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)

PLAUR		ENSSSCG00000003044	6:34639079-34644403		FP015926,CH242-183C8,6:34614693-34644455 (Clone quality: bE183C8 on chr=6; Num_of_Contigs=15; )
PLAUR		ENSSSCG00000003062	6:35027946-35031408		FP102604,CH242-184P4,6:34968039-35068842 (No clone quality info on )
PLAUR		ENSSSCG00000003065	6:35092325-35107861
PLAUR		ENSSSCG00000003073	6:35350245-35354566
PLAUR		ENSSSCG00000015676	15:7491968-7513669		CU915310,CH242-174H6,15:7457917-7555553 (Clone quality: bE174H6 on chr=15; Num_of_Contigs=3; )
PLAUR		location ⇒	6:35092894-35092508		FP102993,CH242-270O18,6:35082446-35099295 (Clone quality: bE270O18 on chr=6; Num_of_Contigs=6; )
PLAUR		location ⇒	6:35094107-35093958		FP102993,CH242-270O18,6:35082446-35099295 (Clone quality: bE270O18 on chr=6; Num_of_Contigs=6; )
PLAUR		location ⇒	6:35094823-35094687		FP102993,CH242-270O18,6:35082446-35099295 (Clone quality: bE270O18 on chr=6; Num_of_Contigs=6; )
PLAUR		location ⇒	6:35095470-35095389		FP102993,CH242-270O18,6:35082446-35099295 (Clone quality: bE270O18 on chr=6; Num_of_Contigs=6; )
PLB1		ENSSSCG00000008541	3:103554744-103573515		CU468182,CH242-232K9,3:103548566-103606520 (Clone quality: bE232K9 on chr=3; Num_of_Contigs=4; )
PLBD2		ENSSSCG00000009872	14:38872267-38898613
PLCB1		ENSSSCG00000007056	17:17191557-17361321
PLCB2		ENSSSCG00000004779	1:137533797-137544390		CU498975,CH242-47C7,1:137533368-137545560 (Clone quality: bE47C7 on chr=1; Num_of_Contigs=13; )
PLCB3		ENSSSCG00000013034	2:6230671-6243362
PLCB3		location ⇒	2:6235388-6235490		CU861533,CH242-1H13,2:6230888-6239573 (Clone quality: bE1H13 on chr=2; Num_of_Contigs=14; )
PLCB3		location ⇒	2:6236082-6236248		CU861533,CH242-1H13,2:6230888-6239573 (Clone quality: bE1H13 on chr=2; Num_of_Contigs=14; )
PLCB3		location ⇒	2:6236327-6236485		CU861533,CH242-1H13,2:6230888-6239573 (Clone quality: bE1H13 on chr=2; Num_of_Contigs=14; )
PLCB3		location ⇒	2:6236770-6236894		CU861533,CH242-1H13,2:6230888-6239573 (Clone quality: bE1H13 on chr=2; Num_of_Contigs=14; )
PLCB4		ENSSSCG00000007058	17:18084144-18284816
PLCD3		ENSSSCG00000017338	12:16148233-16168914
PLCD4		ENSSSCG00000016192	15:113591768-113619299		CU570813,CH242-128B23,15:113581621-113657451 (Clone quality: bE128B23 on chr=15; Num_of_Contigs=4; )
PLCD4		location ⇒	15:113592446-113591772		CU570813,CH242-128B23,15:113581621-113657451 (Clone quality: bE128B23 on chr=15; Num_of_Contigs=4; )
PLCD4		location ⇒	15:113608643-113608408		CU570813,CH242-128B23,15:113581621-113657451 (Clone quality: bE128B23 on chr=15; Num_of_Contigs=4; )
PLCD4		location ⇒	15:113793910-113793675		CU914509,CH242-30J4,15:113791803-113794099 (Clone quality: bE30J4 on chr=15; Num_of_Contigs=25; )
PLCD4		location ⇒	15:113796206-113796880		CU914509,CH242-30J4,15:113794200-113805868 (Clone quality: bE30J4 on chr=15; Num_of_Contigs=25; )
PLCE1		ENSSSCG00000010483	14:110861592-111099030
PLCG1		ENSSSCG00000007356	17:45881829-45914905
PLCG1		location ⇒	17:45905503-45905381		CU062531,CH242-134J5,17:45881829-45961061 (Clone quality: bE134J5 on chr=17; Num_of_Contigs=2; )
PLCG1		location ⇒	17:45906321-45906153		CU062531,CH242-134J5,17:45881829-45961061 (Clone quality: bE134J5 on chr=17; Num_of_Contigs=2; )
PLCG1		location ⇒	17:45906810-45906685		CU062531,CH242-134J5,17:45881829-45961061 (Clone quality: bE134J5 on chr=17; Num_of_Contigs=2; )
PLCG1		location ⇒	17:45907258-45907068		CU062531,CH242-134J5,17:45881829-45961061 (Clone quality: bE134J5 on chr=17; Num_of_Contigs=2; )
PLCG2		ENSSSCG00000002688	6:4701218-4815136
PLCG2		location ⇒	6:4734031-4733528		CU856256,CH242-10B22,6:4696382-4770436 (Clone quality: bE10B22 on chr=6; Num_of_Contigs=4; )
PLCG2		location ⇒	6:4734347-4734170		CU856256,CH242-10B22,6:4696382-4770436 (Clone quality: bE10B22 on chr=6; Num_of_Contigs=4; )
PLCG2		location ⇒	6:4739522-4739351		CU856256,CH242-10B22,6:4696382-4770436 (Clone quality: bE10B22 on chr=6; Num_of_Contigs=4; )
PLCG2		location ⇒	6:4815367-4814944		CU856256,CH242-10B22,6:4809634-4838468 (Clone quality: bE10B22 on chr=6; Num_of_Contigs=4; )
PLCL1		ENSSSCG00000016083	15:95398577-95423950		FP015776,CH242-348I23,15:95320310-95433055 (Clone quality: bE348I23 on chr=15; Num_of_Contigs=1; )
PLCXD2		ENSSSCG00000011934	13:111527747-111527929		CU550693,CH242-88C11,13:111522590-111542052 (Clone quality: bE88C11 on chr=13; Num_of_Contigs=23; )
PLCXD3		ENSSSCG00000016862	16:23553381-23555818		CU570718,CH242-195L1,16:23528300-23606648 (Clone quality: bE195L1 on chr=16; Num_of_Contigs=5; )
PLCZ		ENSSSCG00000000590	5:51990478-52034702
PLCZ		location ⇒	5:52002843-52003076		CU457757,CH242-219O8,5:51933888-52027325 (Clone quality: bE219O8 on chr=5; Num_of_Contigs=1; )
PLCZ		location ⇒	5:52006716-52006919		CU457757,CH242-219O8,5:51933888-52027325 (Clone quality: bE219O8 on chr=5; Num_of_Contigs=1; )
PLCZ		location ⇒	5:52017459-52017702		CU457757,CH242-219O8,5:51933888-52027325 (Clone quality: bE219O8 on chr=5; Num_of_Contigs=1; )
PLCZ		location ⇒	5:52025407-52025580		CU457757,CH242-219O8,5:51933888-52027325 (Clone quality: bE219O8 on chr=5; Num_of_Contigs=1; )
PLCZ1		ENSSSCG00000000590	5:51990478-52034702
PLD1		ENSSSCG00000011750	13:83588488-83687204
PLD1		location ⇒	13:83669377-83669514		CU861962,CH242-265J1,13:83605989-83694135 (Clone quality: bE265J1 on chr=13; Num_of_Contigs=3; )
PLD1		location ⇒	13:83670122-83670235		CU861962,CH242-265J1,13:83605989-83694135 (Clone quality: bE265J1 on chr=13; Num_of_Contigs=3; )
PLD1		location ⇒	13:83684509-83684638		CU861962,CH242-265J1,13:83605989-83694135 (Clone quality: bE265J1 on chr=13; Num_of_Contigs=3; )
PLD1		location ⇒	13:83685374-83685493		CU861962,CH242-265J1,13:83605989-83694135 (Clone quality: bE265J1 on chr=13; Num_of_Contigs=3; )

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, 1851-1900, 1901-1950, 1951-2000, 2001-2050, 2051-2100, 2101-2150, 2151-2200, 2201-21

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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).