Status report on gap closure of the human chromosome 5 BAC map Authentication of C5 BAC maps Map and sequence status Gap status and steps used to close.

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Status report on gap closure of the human chromosome 5 BAC map Authentication of C5 BAC maps Map and sequence status Gap status and steps used to close gaps Status of the centromere and telomeres C5 specific duplications Jan-Fang Cheng Joint Genome Institute May 24, 2001

Authentication of C5 BAC contigs Restriction fragment overlaps FISH data UniSTS matches BAC end matches FPC map Sequence overlaps

C5 map and sequence status Size of chromosome 5: ~200 Mb Coverage of restriction mapped clones: 184,306 Kb Number of JGI committed clones: 1989 Coverage of committed clones: 172,083 Kb Size of JGI sequenced clones: 141,027 Kb –Marked clones: 1,912 Kb –Drafted clones: 77,356 Kb –Finished clones: 61,759 Kb Feb. 10 release of the Golden Path: 165 Mb of sequence and 35 Mb of gap

Gap status and steps used to close gaps Restriction map + FISH STS + Restriction map + FISH (STS + Restriction map + FISH) n Type 3: Gaps with no bridging clones 11 Celera Scaffold 22 Type 2: Gaps with FPC bridging clones FPC How many 95

Map status of C5 centromere and telomeres RP11-811I15 ? Kb 927 Kb BAC YAC RP1-9H3 CTD-2276O24 RP11-236F Kb 600 Kb RP11-324K Kb 8.26 Mb YAC BAC q p

Mapping of tandemly duplicated gene: Protocadherin gene cluster on 5q31 Wu et al., (2001) Genome Research 11:

C5 specific duplications q p RP11-374A4 RP11-96B3 NAIP SMN NAIP 500 Kb 597 Kb (6 BACs) RP11-360I2 15 Mb RP11-3M7 CTD-2021M10 RP11-356O21 RP11-430F16 ??