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)

ADORA3		location ⇒	4:113216094-113215744		CU311186,CH242-230C12,4:113204230-113251493 (Clone quality: bE230C12 on chr=4; Num_of_Contigs=3; )
ADORA3		location ⇒	4:113218089-113217982		CU311186,CH242-230C12,4:113204230-113251493 (Clone quality: bE230C12 on chr=4; Num_of_Contigs=3; )
ADORA3		location ⇒	4:113219215-113219129		CU311186,CH242-230C12,4:113204230-113251493 (Clone quality: bE230C12 on chr=4; Num_of_Contigs=3; )
ADPGK		ENSSSCG00000001925	7:66095219-66103744		CU571030,CH242-26L13,7:66088637-66116298 (Clone quality: bE26L13 on chr=7; Num_of_Contigs=6; )
ADPRH		ENSSSCG00000011896	13:105436786-105442965		CU607003,CH242-303J2,13:105344285-105449516 (Clone quality: bE303J2 on chr=13; Num_of_Contigs=5; )
ADPRHL2		ENSSSCG00000003634	6:62562518-62568158		CU929602,CH242-252C17,6:62540199-62574798 (Clone quality: bE252C17 on chr=6; Num_of_Contigs=6; )
ADRA1A		ENSSSCG00000009661	14:10745520-10839033
ADRA1B		ENSSSCG00000017041	16:61219959-61220915		CU914194,CH242-255E15,16:61187296-61298759 (Clone quality: bE255E15 on chr=16; Num_of_Contigs=5; )
ADRA1D		ENSSSCG00000007139	17:33077686-33097029
ADRA2A		ENSSSCG00000010629	14:127073819-127075213		CT737336,CH242-143P15,14:126897173-127111088 (Clone quality: bE143P15 on chr=14; Num_of_Contigs=1; )
ADRA2B		ENSSSCG00000008122	3:41652712-41654052		CU928101,CH242-269H20,3:41644484-41654273 (Clone quality: bE269H20 on chr=3; Num_of_Contigs=12; )
ADRB1		ENSSSCG00000010647	14:130269574-130270926		CT841536,CH242-339B10,14:130269559-130274109 (Clone quality: bE339B10 on chr=14; Num_of_Contigs=4; )
ADRB2		ENSSSCG00000014429	2:135588742-135590782		CU929854,CH242-92K15,2:135551676-135614413 (Clone quality: bE92K15 on chr=2; Num_of_Contigs=6; )
ADRB3		ENSSSCG00000015821	15:45972043-45981483
ADRBK1		ENSSSCG00000012918	2:3611251-3796691
ADRBK1		location ⇒	2:3612222-3612105		CU914251,CH242-230J11,2:3573735-3623266 (Clone quality: bE230J11 on chr=2; Num_of_Contigs=8; )
ADRBK1		location ⇒	2:3614462-3614331		CU914251,CH242-230J11,2:3573735-3623266 (Clone quality: bE230J11 on chr=2; Num_of_Contigs=8; )
ADRBK1		location ⇒	2:3765125-3765256		CU915632,CH242-307O16,2:3762372-3770122 (Clone quality: bE307O16 on chr=2; Num_of_Contigs=9; )
ADRBK1		location ⇒	2:3767365-3767482		CU915632,CH242-307O16,2:3762372-3770122 (Clone quality: bE307O16 on chr=2; Num_of_Contigs=9; )
ADRBK2		ENSSSCG00000009956	14:43833533-43940600
ADSL		ENSSSCG00000000077	5:4296145-4314026		CU639392,CH242-157D22,5:4238817-4335426 (Clone quality: bE157D22 on chr=5; Num_of_Contigs=2; )
ADSS		ENSSSCG00000010874	10:16777935-16831949
AEBP1		ENSSSCG00000016754	18:49589599-49598777		CU928907,CH242-155A21,18:49534481-49598883 (Clone quality: bE155A21 on chr=18; Num_of_Contigs=2; )
AEBP1		location ⇒	18:49590212-49590063		CU928907,CH242-155A21,18:49534481-49598883 (Clone quality: bE155A21 on chr=18; Num_of_Contigs=2; )
AEBP1		location ⇒	18:49591266-49590914		CU928907,CH242-155A21,18:49534481-49598883 (Clone quality: bE155A21 on chr=18; Num_of_Contigs=2; )
AEBP1		location ⇒	18:49591645-49591462		CU928907,CH242-155A21,18:49534481-49598883 (Clone quality: bE155A21 on chr=18; Num_of_Contigs=2; )
AEBP1		location ⇒	18:49591923-49591725		CU928907,CH242-155A21,18:49534481-49598883 (Clone quality: bE155A21 on chr=18; Num_of_Contigs=2; )
AEBP2		ENSSSCG00000000587	5:51378731-51447999
AECC		location ⇒	4:134516023-134515971	CU469041,CH242-483E7,4:134455245-134516471 (Clone quality: bE483E7 on chr=4; Num_of_Contigs=7; )
AECC		location ⇒	4:134520568-134520620	CU694822,CH242-148M17,4:134520092-134552572 (Clone quality: bE148M17 on chr=4; Num_of_Contigs=8; )
AECC		location ⇒	4:134581874-134581304	CU694822,CH242-148M17,4:134577853-134593566 (Clone quality: bE148M17 on chr=4; Num_of_Contigs=8; )
AECC		location ⇒	4:134588283-134588019	CU694822,CH242-148M17,4:134577853-134593566 (Clone quality: bE148M17 on chr=4; Num_of_Contigs=8; )
AEN		ENSSSCG00000005102	1:200299368-200305255		FP017226,CH242-131P7,1:200286939-200334734 (Clone quality: bE131P7 on chr=1; Num_of_Contigs=4; )
AEP		location ⇒	7:122190892-122190339		CU571237,CH242-75O20,7:122153470-122210392 (Clone quality: bE75O20 on chr=7; Num_of_Contigs=3; )
AEP		location ⇒	7:122196682-122196479		CU571237,CH242-75O20,7:122153470-122210392 (Clone quality: bE75O20 on chr=7; Num_of_Contigs=3; )
AEP		location ⇒	7:122284872-122285075		CU467720,CH242-289F13,7:122284825-122291978 (Clone quality: bE289F13 on chr=7; Num_of_Contigs=18; )
AEP		location ⇒	7:122290662-122291215		CU467720,CH242-289F13,7:122284825-122291978 (Clone quality: bE289F13 on chr=7; Num_of_Contigs=18; )
AFAP1		ENSSSCG00000008717	8:3094881-3312198
AFAP1L1		ENSSSCG00000014431	2:135894712-135958962
AFAP1L2		ENSSSCG00000010650	14:130501487-130541758
AFF1		ENSSSCG00000009224	8:113057608-113315476
AFF2		ENSSSCG00000012730	X:119284387-119584694
AFF3		ENSSSCG00000008177	3:49915308-50055739
AFF3		location ⇒	3:122205397-122205296		FP085404,PigI-598C7,3:122174970-122220734 (Clone quality: bI598C7 on chr=3; Num_of_Contigs=4; )
AFF3		location ⇒	3:122430323-122430424		FP102188,PigI-235E4,3:122383878-122439080 (Clone quality: bI235E4 on chr=3; Note=un_improved;)
AFF3		location ⇒	3:122459714-122459613		FP085403,PigI-13B2,3:122451164-122496687 (Clone quality: bI13B2 on chr=3; Note=un_improved;)
AFF3		location ⇒	3:122570383-122570282		CU928912,CH242-223F14,3:122570112-122580956 (Clone quality: bE223F14 on chr=3; Num_of_Contigs=5; )
AFF4		ENSSSCG00000014291	2:123111769-123194106
AFG3L2		ENSSSCG00000002638	6:135785-142399
AFM		ENSSSCG00000008950	8:59081569-59100317		CU606945,CH242-230P13,8:59079400-59136397 (Clone quality: bE230P13 on chr=8; Num_of_Contigs=3; )

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).