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)

TMEM220		ENSSSCG00000018010	12:52506968-52521767
TMEM221		ENSSSCG00000013877	2:61746038-61752269		CU861959,CH242-254K17,2:61744697-61757411 (Clone quality: bE254K17 on chr=2; Num_of_Contigs=9; )
TMEM222		ENSSSCG00000003571	6:58216899-58228306
TMEM225		ENSSSCG00000015151	9:49267103-49269547		CU855492,CH242-168G23,9:49265654-49275855 (Clone quality: bE168G23 on chr=9; Num_of_Contigs=4; )
TMEM229A		ENSSSCG00000016600	18:21684799-21685908	CU467663,CH242-113A4,18:21660168-21802380 (Clone quality: bE113A4 on chr=18; Num_of_Contigs=6; )
TMEM229B		ENSSSCG00000002291	7:99593542-99594042		CU407266,CH242-470E7,7:99569802-99608440 (Clone quality: bE470E7 on chr=7; Num_of_Contigs=4; )
TMEM231		ENSSSCG00000002708	6:8790715-8812823
TMEM232		ENSSSCG00000014196	2:103781370-104096516
TMEM233		ENSSSCG00000009841	14:33282471-33311272
TMEM26		ENSSSCG00000010217	14:67531617-67575430		CU694510,CH242-17O17,14:67506548-67667389 (Clone quality: bE17O17 on chr=14; Num_of_Contigs=1; )
TMEM27		ENSSSCG00000012139	X:11514627-11696825
TMEM30A		ENSSSCG00000004481	1:95750121-95800364
TMEM30B		ENSSSCG00000005094	1:199179247-199180275		CU856630,CH242-128J23,1:199117213-199208126 (Clone quality: bE128J23 on chr=1; Num_of_Contigs=6; )
TMEM30B		location ⇒	1:199177213-199177089		CU856630,CH242-128J23,1:199117213-199208126 (Clone quality: bE128J23 on chr=1; Num_of_Contigs=6; )
TMEM30B		location ⇒	1:199180335-199179256		CU856630,CH242-128J23,1:199117213-199208126 (Clone quality: bE128J23 on chr=1; Num_of_Contigs=6; )
TMEM33		ENSSSCG00000008800	8:27912888-27931777
TMEM35		ENSSSCG00000012490	X:76098935-76111074		FP015894,CH242-19K5,X:76058643-76129674 (Clone quality: bE19K5 on chr=X; Num_of_Contigs=2; )
TMEM38A		ENSSSCG00000013864	2:61218930-61226864		CU929691,CH242-155H10,2:61196915-61238847 (Clone quality: bE155H10 on chr=2; Num_of_Contigs=7; )
TMEM38B		ENSSSCG00000005429	1:259035270-259085827		CU372900,CH242-201E4,1:258974460-259090674 (Clone quality: bE201E4 on chr=1; Num_of_Contigs=3; )
TMEM39A		ENSSSCG00000011901	13:105556673-105590207
TMEM40		ENSSSCG00000011583	13:57034072-57065362		CU928558,CH242-268K10,13:56979951-57068856 (Clone quality: bE268K10 on chr=13; Num_of_Contigs=3; )
TMEM41A		ENSSSCG00000011792	13:93338013-93341316		CU582974,CH242-334N13,13:93334924-93342805 (Clone quality: bE334N13 on chr=13; Num_of_Contigs=9; )
TMEM41B		ENSSSCG00000014579	9:678798-703168		CU638718,CH242-178L14,9:670144-722820 (Clone quality: bE178L14 on chr=9; Num_of_Contigs=6; )
TMEM42		ENSSSCG00000011302	13:23690741-23694407		CU633692,CH242-274A14,13:23677229-23700829 (Clone quality: bE274A14 on chr=13; Num_of_Contigs=14; )
TMEM43		ENSSSCG00000011603	13:58604002-58620486
TMEM44		ENSSSCG00000011826	13:99145308-99179264		CU468465,CH242-221O22,13:99126848-99200122 (Clone quality: bE221O22 on chr=13; Num_of_Contigs=4; )
TMEM45B		ENSSSCG00000015241	9:55052655-55058475		CU639485,CH242-386H2,9:55051557-55064336 (Clone quality: bE386H2 on chr=9; Num_of_Contigs=20; )
TMEM46		ENSSSCG00000009297	11:2962354-2966077		CU607007,CH242-508H24,11:2959249-2966966 (Clone quality: bE508H24 on chr=11; Num_of_Contigs=17; )
TMEM47		ENSSSCG00000012214	X:30239674-30267263
TMEM49		ENSSSCG00000017668	12:34069469-34200586
TMEM5		ENSSSCG00000000462	5:27999464-28074702
TMEM55A		ENSSSCG00000006121	4:46360835-46424350	CU179670,CH242-299E13,4:46296919-46490242 (Clone quality: bE299E13 on chr=4; Num_of_Contigs=2; )
TMEM55B		ENSSSCG00000002136	7:84885611-84889464		CT955972,CH242-231D20,7:84860540-84904248 (Clone quality: bE231D20 on chr=7; Num_of_Contigs=1; )
TMEM56		ENSSSCG00000006884	4:126853819-126880070
TMEM57		ENSSSCG00000003548	6:57112019-57112219		CU929753,CH242-280A19,6:57110925-57224647 (Clone quality: bE280A19 on chr=6; Num_of_Contigs=3; )
TMEM62		ENSSSCG00000004716	1:134425937-134435421
TMEM63A		ENSSSCG00000010854	10:13975458-14014806
TMEM63B		ENSSSCG00000001697	7:45659823-45685951	CR956360,CH242-245E12,7:45529239-45714745 (No clone quality info on bE245E12)
TMEM63C		ENSSSCG00000002398	7:108370553-108378908
TMEM64		ENSSSCG00000006123	4:47050724-47071443		CU655946,CH242-424L4,4:47011573-47128735 (Clone quality: bE424L4 on chr=4; Num_of_Contigs=7; )
TMEM65		ENSSSCG00000005977	4:14927505-14972281		CU469033,CH242-42C1,4:14909282-15017864 (Clone quality: bE42C1 on chr=4; Num_of_Contigs=2; )
TMEM66		ENSSSCG00000015849	15:51905329-51924571
TMEM67		ENSSSCG00000006108	4:43478274-43550835
TMEM68		ENSSSCG00000006252	4:78839849-78870955		CU467744,CH242-37O14,4:78741713-78909653 (Clone quality: bE37O14 on chr=4; Num_of_Contigs=2; )
TMEM71		ENSSSCG00000005951	4:7436163-7461644
TMEM74		ENSSSCG00000006031	4:28661949-28662860		CU694914,CH242-446C3,4:28590825-28757646 (Clone quality: bE446C3 on chr=4; Num_of_Contigs=1; )
TMEM79		ENSSSCG00000006489	4:97666295-97671066		CU468654,CH242-228K10,4:97649767-97712830 (Clone quality: bE228K10 on chr=4; Num_of_Contigs=7; )
TMEM8		ENSSSCG00000007985	3:35438424-35444553
TMEM8		location ⇒	3:35440555-35440406		FP103065,CH242-393N23,3:35429454-35444197 (Clone quality: bE393N23 on chr=3; Num_of_Contigs=5; )
TMEM8		location ⇒	3:35440811-35440630		FP103065,CH242-393N23,3:35429454-35444197 (Clone quality: bE393N23 on chr=3; Num_of_Contigs=5; )

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, 701-750, 751-800, 801-850, 851-900, 901-950, 951-1000, 1001-1050, 1051-1100, 1101-1150, 1151-1200, 1201-1250, 1251-1300, 1301-1350, 1351-1400, 1401-1450, 1451-1500, 1501-1550, 1551-1600, 1601-1650, 1651-1700, 1701-1750, 1751-1800, 1801-1850, 1851-8

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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).