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)

TIMP2		location ⇒	12:1917660-1917355	CU942393,CH242-200M2,12:1864056-2044534 (Clone quality: bE200M2 on chr=14; Num_of_Contigs=6; )
TIMP3		ENSSSCG00000000155	5:10406881-10459980
TIMP3		location ⇒	5:10407077-10406957		CU633408,CH242-374H15,5:10378946-10410538 (Clone quality: bE374H15 on chr=5; Num_of_Contigs=8; )
TIMP3		location ⇒	5:10408315-10408192		CU633408,CH242-374H15,5:10378946-10410538 (Clone quality: bE374H15 on chr=5; Num_of_Contigs=8; )
TIMP3		location ⇒	5:10409112-10408998		CU633408,CH242-374H15,5:10378946-10410538 (Clone quality: bE374H15 on chr=5; Num_of_Contigs=8; )
TIMP3		location ⇒	5:10416413-10416330		CU633408,CH242-374H15,5:10410639-10460458 (Clone quality: bE374H15 on chr=5; Num_of_Contigs=8; )
TINAG		ENSSSCG00000001484	7:30938973-30970979
TINAG		location ⇒	7:30812666-30812268		CU633761,CH242-86K3,7:30810399-30844816 (Clone quality: bE86K3 on chr=7; Num_of_Contigs=10; )
TINAG		location ⇒	7:30940168-30939986		CU407337,CH242-195F6,7:30935766-30942660 (Clone quality: bE195F6 on chr=7; Num_of_Contigs=9; )
TINAGL1		ENSSSCG00000003600	6:60374014-60402308
TINF2		ENSSSCG00000001994	7:81397743-81400706		CU019590,CH242-406B17,7:81281809-81421007 (Clone quality: bE406B17 on chr=7; Num_of_Contigs=4; )
TINP1		ENSSSCG00000014075	2:72774741-72782022		CU657963,CH242-277N12,2:72737817-72842780 (Clone quality: bE277N12 on chr=2; Num_of_Contigs=6; )
TIPIN		ENSSSCG00000004942	1:171507081-171523820		CU062652,CH242-108M5,1:171491799-171560282 (Clone quality: bE108M5 on chr=1; Num_of_Contigs=3; )
TIPRL		ENSSSCG00000006301	4:86049538-86082876	CU151849,CH242-198O5,4:85931827-86135389 (Clone quality: bE198O5 on chr=4; Num_of_Contigs=5; )
TIRAP		location ⇒	9:5654387-5654496		CU914666,CH242-341A4,9:5647058-5654652 (Clone quality: bE341A4 on chr=9; Num_of_Contigs=11; )
TIRAP		location ⇒	9:5733246-5733355		FP103078,CH242-97F1,9:5725910-5734266 (Clone quality: bE97F1 on chr=9; Num_of_Contigs=12; )
TIRAP		location ⇒	9:6135088-6135189		FP102867,CH242-179D20,9:6122096-6143981 (Clone quality: bE179D20 on chr=9; Num_of_Contigs=3; )
TIRAP		location ⇒	9:7017105-7017222		CU694608,CH242-349P16,9:7004375-7059805 (Clone quality: bE349P16 on chr=9; Num_of_Contigs=4; )
TITIN		ENSSSCG00000017500	12:20615599-20616848		CU640399,CH242-251F23,12:20578579-20644206 (Clone quality: bE251F23 on chr=12; Num_of_Contigs=5; )
TITIN		ENSSSCG00000015747	15:30805632-30891963
TITIN		ENSSSCG00000014324	2:126969357-126989069
TITIN		ENSSSCG00000010144	14:55841319-55911445
TITIN		ENSSSCG00000003693	6:70794741-70931819
TITIN		ENSSSCG00000016001	15:79179921-79454720
TITIN		location ⇒	15:79222709-79220998		CU929649,CH242-45A12,15:79206661-79247726 (Clone quality: bE45A12 on chr=15; Num_of_Contigs=2; )
TJP1		ENSSSCG00000004854	1:152847711-153065870
TJP2		ENSSSCG00000005247	1:232780879-232925724
TJP3		ENSSSCG00000013491	2:48235098-48258141		FP102497,CH242-307J7,2:48199823-48346436 (Clone quality: bE307J7 on chr=2; Num_of_Contigs=2; )
TKT		ENSSSCG00000006338	4:91510539-91665778
TLCD1		ENSSSCG00000017767	12:42631449-42633236		FP016171,CH242-62B5,12:42618725-42654541 (Clone quality: bE62B5 on chr=12; Num_of_Contigs=5; )
TLE1		ENSSSCG00000005291	1:245347992-245459515
TLE4		ENSSSCG00000005288	1:243320848-243391371
TLK1		ENSSSCG00000015944	15:72347163-72504336
TLL1		ENSSSCG00000008853	8:36835650-36910460
TLL2		ENSSSCG00000010507	14:112915034-112975212
TLN1		ENSSSCG00000005317	1:247508379-247543258		CU062658,CH242-97C14,1:247426659-247546707 (Clone quality: bE97C14 on chr=1; Num_of_Contigs=2; )
TLN1		location ⇒	1:112602179-112602074		CU210863,CH242-150C21,1:112479346-112636130 (Clone quality: bE150C21 on chr=1; Num_of_Contigs=2; )
TLN1		location ⇒	1:247508952-247508380		CU062658,CH242-97C14,1:247426659-247546707 (Clone quality: bE97C14 on chr=1; Num_of_Contigs=2; )
TLN1		location ⇒	1:247509814-247509631		CU062658,CH242-97C14,1:247426659-247546707 (Clone quality: bE97C14 on chr=1; Num_of_Contigs=2; )
TLN1		location ⇒	1:247511697-247511510		CU062658,CH242-97C14,1:247426659-247546707 (Clone quality: bE97C14 on chr=1; Num_of_Contigs=2; )
TLN2		ENSSSCG00000004571	1:112597000-112799014
TLN2		location ⇒	1:112796446-112796346		CU571194,CH242-15J7,1:112743517-112914181 (Clone quality: bE15J7 on chr=1; Num_of_Contigs=1; )
TLN2		location ⇒	1:112799052-112798879		CU571194,CH242-15J7,1:112743517-112914181 (Clone quality: bE15J7 on chr=1; Num_of_Contigs=1; )
TLN2		location ⇒	1:112864106-112864034		CU571194,CH242-15J7,1:112743517-112914181 (Clone quality: bE15J7 on chr=1; Num_of_Contigs=1; )
TLN2		location ⇒	1:113007438-113007531		CU929584,CH242-18J11,1:112996938-113012276 (Clone quality: bE18J11 on chr=1; Num_of_Contigs=22; )
TLR1		location ⇒	8:25568351-25569382		FP089508,CH242-63B6,8:25543927-25603877 (Clone quality: bE63B6 on chr=8; Num_of_Contigs=4; )
TLR1		location ⇒	8:25581307-25583946		FP089508,CH242-63B6,8:25543927-25603877 (Clone quality: bE63B6 on chr=8; Num_of_Contigs=4; )
TLR1		location ⇒	8:25711348-25708709		CU694791,CH242-295G5,8:25655285-25835574 (Clone quality: bE295G5 on chr=8; Num_of_Contigs=1; )
TLR1		location ⇒	8:25724304-25723273		CU694791,CH242-295G5,8:25655285-25835574 (Clone quality: bE295G5 on chr=8; Num_of_Contigs=1; )
TLR10		location ⇒	8:21130-21219		FP102972,CH242-47L5,8:17398-21329 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )

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, 1851-8

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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).