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)

AMH		ENSSSCG00000013452	2:47042615-47137986
AMHR2		ENSSSCG00000000271	5:17125841-17131706
AMHR2		location ⇒	5:17126105-17125756		CU570852,CH242-3N12,5:17121211-17130262 (Clone quality: bE3N12 on chr=5; Num_of_Contigs=3; )
AMHR2		location ⇒	5:17127745-17127596		CU570852,CH242-3N12,5:17121211-17130262 (Clone quality: bE3N12 on chr=5; Num_of_Contigs=3; )
AMHR2		location ⇒	5:17128096-17127925		CU570852,CH242-3N12,5:17121211-17130262 (Clone quality: bE3N12 on chr=5; Num_of_Contigs=3; )
AMHR2		location ⇒	5:17131552-17130936		CU570852,CH242-3N12,5:17130363-17155278 (Clone quality: bE3N12 on chr=5; Num_of_Contigs=3; )
AMICA1		ENSSSCG00000015089	9:44392087-44420224
AMICA1		location ⇒	9:44403708-44403540		FP102383,CH242-195F19,9:44362091-44419833 (Clone quality: bE195F19 on chr=9; Num_of_Contigs=1; )
AMICA1		location ⇒	9:44405279-44405204		FP102383,CH242-195F19,9:44362091-44419833 (Clone quality: bE195F19 on chr=9; Num_of_Contigs=1; )
AMICA1		location ⇒	9:44410436-44410206		FP102383,CH242-195F19,9:44362091-44419833 (Clone quality: bE195F19 on chr=9; Num_of_Contigs=1; )
AMICA1		location ⇒	9:44411851-44411776		FP102383,CH242-195F19,9:44362091-44419833 (Clone quality: bE195F19 on chr=9; Num_of_Contigs=1; )
AMIGO1		ENSSSCG00000006826	4:115137411-115138889		CU633714,CH242-413N19,4:115062764-115147480 (Clone quality: bE413N19 on chr=4; Num_of_Contigs=4; )
AMIGO1		location ⇒	4:115138296-115138805		CU633714,CH242-413N19,4:115062764-115147480 (Clone quality: bE413N19 on chr=4; Num_of_Contigs=4; )
AMIGO2		ENSSSCG00000000810	5:73096930-73097880		FP102336,CH242-82H14,5:73096927-73252218 (Clone quality: bE82H14 on chr=5; Num_of_Contigs=1; )
AMIGO2		location ⇒	5:73096927-73097299
AMIGO3		ENSSSCG00000011388	13:27006899-27008425		CU914539,CH242-222N14,13:26945819-27078203 (Clone quality: bE222N14 on chr=13; Num_of_Contigs=2; )
AMIGO3		location ⇒	13:27007487-27006957		CU914539,CH242-222N14,13:26945819-27078203 (Clone quality: bE222N14 on chr=13; Num_of_Contigs=2; )
AMMECR1		ENSSSCG00000012574	X:87495384-87606210
AMMECR1L		ENSSSCG00000012529	X:82011274-82014331		FP102487,CH242-220O15,X:81971924-82031111 (Clone quality: bE220O15 on chr=X; Num_of_Contigs=2; )
AMN		ENSSSCG00000002524	7:130928666-130936789		CT998550,CH242-445C19,7:130928637-130997560 (Clone quality: bE445C19 on chr=7; Num_of_Contigs=6; )
AMOT		ENSSSCG00000012591	X:90548473-90593546
AMOT		location ⇒	X:90546265-90544747	CU464172,CH242-63P10,X:90522245-90559514 (Clone quality: bE63P10 on chr=X; Num_of_Contigs=2; )
AMOT		location ⇒	X:90550991-90550756	CU464172,CH242-63P10,X:90522245-90559514 (Clone quality: bE63P10 on chr=X; Num_of_Contigs=2; )
AMOT		location ⇒	X:90585974-90585720	CU207356,CH242-412O5,X:90559515-90618169 (Clone quality: bE412O5 on chr=X; Num_of_Contigs=3; )
AMOT		location ⇒	X:90593546-90592674	CU207356,CH242-412O5,X:90559515-90618169 (Clone quality: bE412O5 on chr=X; Num_of_Contigs=3; )
AMOTL1		ENSSSCG00000014960	9:27236250-27311405
AMOTL2		ENSSSCG00000011643	13:61903374-61915512
AMPD3		location ⇒	4:110249099-110249154		CU393558,CH242-266G7,4:110202821-110378185 (Clone quality: bE266G7 on chr=4; Num_of_Contigs=1; )
AMPD3		location ⇒	4:110252228-110252271		CU393558,CH242-266G7,4:110202821-110378185 (Clone quality: bE266G7 on chr=4; Num_of_Contigs=1; )
AMPKA2		location ⇒	6:110604304-110603630		FP102847,CH242-189G19,6:110589711-110609177 (Clone quality: bE189G19 on chr=6; Num_of_Contigs=10; )
AMPKA2		location ⇒	6:110608013-110607503		FP102847,CH242-189G19,6:110589711-110609177 (Clone quality: bE189G19 on chr=6; Num_of_Contigs=10; )
AMPKA2		location ⇒	6:110623487-110623261		FP102847,CH242-189G19,6:110620219-110631298 (Clone quality: bE189G19 on chr=6; Num_of_Contigs=10; )
AMPKA2		location ⇒	6:110627963-110627817		FP102847,CH242-189G19,6:110620219-110631298 (Clone quality: bE189G19 on chr=6; Num_of_Contigs=10; )
AMT		location ⇒	X:94762649-94762543	CU207357,CH242-478E14,X:94762541-94917907 (Clone quality: bE478E14 on chr=X; Num_of_Contigs=2; )
AMTN		ENSSSCG00000008936	8:57214510-57219079		CU928399,CH242-512L3,8:57209088-57219916 (Clone quality: bE512L3 on chr=8; Num_of_Contigs=3; )
AMYP_PIG		ENSSSCG00000006854	4:119881724-119889927		CU480856,CH242-482F18,4:119881561-119939844 (Clone quality: bE482F18 on chr=4; Num_of_Contigs=8; )
AMZ1		ENSSSCG00000007564	3:1396304-1424849
AMZ2		ENSSSCG00000017264	12:10257746-10265879		FP067366,CH242-80E11,12:10256917-10265943 (Clone quality: bE80E11 on chr=12; Num_of_Contigs=7; )
ANAPC10		ENSSSCG00000009044	8:72013024-72064935
ANAPC13		ENSSSCG00000011644	13:62050889-62055013
ANAPC4		ENSSSCG00000008757	8:15626899-15663169
ANAPC5		ENSSSCG00000009814	14:31299502-31347494
ANFB_PIG		ENSSSCG00000003431	6:48802888-48804381		CU695168,CH242-2E14,6:48789218-48811910 (Clone quality: bE2E14 on chr=6; Num_of_Contigs=4; )
ANG		ENSSSCG00000015753	15:34591356-34702700
ANG		ENSSSCG00000010184	14:62045553-62049221
ANG		ENSSSCG00000006035	4:30187582-30312928
ANG		ENSSSCG00000007198	17:36122402-36167016
ANGEL1		ENSSSCG00000002390	7:107955365-107962277		CU062448,CH242-200H14,7:107950136-107965256 (Clone quality: bE200H14 on chr=7; Num_of_Contigs=5; )
ANGEL2		ENSSSCG00000015588	9:122925324-122942443		CU928431,CH242-12J10,9:122912528-122996434 (Clone quality: bE12J10 on chr=9; Num_of_Contigs=5; )
ANGPT1		ENSSSCG00000006035	4:30187582-30312928

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, 1751-32

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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).