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)

HTR3B		ENSSSCG00000015053	9:40437322-40459481
HTR3D		ENSSSCG00000011784	13:92498341-92502934
HTR4		ENSSSCG00000014428	2:135325159-135464002
HTR5A		ENSSSCG00000016422	18:2357170-2360765		CU929907,CH242-27G17,18:2327307-2364275 (Clone quality: bE27G17 on chr=18; Num_of_Contigs=2; )
HTR7		ENSSSCG00000010459	14:107388267-107490824		CT954288,CH242-71J14,14:107387604-107512154 (Clone quality: bE71J14 on chr=14; Num_of_Contigs=1; )
HTRA1		ENSSSCG00000010703	14:138468111-138528927
HTRA2		ENSSSCG00000008267	3:62906833-62908498		CU633183,CH242-294E8,3:62905101-62908551 (Clone quality: bE294E8 on chr=3; Num_of_Contigs=14; )
HTRA3		ENSSSCG00000008723	8:3520654-3545096
HTRA4		ENSSSCG00000015810	15:44974608-44987531		CU469515,CH242-238L24,15:44884786-44988021 (Clone quality: bE238L24 on chr=15; Num_of_Contigs=5; )
HTT		ENSSSCG00000008697	8:1164042-1436474
HUMINAE		ENSSSCG00000017869	12:47092987-47136476
HUWE1		ENSSSCG00000012328	X:45699108-45827208
HVCN1		ENSSSCG00000009827	14:32036191-32065412		CT737176,CH242-22G23,14:31959545-32075293 (Clone quality: bE22G23 on chr=14; Num_of_Contigs=3; )
HVEC		ENSSSCG00000015124	9:45499515-45554433
HVEC		location ⇒	9:45511420-45511111		CU655927,CH242-310G5,9:45476440-45516542 (Clone quality: bE310G5 on chr=9; Num_of_Contigs=10; )
HVEC		location ⇒	9:45512313-45511959		CU655927,CH242-310G5,9:45476440-45516542 (Clone quality: bE310G5 on chr=9; Num_of_Contigs=10; )
HVEC		location ⇒	9:45563383-45563737		CU914735,CH242-399D9,9:45561157-45575140 (Clone quality: bE399D9 on chr=9; Num_of_Contigs=21; )
HVEC		location ⇒	9:45564276-45564584		CU914735,CH242-399D9,9:45561157-45575140 (Clone quality: bE399D9 on chr=9; Num_of_Contigs=21; )
HYAL1		ENSSSCG00000011404	13:27459186-27461874		CU861907,CH242-10C8,13:27455563-27490719 (Clone quality: bE10C8 on chr=13; Num_of_Contigs=3; )
HYAL2		ENSSSCG00000011405	13:27466272-27468921		CU861907,CH242-10C8,13:27455563-27490719 (Clone quality: bE10C8 on chr=13; Num_of_Contigs=3; )
HYAL2		location ⇒	13:27466986-27466548		CU861907,CH242-10C8,13:27455563-27490719 (Clone quality: bE10C8 on chr=13; Num_of_Contigs=3; )
HYAL2		location ⇒	13:27467478-27467386		CU861907,CH242-10C8,13:27455563-27490719 (Clone quality: bE10C8 on chr=13; Num_of_Contigs=3; )
HYAL2		location ⇒	13:27468922-27467989		CU861907,CH242-10C8,13:27455563-27490719 (Clone quality: bE10C8 on chr=13; Num_of_Contigs=3; )
HYAL3		ENSSSCG00000011402	13:27452030-27453880		CU468071,CH242-427D1,13:27424139-27455562 (Clone quality: bE427D1 on chr=13; Num_of_Contigs=7; )
HYAL4		ENSSSCG00000016602	18:21780086-21787778	CU467663,CH242-113A4,18:21660168-21802380 (Clone quality: bE113A4 on chr=18; Num_of_Contigs=6; )
HYI		ENSSSCG00000003940	6:120039272-120041769		CU463920,CH242-310K18,6:120039132-120050665 (Clone quality: bE310K18 on chr=6; Num_of_Contigs=10; )
HYOU1		ENSSSCG00000015106	9:44856225-44867504		CU695209,CH242-241K21,9:44853505-44878051 (Clone quality: bE241K21 on chr=9; Num_of_Contigs=5; )
HYOU1		ENSSSCG00000015106	9:44856225-44867504		CU695209,CH242-241K21,9:44853505-44878051 (Clone quality: bE241K21 on chr=9; Num_of_Contigs=5; )
HYOU1		location ⇒	9:44855986-44855921		CU695209,CH242-241K21,9:44853505-44878051 (Clone quality: bE241K21 on chr=9; Num_of_Contigs=5; )
HYOU1		location ⇒	9:44857724-44857482		CU695209,CH242-241K21,9:44853505-44878051 (Clone quality: bE241K21 on chr=9; Num_of_Contigs=5; )
HYOU1		location ⇒	9:44860434-44860373		CU695209,CH242-241K21,9:44853505-44878051 (Clone quality: bE241K21 on chr=9; Num_of_Contigs=5; )
HYOU1		location ⇒	9:44865470-44865394		CU695209,CH242-241K21,9:44853505-44878051 (Clone quality: bE241K21 on chr=9; 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, 701-32

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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).