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)

C4B		location ⇒	7:4665-4758		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
C4B		location ⇒	7:89313-89398		CU657920,CH242-367F14,7:75360-95741 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
C4B		location ⇒	7:99895-99814		CU657920,CH242-367F14,7:95842-128080 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
C4BPA		ENSSSCG00000015662	9:132270922-132283647		CU633410,CH242-391L17,9:132252384-132466044 (Clone quality: bE391L17 on chr=9; Num_of_Contigs=2; )
C4BPA		location ⇒	9:132295438-132295612		CU633410,CH242-391L17,9:132252384-132466044 (Clone quality: bE391L17 on chr=9; Num_of_Contigs=2; )
C4BPA		location ⇒	9:132355933-132356107		CU633410,CH242-391L17,9:132252384-132466044 (Clone quality: bE391L17 on chr=9; Num_of_Contigs=2; )
C4BPA		location ⇒	9:132357108-132357286		CU633410,CH242-391L17,9:132252384-132466044 (Clone quality: bE391L17 on chr=9; Num_of_Contigs=2; )
C4BPA		location ⇒	9:132357837-132358114		CU633410,CH242-391L17,9:132252384-132466044 (Clone quality: bE391L17 on chr=9; Num_of_Contigs=2; )
C4BPB		ENSSSCG00000015661	9:132246494-132255986
C4BPB		location ⇒	9:132247004-132247200		CU694720,CH242-352B19,9:132244670-132252383 (Clone quality: bE352B19 on chr=9; Num_of_Contigs=11; )
C4BPB		location ⇒	9:132247798-132247972		CU694720,CH242-352B19,9:132244670-132252383 (Clone quality: bE352B19 on chr=9; Num_of_Contigs=11; )
C4BPB		location ⇒	9:132249053-132249229		CU694720,CH242-352B19,9:132244670-132252383 (Clone quality: bE352B19 on chr=9; Num_of_Contigs=11; )
C4BPB		location ⇒	9:132254738-132254866		CU633410,CH242-391L17,9:132252384-132466044 (Clone quality: bE391L17 on chr=9; Num_of_Contigs=2; )
C4MRC5_PIG		ENSSSCG00000000178	5:13531196-13616993
C4MXZ1_PIG		ENSSSCG00000013992	2:66564101-66582084	FP085478,CH242-132B19,2:66476472-66645587 (Clone quality: bE132B19 on chr=2; Num_of_Contigs=3; )
C4orf16		ENSSSCG00000009128	8:94766037-94836769
C4orf17		ENSSSCG00000009181	8:103583916-103621553
C4orf19		ENSSSCG00000008771	8:24422789-24509347
C4orf21		ENSSSCG00000009120	8:92272536-92289194
C4orf22		ENSSSCG00000009252	8:118046935-118108926
C4orf29		ENSSSCG00000009074	8:83447686-83482688		FP102002,CH242-142F22,8:83402725-83532947 (Clone quality: bE142F22 on chr=8; Num_of_Contigs=3; )
C4orf31		ENSSSCG00000009099	8:88686021-88694965		CU655981,CH242-199N6,8:88631142-88699518 (Clone quality: bE199N6 on chr=8; Num_of_Contigs=3; )
C4orf31		location ⇒	8:88686018-88686213		CU655981,CH242-199N6,8:88631142-88699518 (Clone quality: bE199N6 on chr=8; Num_of_Contigs=3; )
C4orf31		location ⇒	8:88691808-88691938		CU655981,CH242-199N6,8:88631142-88699518 (Clone quality: bE199N6 on chr=8; Num_of_Contigs=3; )
C4orf31		location ⇒	8:88693570-88695587		CU655981,CH242-199N6,8:88631142-88699518 (Clone quality: bE199N6 on chr=8; Num_of_Contigs=3; )
C4orf32		ENSSSCG00000009130	8:94868726-94868971		CU928659,CH242-251I11,8:94867747-94873503 (Clone quality: bE251I11 on chr=8; Num_of_Contigs=13; )
C4orf33		ENSSSCG00000009069	8:82431211-82449372		FP236670,CH242-154K1,8:82291083-82483660 (Clone quality: bE154K1 on chr=8; Num_of_Contigs=1; )
C4orf37		ENSSSCG00000009188	8:104591513-104625541
C4orf40		ENSSSCG00000009264	8:119846554-119851599		CU929598,CH242-240J23,8:119846441-119862845 (Clone quality: bE240J23 on chr=8; Num_of_Contigs=8; )
C4orf41		ENSSSCG00000015777	15:41989098-42127901
C4orf43		ENSSSCG00000008890	8:45187492-45214947		FP104560,CH242-341A23,8:45178229-45225802 (Clone quality: bE341A23 on chr=8; Num_of_Contigs=13; )
C4orf44		ENSSSCG00000008696	8:1146004-1151706
C4orf45		ENSSSCG00000008880	8:41417042-41597034
C4orf46		ENSSSCG00000008876	8:41184891-41188690		CU896689,CH242-1N13,8:41180262-41282411 (Clone quality: bE1N13 on chr=8; Num_of_Contigs=4; )
C4orf47		ENSSSCG00000015794	15:43718678-43737823		CU571359,CH242-312E7,15:43699298-43786916 (Clone quality: bE312E7 on chr=15; Num_of_Contigs=3; )
C4orf48		ENSSSCG00000008686	8:558534-560408		FP089546,CH242-195I13,8:553190-569443 (Clone quality: bE195I13 on chr=8; Num_of_Contigs=10; )
C4orf49		ENSSSCG00000009062	8:75404286-75418204		CU914334,CH242-117F10,8:75402516-75448657 (Clone quality: bE117F10 on chr=8; Num_of_Contigs=8; )
C4orf50		ENSSSCG00000008709	8:2155592-2177321
C4orf51		ENSSSCG00000009038	8:71484809-71489803
C4orf7		location ⇒	8:119956377-119956307		CU929598,CH242-240J23,8:119950665-119962431 (Clone quality: bE240J23 on chr=8; Num_of_Contigs=8; )
C4P6P6_PIG		ENSSSCG00000004977	1:176908290-176909448		CU075430,CH242-172H17,1:176902535-176915481 (Clone quality: bE172H17 on chr=1; Num_of_Contigs=4; )
C5		ENSSSCG00000000286	5:17932916-17934404		CU633419,CH242-45O15,5:17919632-17935223 (Clone quality: bE45O15 on chr=5; Num_of_Contigs=9; )
C5		ENSSSCG00000005512	1:274568890-274654777
C5		ENSSSCG00000007840	3:21672716-21694067		CU972409,CH242-221O18,3:21666086-21697171 (Clone quality: bE221O18 on chr=3; Num_of_Contigs=8; )
C5		ENSSSCG00000001422	7:27842472-27862549	CT956038,CH242-183N12,7:27767223-27953076 (Clone quality: bE183N12 on chr=7; Num_of_Contigs=3; )
C5		location ⇒	1:274569418-274568894		CU571013,CH242-185E21,1:274559464-274569714 (Clone quality: bE185E21 on chr=1; Num_of_Contigs=9; )
C5		location ⇒	1:274589560-274589352		CU571013,CH242-185E21,1:274577449-274649571 (Clone quality: bE185E21 on chr=1; Num_of_Contigs=9; )
C5		location ⇒	1:274609608-274609380		CU571013,CH242-185E21,1:274577449-274649571 (Clone quality: bE185E21 on chr=1; Num_of_Contigs=9; )
C5		location ⇒	1:274625967-274625755		CU571013,CH242-185E21,1:274577449-274649571 (Clone quality: bE185E21 on chr=1; Num_of_Contigs=9; )
C5A		ENSSSCG00000001768	7:54032166-54034261		CU326382,CH242-204O9,7:54016934-54044053 (Clone quality: bE204O9 on chr=7; Num_of_Contigs=8; )

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, 2201-2250, 2251-2300, 2301-2350, 2351-2400, 2401-2450, 2451-2500, 2501-2550, 2551-2600, 2601-2650, 2651-2700, 2701-2750, 2751-2800, 2801-2850, 2851-2900, 2901-2950, 2951-3000, 3001-3050, 3051-3100, 3101-3150, 3151-3200, 3201-3250, 3251-3300, 3301-3350, 3351-3400, 3401-3450, 3451-3500, 3501-3550, 3551-3600, 3601-3650, 3651-3700, 3701-3750, 3751-3800, 3801-3850, 3851-3900, 3901-12

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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).