Pig genome annotation: A Gene Wish List

A Wish List of Genes for Annotation (version 3.26)

(Matches to BACs by their Genome Locations Based on Pig Genome Build v.9 (Data Downloads as of Mar. 7, 2010 )

Info:

Purpose: Help users to find where to go from gene names to their genome locations/BACs in order to locate a starting spot in the pig genome to bring into Otterlace for annotations.
Methods: The gene locations are determined in 2 ways: Ensembl predictions and Blasts. Clones are sought based on their overlapping genome locations with that of your gene.
Terms: Finished BACs: A total of 811 "finished" clones that met the "golden standard" of finished sequencing quality. Unfinished clones: Out of 15,837 clones on the "unfinished clones" list, only 1,769 have been processed to have genome locations. FPC clones: 254K+ of those clones in the sequencing pipeline
Related links:

HINTS:

Owner/Status info: : Someone has this gene on their wish-list to annotate. : This gene is to be annotated. : This gene has been annotated (click to check for details - maybe only a gene variant is annotated. The ultimate annotator list is from Otterlace entries; This list only provides a working reference).
Additional info: : have orthologous gene information. : have refseq information. : details (click for more)
Ensembl Gene ID, Genome Locations, and BAC names are all hyper-linked to Ensembl database

( Go to genes whose symbol start with: 1, 5, 7, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z )
Search results:	Show Finished BAC Show unFinished BAC

User Gene List			Genome Location (Chr.:start-end)	Fell within Finished BACs (Contig, BACname, Chr.:Start-End)	Fell within Unfinished Clones (SeqName, Chr.:Start-End)
Symbol	Owner/ Status	Ensembl Gene ID	Genome Location (Chr.:start-end)	Fell within Finished BACs (Contig, BACname, Chr.:Start-End)	Fell within Unfinished Clones (SeqName, Chr.:Start-End)

HDAC7A		location ⇒	9:82551230-82551120		CU928566,CH242-391H7,9:82544749-82554252 (Clone quality: bE391H7 on chr=9; Num_of_Contigs=12; )
HDAC7A		location ⇒	9:82551685-82551539		CU928566,CH242-391H7,9:82544749-82554252 (Clone quality: bE391H7 on chr=9; Num_of_Contigs=12; )
HDAC7A		location ⇒	9:82650984-82650841		CU928566,CH242-391H7,9:82644951-82654627 (Clone quality: bE391H7 on chr=9; Num_of_Contigs=12; )
HDAC7A		location ⇒	9:82660122-82660015		CU928566,CH242-391H7,9:82654728-82668006 (Clone quality: bE391H7 on chr=9; Num_of_Contigs=12; )
HDAC8		ENSSSCG00000012410	X:57656340-57688846
HDAC9		ENSSSCG00000015369	9:82551135-82557665
HDAC9		location ⇒	9:82399836-82399954		FP101872,CH242-507H15,9:82393975-82400140 (Clone quality: bE507H15 on chr=9; Num_of_Contigs=5; )
HDAC9		location ⇒	9:82411435-82411560		FP101872,CH242-507H15,9:82400241-82413669 (Clone quality: bE507H15 on chr=9; Num_of_Contigs=5; )
HDAC9		location ⇒	9:82414361-82414573		FP101872,CH242-507H15,9:82413770-82431877 (Clone quality: bE507H15 on chr=9; Num_of_Contigs=5; )
HDC		ENSSSCG00000004644	1:126675499-126694471		CU571408,CH242-238O3,1:126668216-126711956 (Clone quality: bE238O3 on chr=1; Num_of_Contigs=8; )
HDDC2		ENSSSCG00000004224	1:39276124-39295821		CU638834,CH242-181N21,1:39273364-39300832 (Clone quality: bE181N21 on chr=1; Num_of_Contigs=13; )
HDDC3		ENSSSCG00000001820	7:59067458-59068906	CT868688,CH242-510G16,7:59026976-59242142 (Clone quality: bE510G16 on chr=7; Num_of_Contigs=3; )
HDGFL1		ENSSSCG00000001083	7:18421679-18422365		CT867955,CH242-341F11,7:18382378-18428874 (Clone quality: bE341F11 on chr=7; Num_of_Contigs=2; )
HDHD2		ENSSSCG00000005771	1:290563921-290609836		CU928359,CH242-451N13,1:290552874-290612650 (Clone quality: bE451N13 on chr=1; Num_of_Contigs=4; )
HDLBP		ENSSSCG00000016379	15:132099305-132123978
HDX		ENSSSCG00000012457	X:66669585-66732946
HEATR1		ENSSSCG00000010145	14:56026771-56075441		CU406971,CH242-320A14,14:56012844-56141165 (Clone quality: bE320A14 on chr=14; Num_of_Contigs=6; )
HEATR2		ENSSSCG00000007543	3:121339-183552
HEATR3		ENSSSCG00000013971	2:65286545-65396448
HEATR4		ENSSSCG00000002343	7:104742583-104742756		CU861939,CH242-201I13,7:104739745-104749313 (Clone quality: bE201I13 on chr=7; Num_of_Contigs=14; )
HEATR5A		ENSSSCG00000001970	7:74443384-74558332		CU606921,CH242-219J21,7:74434749-74610194 (Clone quality: bE219J21 on chr=7; Num_of_Contigs=1; )
HEATR5B		ENSSSCG00000008498	3:96206351-96324305
HEATR7B1		ENSSSCG00000016311	15:126796788-126814692		CU856250,CH242-89G11,15:126791650-126831068 (Clone quality: bE89G11 on chr=15; Num_of_Contigs=6; )
HEATR7B2		ENSSSCG00000016860	16:23323519-23345407		CU861949,CH242-227N6,16:23315381-23345595 (Clone quality: bE227N6 on chr=16; Num_of_Contigs=5; )
HEBP1		ENSSSCG00000000620	5:56653818-56655302		CU915473,CH242-275K16,5:56652542-56656206 (Clone quality: bE275K16 on chr=5; Num_of_Contigs=20; )
HEBP2		ENSSSCG00000004150	1:27327909-27335277		CU457402,CH242-189P20,1:27319624-27348075 (Clone quality: bE189P20 on chr=1; Num_of_Contigs=3; )
HECA		ENSSSCG00000004144	1:26676124-26686980		CU928956,CH242-485L3,1:26662133-26689332 (Clone quality: bE485L3 on chr=1; Num_of_Contigs=8; )
HECTD1		ENSSSCG00000001971	7:74706414-74808309
HECTD2		ENSSSCG00000010463	14:108226061-108298471		CU570916,CH242-171J18,14:108187691-108300820 (Clone quality: bE171J18 on chr=14; Num_of_Contigs=2; )
HECTD3		ENSSSCG00000003923	6:119167141-119175016		FP102605,CH242-186A16,6:119120152-119190598 (Clone quality: bE186A16 on chr=6; Num_of_Contigs=3; )
HECW1		ENSSSCG00000016759	18:49972682-50249750
HECW2		ENSSSCG00000016068	15:93717378-93871058
HEG1		ENSSSCG00000011859	13:101613738-101764960
HELB		ENSSSCG00000000477	5:30591883-30636962		FP067340,CH242-169A6,5:30518810-30705424 (Clone quality: bE169A6 on chr=5; Num_of_Contigs=1; )
HELLS		ENSSSCG00000010486	14:111246529-111288949		CU468514,CH242-226D12,14:111244933-111297988 (Clone quality: bE226D12 on chr=14; Num_of_Contigs=3; )
HELQ		ENSSSCG00000009236	8:116144462-116179090
HELT		ENSSSCG00000015788	15:43356384-43356773		FP102719,CH242-512M14,15:43356382-43358805 (Clone quality: bE512M14 on chr=15; Num_of_Contigs=25; )
HELZ		ENSSSCG00000017272	12:11512620-11646654
HEMGN		ENSSSCG00000005371	1:251343331-251366031		CU074406,CH242-147C20,1:251334484-251393530 (Clone quality: bE147C20 on chr=1; Num_of_Contigs=8; )
HEPACAM		ENSSSCG00000015319	9:68337103-68488985
HEPACAM		ENSSSCG00000015205	9:50575128-50589227		CU656002,CH242-314J3,9:50466714-50627914 (Clone quality: bE314J3 on chr=9; Num_of_Contigs=1; )
HEPACAM		location ⇒	9:50577542-50577328		CU656002,CH242-314J3,9:50466714-50627914 (Clone quality: bE314J3 on chr=9; Num_of_Contigs=1; )
HEPACAM		location ⇒	9:50578673-50578328		CU656002,CH242-314J3,9:50466714-50627914 (Clone quality: bE314J3 on chr=9; Num_of_Contigs=1; )
HEPACAM		location ⇒	9:50589227-50589108		CU656002,CH242-314J3,9:50466714-50627914 (Clone quality: bE314J3 on chr=9; Num_of_Contigs=1; )
HEPACAM2		ENSSSCG00000015319	9:68337103-68488985
HEPH		ENSSSCG00000012363	X:51024196-51095604
HEPHL1		ENSSSCG00000014953	9:26795159-26836774
HERC1		ENSSSCG00000004561	1:111580881-111792306
HERC2		ENSSSCG00000015853	15:53257004-53467275
HERC3		ENSSSCG00000009208	8:112041032-112114116

Go to records:
1-49, 50-100, 101-150, 151-200, 201-250, 251-300, 301-350, 351-400, 401-450, 451-500, 501-550, 551-600, 601-650, 651-700, 701-32

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$version: 3.26; Updates: Mar. 6, 2010; Apr. 20, 2010; Aug 21, 2010

Related publications:

Martien Groenen, Alan Archibald, Hirohide Uenishi, Christopher Tuggle, Yasuhiro Takeuchi, Max Rothschild, Claire Rogel-Gaillard, ... Denis Milan, Hendrik-Jan Megens, ... Zhi-Liang Hu, Sean J. Humphray, ... James M. Reecy, ..., Gary A. Rohrer, ... Shuhong Zhao, Jane Rogers, Carol Churcher & Lawrence B. Schook. (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491, 393-398 (15 November 2012).