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)

INDO		location ⇒	17:9681681-9681546		CU927892,CH242-110P10,17:9643188-9702145 (Clone quality: bE110P10 on chr=17; Num_of_Contigs=5; )
ING1		ENSSSCG00000009549	11:77694750-77699940		FP016099,CH242-239C16,11:77694687-77728793 (Clone quality: bE239C16 on chr=11; Num_of_Contigs=7; )
ING2		ENSSSCG00000015778	15:42062262-42068470		CU694719,CH242-351H16,15:42053595-42068991 (Clone quality: bE351H16 on chr=15; Num_of_Contigs=9; )
ING3		ENSSSCG00000016619	18:24106624-24134650	CU463290,CH242-211E24,18:24073727-24213322 (Clone quality: bE211E24 on chr=18; Num_of_Contigs=1; )
ING4		ENSSSCG00000000701	5:60144356-60148069
INHBA		ENSSSCG00000016764	18:51533803-51544277
INHBA		location ⇒	12:12201958-12201873		CU606903,CH242-358O17,12:12168415-12217906 (Clone quality: bE358O17 on chr=12; Num_of_Contigs=4; )
INHBA		location ⇒	12:4068644-4068713	CU928968,CH242-19M24,12:4017937-4068721 (Clone quality: bE19M24 on chr=12; Num_of_Contigs=4; )
INHBA		location ⇒	12:817558-817663		CU993801,CH242-26A11,12:808758-830529 (Clone quality: bE26A11 on chr=12; Num_of_Contigs=7; )
INHBA		location ⇒	12:87488-87581	FP085448,CH242-272C22,12:58856-90407 (Clone quality: bE272C22 on chr=12; Num_of_Contigs=8; )
INHBE		ENSSSCG00000000442	5:21842774-21844324		FP016095,CH242-213I11,5:21833344-21844996 (Clone quality: bE213I11 on chr=5; Num_of_Contigs=19; )
INMT		ENSSSCG00000016676	18:40717885-40722614
INO80		ENSSSCG00000004756	1:136862404-136866322		CU571034,CH242-27B2,1:136862277-136867311 (Clone quality: bE27B2 on chr=1; Num_of_Contigs=24; )
INO80C		ENSSSCG00000003742	6:82878331-82887917		FP245424,CH242-81K21,6:82875697-82888942 (Clone quality: bE81K21 on chr=6; Num_of_Contigs=4; )
INO80D		ENSSSCG00000016125	15:102084002-102124382
iNOS		ENSSSCG00000017755	12:42108512-42147251
iNOS		location ⇒	12:42128677-42128574		CU972495,CH242-385A7,12:42119149-42130490 (Clone quality: bE385A7 on chr=12; Num_of_Contigs=10; )
iNOS		location ⇒	12:42128942-42128767		CU972495,CH242-385A7,12:42119149-42130490 (Clone quality: bE385A7 on chr=12; Num_of_Contigs=10; )
iNOS		location ⇒	12:42130411-42130267		CU972495,CH242-385A7,12:42119149-42130490 (Clone quality: bE385A7 on chr=12; Num_of_Contigs=10; )
iNOS		location ⇒	12:42130759-42130616		CU972495,CH242-385A7,12:42130591-42147954 (Clone quality: bE385A7 on chr=12; Num_of_Contigs=10; )
INPP1		ENSSSCG00000016050	15:89551458-89581886
INPP4A		ENSSSCG00000008190	3:51305267-51352304
INPP4B		ENSSSCG00000009050	8:73247726-73520856
INPP5A		ENSSSCG00000010765	14:147411997-147574963
INPP5B		ENSSSCG00000003642	6:63462372-63519857	CR956649,PigE-92E11,6:63451761-63579213 (No clone quality info on bT92E11)
INPP5D		ENSSSCG00000016298	15:126094735-126191031
INPP5D		location ⇒	15:125958539-125958430		CU928130,CH242-481I23,15:125954436-125963411 (Clone quality: bE481I23 on chr=15; Num_of_Contigs=18; )
INPP5D		location ⇒	15:125960248-125960107		CU928130,CH242-481I23,15:125954436-125963411 (Clone quality: bE481I23 on chr=15; Num_of_Contigs=18; )
INPP5D		location ⇒	15:126111316-126111200		FP102656,CH242-26J3,15:126092166-126115941 (Clone quality: bE26J3 on chr=15; Num_of_Contigs=12; )
INPP5D		location ⇒	15:126122471-126122330		FP102656,CH242-26J3,15:126116042-126125764 (Clone quality: bE26J3 on chr=15; Num_of_Contigs=12; )
INPP5F		ENSSSCG00000010687	14:135561993-135653575
INPPL1		ENSSSCG00000014811	9:6293214-6303491		FP090889,CH242-166B16,9:6292210-6303906 (Clone quality: bE166B16 on chr=9; Num_of_Contigs=3; )
INS		ENSSSCG00000009567	11:79213291-79288711
INS		ENSSSCG00000008076	3:37680437-37715420		FP016002,CH242-245P15,3:37670882-37732166 (Clone quality: bE245P15 on chr=3; Num_of_Contigs=9; )
INS		ENSSSCG00000002457	7:122500435-122566510		CU468886,CH242-145B2,7:122436020-122571421 (Clone quality: bE145B2 on chr=7; Num_of_Contigs=2; )
INS		ENSSSCG00000000739	5:63124994-63138294
INSC		ENSSSCG00000013385	2:41061542-41156784
INSIG1		ENSSSCG00000016420	18:2106766-2225274
INSL3		ENSSSCG00000013887	2:62079012-62080810		CU928970,CH242-349K2,2:62018597-62084904 (Clone quality: bE349K2 on chr=2; Num_of_Contigs=3; )
INSL6		ENSSSCG00000005214	1:226745292-226745558		CU302244,CH242-254J19,1:226615674-226772700 (Clone quality: bE254J19 on chr=1; Num_of_Contigs=1; )
INSM1		ENSSSCG00000007106	17:29318401-29319528		CU302380,CH242-225D21,17:29318400-29361881 (Clone quality: bE225D21 on chr=17; Num_of_Contigs=3; )
INSM2		ENSSSCG00000001949	7:70359878-70361274
INSR		ENSSSCG00000013560	2:50473534-50476068		CU986279,CH242-45E14,2:50473212-50490770 (Clone quality: bE45E14 on chr=2; Num_of_Contigs=23; )
INSRR		ENSSSCG00000006465	4:96937361-96950761		CU151867,CH242-283E3,4:96858244-96970867 (Clone quality: bE283E3 on chr=4; Num_of_Contigs=3; )
INTS1		ENSSSCG00000007558	3:731686-757759
INTS10		ENSSSCG00000007004	17:8429754-8474503
INTS2		ENSSSCG00000017673	12:34572633-34602671		CU929908,CH242-288F7,12:34563929-34620377 (Clone quality: bE288F7 on chr=12; Num_of_Contigs=8; )
INTS3		ENSSSCG00000006571	4:100048786-100088155
INTS4		ENSSSCG00000014884	9:12197361-12276302
INTS6		ENSSSCG00000009384	11:16445682-16535071

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, 1101-33

Report problems to zhu

iastate.edu

$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).