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)

CCRL1		location ⇒	13:60584384-60584509		CU463338,CH242-512O15,13:60561420-60652606 (Clone quality: bE512O15 on chr=13; Num_of_Contigs=4; )
CCRL1		location ⇒	13:60585233-60585405		CU463338,CH242-512O15,13:60561420-60652606 (Clone quality: bE512O15 on chr=13; Num_of_Contigs=4; )
CCRL1		location ⇒	13:60587794-60588970		CU463338,CH242-512O15,13:60561420-60652606 (Clone quality: bE512O15 on chr=13; Num_of_Contigs=4; )
CCRL2		location ⇒	8:21223-21118		FP102972,CH242-47L5,8:17398-21329 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
CCRL2		location ⇒	8:48273-48212		FP102972,CH242-47L5,8:43508-48739 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
CCRL2		location ⇒	8:7304-7413		FP102972,CH242-47L5,8:6630-11538 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
CCRL2		location ⇒	8:79830-79721		FP102972,CH242-47L5,8:79654-82980 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
CCS		ENSSSCG00000012934	2:4121849-4163669
CCT2		ENSSSCG00000000496	5:32702669-32717722
CCT3		ENSSSCG00000006487	4:97601379-97656994
CCT4		ENSSSCG00000008377	3:73478929-73496364
CCT7		ENSSSCG00000008303	3:63887995-63907404
CD		ENSSSCG00000002997	6:33691277-33692709		CU928654,CH242-130A3,6:33678287-33731769 (Clone quality: bE130A3 on chr=6; Num_of_Contigs=6; )
CD		ENSSSCG00000000662	5:59228332-59239308
CD1.1		location ⇒	4:95649188-95648951		CU570749,CH242-3I5,4:95632910-95650891 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1.1		location ⇒	4:95670877-95670604		CU570749,CH242-3I5,4:95650992-95680714 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1.1		location ⇒	4:95702920-95702862		CU570749,CH242-3I5,4:95680815-95725403 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1.1		location ⇒	4:95730123-95729850		CU570749,CH242-3I5,4:95725504-95735613 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD100		ENSSSCG00000009584	14:1167125-1208885		CU469368,CH242-181M10,14:1134838-1275802 (Clone quality: bE181M10 on chr=14; Num_of_Contigs=3; )
CD101		ENSSSCG00000006734	4:107816226-107847307		CU468873,CH242-284J24,4:107815328-107859077 (Clone quality: bE284J24 on chr=4; Num_of_Contigs=15; )
CD103		ENSSSCG00000017869	12:47092987-47136476
CD104		ENSSSCG00000017204	12:4001967-4036159
CD105		ENSSSCG00000005625	1:282803569-282837580
CD107b		ENSSSCG00000012604	X:95827889-95864680
CD109		ENSSSCG00000004485	1:97276232-97430354
CD109		location ⇒	1:97393264-97393079		CU062592,CH242-68N19,1:97301165-97467017 (Clone quality: bE68N19 on chr=1; Num_of_Contigs=1; )
CD109		location ⇒	1:97428953-97428779		CU062592,CH242-68N19,1:97301165-97467017 (Clone quality: bE68N19 on chr=1; Num_of_Contigs=1; )
CD109		location ⇒	1:97430354-97430224		CU062592,CH242-68N19,1:97301165-97467017 (Clone quality: bE68N19 on chr=1; Num_of_Contigs=1; )
CD11		location ⇒	6:41340204-41340281		FP245423,CH242-507H20,6:41335911-41340618 (Clone quality: bE507H20 on chr=6; Num_of_Contigs=16; )
CD11		location ⇒	6:41340814-41340986		FP245423,CH242-507H20,6:41340719-41344988 (Clone quality: bE507H20 on chr=6; Num_of_Contigs=16; )
CD11		location ⇒	6:41341168-41341244		FP245423,CH242-507H20,6:41340719-41344988 (Clone quality: bE507H20 on chr=6; Num_of_Contigs=16; )
CD11		location ⇒	6:41341374-41341538		FP245423,CH242-507H20,6:41340719-41344988 (Clone quality: bE507H20 on chr=6; Num_of_Contigs=16; )
CD110		ENSSSCG00000003947	6:120231429-120237080		CU694684,CH242-210N13,6:120225876-120239718 (Clone quality: bE210N13 on chr=6; Num_of_Contigs=11; )
CD111		ENSSSCG00000015124	9:45499515-45554433
CD113		ENSSSCG00000011933	13:111141197-111166125		CU914400,CH242-126E9,13:111116261-111220774 (Clone quality: bE126E9 on chr=13; Num_of_Contigs=5; )
CD115		ENSSSCG00000014441	2:136526706-136552808
CD117		ENSSSCG00000008842	8:35758931-35827981
CD119		ENSSSCG00000004156	1:28492000-28512144		CU302366,CH242-266L9,1:28341732-28512176 (Clone quality: bE266L9 on chr=1; Num_of_Contigs=1; )
CD11a		ENSSSCG00000007797	3:16488603-16527995
CD120a		ENSSSCG00000000708	5:60337243-60349834
CD121a		ENSSSCG00000008162	3:47896450-47909993		CU856003,CH242-200C14,3:47889549-47912820 (Clone quality: bE200C14 on chr=3; Num_of_Contigs=5; )
CD121b		ENSSSCG00000008163	3:48048433-48111836
CD124		ENSSSCG00000007817	3:17689919-17711751
CD127		ENSSSCG00000016832	16:18632640-18662644		CU463889,CH242-401A5,16:18594462-18700254 (Clone quality: bE401A5 on chr=16; Num_of_Contigs=7; )
CD129		ENSSSCG00000007973	3:35184957-35192998		FP103025,CH242-371L21,3:35180882-35196238 (No clone quality info on )
CD13		ENSSSCG00000001849	7:60775665-60790582		CT737411,CH242-149F11,7:60738915-60829656 (Clone quality: bE149F11 on chr=7; Num_of_Contigs=3; )
CD131		ENSSSCG00000000136	5:7187547-7201962		CU407327,CH242-127L5,5:7172124-7252136 (Clone quality: bE127L5 on chr=5; Num_of_Contigs=4; )
CD134		ENSSSCG00000003331	6:42795165-42797753		FP102596,CH242-173K23,6:42793613-42821104 (Clone quality: bE173K23 on chr=6; Num_of_Contigs=10; )
CD135		ENSSSCG00000009314	11:4780073-4815356
CD137		ENSSSCG00000003386	6:46287255-46302434

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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).