RP11-368i7 / 245 / AC010538 / D / JGI
RP11-8j19 / AC012430 / D / WIBR
NT_000743 / 109 / F / JGI / 109 kb FANCA cosmid ctg
RP11-372e5 / connects FANCA ctg with subtelomeric cosmid ctg (BAC end sequence data), no drft seq
c344G2 / 41 / AC006838 / D / JGI / subtelomeric cosmid ctg
c439G8 / 35 / AC007046 / D / JGI / subtelomeric cosmid ctg
c372B12 / 35 / AC007181 / D / JGI / subtelomeric cosmid ctg
c425e4 / 36 / AC007657 / D / JGI
RARE, Srpt / y
yRM2111 / 105 / S / HR_RKM / 105 kb half-YAC spanning 17ptel region
17ptel cosmids
RP11-337D6 / no sequence / contains 2111V-I (hyb and PCR), extends into yRM2111 seq
CTD-2348K1 / no sequence / contains 2111V-I (hyb and PCR), extends into yRM2111 seq
yRM2111 cos ctg / AF240580 / D / Moyzis, HR_RKM / contiguous sequence to within 20 kb of 17p telomere
RARE, Srpt / unk / 17qtel-derived sequences contain a low-copy repeat segment associated with the Tre17 oncogene which is duplicated several times on chr 17. Single-copy sequences from the half-YACs do not match any sequence from the Working Draft
yB37 / 90 / 90 kb half-YAC spanning 17qtel region
yRM2009 / 140 / S / HR_RKM / 140 kb half-YAC spanning 17qtel region
17qtel cosmids / S / HR_RKM
chr 17 repeat in half-YAC / Many apparent chr 17 BAC overlaps, low-copy 17-specific repeat (Tre17-associated)
RARE, Srpt / n / Distal 100 kb of working draft sequence is Srpt
yRM2102 / 220 / S / HR_RKM / 220 kb half-YAC spanning 18ptel region
yRM2011 / 140 / S / HR_RKM / 140 kb half-YAC spanning 18ptel region
yRM2141 / S / HR_RKM / 18ptel half-YAC containing internal deletion(s)
18ptel cosmids / S / HR_RKM
RP11-720L2 / 189 / AP000915 / D / RIKEN / BAC clone containing 2141V-I
RP11-398L3 / 170 / AC015567 / D / WIBR / BAC clone containing 2141V-I, 2102V-I
RP11-324G2 / 168 / AC016128 / D / WIBR / BAC clone containing 2141V-I, 2102V-I
RP11-815L4 / 184 / AP001022 / D / RIKEN / BAC clone containing 2141V-I, 2102V-I
RP11-839o23 / 185 / AP000939 / D / RIKEN
RP11-683J11 / 176 / AP000900 / D / RIKEN / BAC clone containing 2141V-I, 2102V-I
RP11-464L8 / 225 / BAC clone containing 2141V-I, 2102V-I, and 2011V-I
RP11-558F13 / 180 / BAC clone containing 2141V-I, 2102V-I, and 2011V-I
RP11-705o1 / 164 / AP000845 / D / RIKEN / BAC clone containing 2102V-I, 2011V-I
RP11-417H13 / 150 / BAC clone containing 2102V-I, 2011V-I
RP11-550F2 / 160 / BAC clone containing 2102V-I, 2011V-I
RP11-271E15 / 160 / BAC clone containing 2102V-I, 2011V-I
RP11-191N4 / 162 / BAC clone containing 2102V-I, 2011V-I
RP11-683L23 / 163 / AP001005 / D / RIKEN / BAC clone containing 2011V-I, extends to within 10 kb of 18p telomere
RARE, Srpt / n
yRM2050 / 290 / S / HR_RKM / 290 kb half-YAC spanning 18qtel region
18qtel cosmids / S / HR_RKM
RP11-7C10 / 147 / AC010958 / D / WIBR / contains 2050V-I
RP11-7C9 / AC015668 / D / WIBR
RP11-507P3 / AC018747 / D / CSH / contains 2050V-I
RP11-680N10 / 160 / AP001522 / D / RIKEN / contains 2050V-I
RP11-565D23 / 146 / AC068530 / D / WIBR / most telomeric
RARE, Srpt / y
yRM2001 / S / HR_RKM / 50 kb half-YAC spanning 19ptel region
19ptel cosmids / S / HR_RKM
Znf-sequence containing clones / Pile-up of chr 19 BACs from 19q and 19p that contain Znf sequences, need to sort out…..
CTD-2102P23 / 180 / AC008813 / D / JGI / contains 2001V-I, extends centromerically, contains Znf sequences
F7501 / 36 / L78442 / F / Trask / contains 2001V-I
LLNLR-222A1 / 38 / AC008993 / F / JGI / contains 2001V-I and HC1103, most telomeric (about 25 kb from 19p telomere)
Srpt / y
Znf-sequence containing clones / Pile-up of BACs from 19q , 19p, chr 5, and possibly elsewhere that contain Znf sequences, difficult to sort out
LLNLR-305D11 / 40 / AC016630 / D / JGI
LLNLR-271e8 / 44 / AC016629 / D / JGI / extends into subtelomeric repeats, IL9R pseudogene
Srpt / unk
yRM2005 / 180 / S / HR_RKM / 180 kb half-YAC spanning 20ptel region
20ptel cosmids / S / HR_RKM
RP5-852M4 / 164 / AL121747 / D / SC
RP5-1103G7 / 153 / AL034548 / F / SC / overlaps with RP11-530N10
RP11-239K9 / 160 / AL365339 / D / SC / contains 2005V-I, incorrectly listed as chr 1 clone
RP11-530N10 / 191 / AL360078 / D / SC / contains 2005V-I, most telomeric
Srpt / y
RP4-591C20 / AL118506 / F / SC
RP11-238j15 / AL356790 / F / SC
RP13-152o15 / 118 / AL355803 / D / SC
RP5-1022e24 / 160 / AL121581 / D / SC
RP11-476i15 / AL137028 / F / SC / contains subtelomeric repeats and IL9R pseudogene, most telomeric
RARE, Srpt / n / contains 2208V-I and 2029V-I sequences, extends to telomere; distal region matches yRM2208 and yRM2029 physical maps
yRM2208 / 290 / S / HR_RKM / 290 kb half-YAC spanning 21qtel region
yRM2029 / 175 / S / HR_RKM / 175 kb half-YAC spanning distal 21qtel region
21qtel cosmids / S / HR_RKM
Tel part of NT_002835 clone ctg / 340 / AP001759 / F / 21c / NT_002835 contains 3,430 kb of contiguous sequence from the 21q telomere towards cen
Tel part of NT_002835 clone ctg / 340 / AP001760 / F / 21c / contains 2208V-I and 2029V-I sequences
Tel part of NT_002835 clone ctg / 40 / AP001761 / F / 21c / extends to 21q telomere; distal region of NT_002835 matches yRM2208 and yRM2029 physical maps
Srpt / unk
yRM2117 / 75 / S / HR_RKM / contains 2117V-I sequence, half-YAC extends about 50 kb beyond sequence
RP4-579N16 / 67 / AL096767 / F / SC / NT_001128; 382 kb of contiguous sequence extending into 22q Srpt region
CTA-999D10 / 9.5 / Z94802 / F / SC
140 / U62317 / F / TIGR
0.2 / Z82168 / F / SC
23 / Z82245 / F / SC
n66c4 / 42 / AC000050 / F / UOKNOR
n85a3 / 43 / AC000036 / F / UOKNOR
n94h12 / 44 / AC002056 / F / UOKNOR
n1g3 / 41 / AC002055 / F / UOKNOR / most telomeric
PFGE, Srpt / unk / No BAC working draft sequence detected distal to SHOX gene (approx 500 kb from Xp/Yp tel), markers DXYS14, DXYS14, PGPL gene tested; cosmid contig covers entire region (Gianfrancesco et al., Hum Mol Genet 1998, Vol 7, 407-414.
no half-YAC
SHOX cosmid ctg / U82668 / F / IMB / NT_ 001151, 500 kb from Xp/Yp tel
PFGE, Srpt / unk
yRM2195 / 320 / S / HR_RKM
RP11-431N21* / 195 / AC009620 / D / WIBR / *listed incorrectly as chr 4, contains 2195V-I sequence and Xq_variant2 pseudoautosomal boundary sequence
IIGB-CNR clone ctg / 240 / AJ271735 / F / IIGB-CNR / NT_004184; contains 2195V-I; contiguous 359 kb finished sequence extends from XqYq telomere through the Xq/Yq pseudoatosomal region to Xq28-specific DNA
IIGB-CNR clone ctg / 159 / AJ271736 / F / IIGB-CNR / NT_004184; contains Xq/Yq telomere
PFGE, Srpt / unk / yRM2195 / 320 / S / HR_RKM
RP11-57J19 / 168 / AC025226 / F / WUGSC / * listed incorrectly as chr 4, contains Yq -sequences, 2195V-I sequence and Yq pseudoautosomal boundary sequence, extends into Xq/Yq pseudo-autosomal sequence NT_004184 which extends to Xq/Yq telomere

aGolden Path Working Draft Sequence contigs which overlap with the indicated subtelomeric regions can be accessed from (Oct 7, 2000 freeze).