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)

UBE2C		ENSSSCG00000007423	17:50082565-50085707		CU076086,CH242-56C16,17:49960216-50115189 (Clone quality: bE56C16 on chr=17; Num_of_Contigs=2; )
UBE2D1		ENSSSCG00000010419	14:96895555-96905796
UBE2D2		ENSSSCG00000014358	2:128671505-128690127
UBE2D3		ENSSSCG00000009167	8:101415843-101427461		CU972368,CH242-513E6,8:101410807-101442931 (Clone quality: bE513E6 on chr=8; Num_of_Contigs=4; )
UBE2D4		ENSSSCG00000016722	18:47377877-47398530
UBE2E2		ENSSSCG00000011209	13:8633044-8723679		CU633903,CH242-265H17,13:8624321-8769900 (Clone quality: bE265H17 on chr=13; Num_of_Contigs=2; )
UBE2G1		ENSSSCG00000017878	12:47515462-47598747
UBE2G1		location ⇒	12:47515505-47515869		FP067370,CH242-167N15,12:47507154-47581446 (Clone quality: bE167N15 on chr=12; Num_of_Contigs=3; )
UBE2G1		location ⇒	12:47588996-47589175		FP067370,CH242-167N15,12:47581547-47628595 (Clone quality: bE167N15 on chr=12; Num_of_Contigs=3; )
UBE2G1		location ⇒	12:47592479-47592604		FP067370,CH242-167N15,12:47581547-47628595 (Clone quality: bE167N15 on chr=12; Num_of_Contigs=3; )
UBE2G1		location ⇒	12:47598249-47599348		FP067370,CH242-167N15,12:47581547-47628595 (Clone quality: bE167N15 on chr=12; Num_of_Contigs=3; )
UBE2H		ENSSSCG00000016564	18:16930378-17082949
UBE2H		location ⇒	18:1464459-1464567		CU929830,CH242-52F22,18:1436419-1468077 (Clone quality: bE52F22 on chr=18; Num_of_Contigs=8; )
UBE2H		location ⇒	18:3958924-3959037		FP103034,CH242-8F9,18:3954880-3959963 (Clone quality: bE8F9 on chr=18; Num_of_Contigs=4; )
UBE2H		location ⇒	18:4255096-4255193		CU681827,CH242-261E23,18:4254698-4255402 (Clone quality: bE261E23 on chr=18; Num_of_Contigs=28; )
UBE2H		location ⇒	18:4961584-4961496		FP236681,CH242-196C2,18:4922748-4962653 (Clone quality: bE196C2 on chr=18; Num_of_Contigs=5; )
UBE2J2		ENSSSCG00000003334	6:42827546-42839848
UBE2K		ENSSSCG00000008791	8:26170493-26242359
UBE2L3		ENSSSCG00000010088	14:51339903-51389142		CU633431,CH242-79C11,14:51180713-51414471 (Clone quality: bE79C11 on chr=14; Num_of_Contigs=4; )
UBE2N		ENSSSCG00000000908	5:84008035-84009996		CU915373,CH242-67L15,5:84003378-84016228 (Clone quality: bE67L15 on chr=5; Num_of_Contigs=3; )
UBE2NL		ENSSSCG00000004151	1:27365895-27366353		CU457402,CH242-189P20,1:27348176-27448920 (Clone quality: bE189P20 on chr=1; Num_of_Contigs=3; )
UBE2Q1		ENSSSCG00000006544	4:99262524-99296581	CU469085,CH242-42I4,4:99200352-99380372 (Clone quality: bE42I4 on chr=4; Num_of_Contigs=1; )
UBE2QL1		ENSSSCG00000017105	16:72812055-72857673
UBE2R2		ENSSSCG00000010989	10:31508071-31523087		CU633320,CH242-86P2,10:31485466-31523504 (Clone quality: bE86P2 on chr=10; Num_of_Contigs=12; )
UBE2S		ENSSSCG00000003291	6:41318106-41323204		FP245423,CH242-507H20,6:41317281-41333293 (Clone quality: bE507H20 on chr=6; Num_of_Contigs=16; )
UBE2T		ENSSSCG00000010924	10:24508005-24512563		CU929522,CH242-133L15,10:24469362-24590809 (Clone quality: bE133L15 on chr=10; Num_of_Contigs=3; )
UBE2U		ENSSSCG00000003810	6:104416813-104514987
UBE2W		ENSSSCG00000006177	4:64197630-64267878		CU210930,CH242-386B23,4:64175433-64296491 (Clone quality: bE386B23 on chr=4; Num_of_Contigs=3; )
UBE3A		ENSSSCG00000004832	1:149311628-149409522		CU856472,CH242-6D24,1:149309067-149483598 (Clone quality: bE6D24 on chr=1; Num_of_Contigs=1; )
UBE3B		ENSSSCG00000009933	14:41614115-41671338
UBE3C		ENSSSCG00000016409	18:645622-764163
UBE4A		ENSSSCG00000015095	9:44546462-44587222		CU914235,CH242-177G19,9:44486144-44604301 (Clone quality: bE177G19 on chr=9; Num_of_Contigs=2; )
UBE4B		ENSSSCG00000003398	6:47304653-47337410
UBFD1		ENSSSCG00000010796	10:74265-86228		CU929008,CH242-207N16,10:36882-91422 (Clone quality: bE207N16 on chr=10; Num_of_Contigs=6; )
UBIM_PIG		ENSSSCG00000013002	2:5471274-5473282	CU457406,CH242-284K16,2:5352106-5575890 (Clone quality: bE284K16 on chr=2; Num_of_Contigs=20; )
UBIQ_PIG		ENSSSCG00000008403	3:79884471-79887087		CU915675,CH242-7O5,3:79883143-79902708 (Clone quality: bE7O5 on chr=3; Num_of_Contigs=16; )
UBL3		ENSSSCG00000009325	11:6136893-6198799
UBL3		location ⇒	11:5994896-5994017		CU856043,CH242-351N22,11:5973804-6004593 (Clone quality: bE351N22 on chr=11; Num_of_Contigs=7; )
UBL3		location ⇒	11:6135732-6136611		CU469120,CH242-144O22,11:6125526-6179812 (Clone quality: bE144O22 on chr=11; Num_of_Contigs=6; )
UBL5		ENSSSCG00000016886	16:29397538-29397759		CU856099,CH242-229O6,16:29395398-29401618 (Clone quality: bE229O6 on chr=16; Num_of_Contigs=11; )
UBL7		ENSSSCG00000001907	7:64613269-64626634		CU638715,CH242-118M5,7:64531973-64634730 (Clone quality: bE118M5 on chr=7; Num_of_Contigs=2; )
UBLCP1		ENSSSCG00000017042	16:61854613-61876683		CU570833,CH242-250F18,16:61833703-61916627 (Clone quality: bE250F18 on chr=16; Num_of_Contigs=7; )
UBN1		ENSSSCG00000007924	3:33395490-33406823
UBN2		ENSSSCG00000016510	18:8578867-8621308
UBOX5		ENSSSCG00000007162	17:34094978-34133688
UBP		ENSSSCG00000016994	16:49319605-49383853
UBP		ENSSSCG00000013467	2:47393028-47409568		CU972376,CH242-107L7,2:47367584-47461889 (Clone quality: bE107L7 on chr=2; Num_of_Contigs=6; )
UBP		ENSSSCG00000001907	7:64613269-64626634		CU638715,CH242-118M5,7:64531973-64634730 (Clone quality: bE118M5 on chr=7; Num_of_Contigs=2; )
UBP		location ⇒	5:66010992-66010791		CU914454,CH242-45H20,5:66007355-66013978 (Clone quality: bE45H20 on chr=5; Num_of_Contigs=14; )
UBP		location ⇒	5:66011381-66011049		CU914454,CH242-45H20,5:66007355-66013978 (Clone quality: bE45H20 on chr=5; Num_of_Contigs=14; )

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, 1001-33

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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).