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)

CRADD		location ⇒	5:84220508-84220811		CU914474,CH242-208I20,5:84214277-84228332 (Clone quality: bE208I20 on chr=5; Num_of_Contigs=13; )
CRADD		location ⇒	5:84438432-84438238		CU633711,CH242-3G2,5:84418699-84452417 (Clone quality: bE3G2 on chr=5; Num_of_Contigs=4; )
CRADD		location ⇒	5:84438855-84438469		CU633711,CH242-3G2,5:84418699-84452417 (Clone quality: bE3G2 on chr=5; Num_of_Contigs=4; )
CRAMP1L		ENSSSCG00000008026	3:36137562-36164366		CU694571,CH242-220O7,3:36133262-36166327 (Clone quality: bE220O7 on chr=3; Num_of_Contigs=5; )
CRAT		ENSSSCG00000005671	1:284061844-284075655
CRB1		ENSSSCG00000010899	10:21375031-21466030
CRB2		ENSSSCG00000005584	1:278821324-278842440
CRB3		ENSSSCG00000013547	2:49944924-49949715		CU929921,CH242-352E11,2:49929530-49957978 (Clone quality: bE352E11 on chr=2; Num_of_Contigs=12; )
CRBN		ENSSSCG00000011530	13:50309326-50328368
CRCT1		ENSSSCG00000006603	4:100720247-100721514	CU076058,CH242-126J8,4:100634937-100826648 (Clone quality: bE126J8 on chr=4; Num_of_Contigs=7; )
CREB1		ENSSSCG00000016138	15:103667511-103715563
CREB1		location ⇒	15:103667657-103667504		CU928271,CH242-512M8,15:103648115-103683036 (Clone quality: bE512M8 on chr=15; Num_of_Contigs=11; )
CREB1		location ⇒	15:103676979-103676826		CU928271,CH242-512M8,15:103648115-103683036 (Clone quality: bE512M8 on chr=15; Num_of_Contigs=11; )
CREB1		location ⇒	15:103679188-103679006		CU928271,CH242-512M8,15:103648115-103683036 (Clone quality: bE512M8 on chr=15; Num_of_Contigs=11; )
CREB1		location ⇒	15:103715572-103715446		CU928271,CH242-512M8,15:103715242-103720211 (Clone quality: bE512M8 on chr=15; Num_of_Contigs=11; )
CREB3		ENSSSCG00000005318	1:247543400-247548873
CREB3L1		ENSSSCG00000013263	2:14412112-14445749		CU468152,CH242-296I23,2:14412037-14569781 (Clone quality: bE296I23 on chr=2; Num_of_Contigs=2; )
CREB3L2		ENSSSCG00000016520	18:9881888-10007524
CREB3L3		ENSSSCG00000013501	2:48503321-48512828		CU929466,CH242-60A20,2:48498879-48517822 (Clone quality: bE60A20 on chr=2; Num_of_Contigs=5; )
CREB5		ENSSSCG00000016690	18:42269389-42779066
CREBBP		ENSSSCG00000007951	3:34439678-34548590
CREBBP		location ⇒	3:34533501-34533378		FP067388,CH242-65E7,3:34522757-34560903 (Clone quality: bE65E7 on chr=3; Num_of_Contigs=5; )
CREBBP		location ⇒	3:34534304-34534186		FP067388,CH242-65E7,3:34522757-34560903 (Clone quality: bE65E7 on chr=3; Num_of_Contigs=5; )
CREBBP		location ⇒	3:34535536-34535390		FP067388,CH242-65E7,3:34522757-34560903 (Clone quality: bE65E7 on chr=3; Num_of_Contigs=5; )
CREBBP		location ⇒	3:34535905-34535802		FP067388,CH242-65E7,3:34522757-34560903 (Clone quality: bE65E7 on chr=3; Num_of_Contigs=5; )
CREBL1		ENSSSCG00000001430	7:28000405-28011087	CT954269,CH242-404E7,7:27953077-28153182 (Clone quality: bE404E7 on chr=7; Num_of_Contigs=12; )
CREBZF		ENSSSCG00000014907	9:19844512-19845576		CU928672,CH242-451F17,9:19839178-19863160 (Clone quality: bE451F17 on chr=9; Num_of_Contigs=3; )
CREG1		ENSSSCG00000006308	4:86763461-86773439	CU151848,CH242-192N14,4:86700413-86905931 (Clone quality: bE192N14 on chr=4; Num_of_Contigs=2; )
CREG2		ENSSSCG00000008166	3:48582289-48636307		CU463188,CH242-163A11,3:48487582-48648441 (Clone quality: bE163A11 on chr=3; Num_of_Contigs=2; )
CRELD1		ENSSSCG00000011560	13:55382148-55390735		CU464019,CH242-82C2,13:55347452-55391174 (Clone quality: bE82C2 on chr=13; Num_of_Contigs=5; )
CRELD2		ENSSSCG00000000981	5:100015073-100022777		FP102108,CH242-165O15,5:100011427-100040403 (Clone quality: bE165O15 on chr=5; Num_of_Contigs=15; )
CREM		ENSSSCG00000004340	1:66966131-67012861
CREM		ENSSSCG00000011106	10:54799896-54865883
CREM		location ⇒	10:54852756-54852919		CU571035,CH242-280P3,10:54822123-54879331 (Clone quality: bE280P3 on chr=10; Num_of_Contigs=7; )
CREM		location ⇒	10:54861613-54861772		CU571035,CH242-280P3,10:54822123-54879331 (Clone quality: bE280P3 on chr=10; Num_of_Contigs=7; )
CREM		location ⇒	10:54864958-54866123		CU571035,CH242-280P3,10:54822123-54879331 (Clone quality: bE280P3 on chr=10; Num_of_Contigs=7; )
CRF		ENSSSCG00000011043	10:43502285-43508918		CU694240,CH242-232P13,10:43502230-43519179 (Clone quality: bE232P13 on chr=10; Num_of_Contigs=2; )
CRF		ENSSSCG00000006215	4:71073497-71075565		CU550675,CH242-329I16,4:71045167-71242427 (Clone quality: bE329I16 on chr=4; Num_of_Contigs=1; )
CRF		ENSSSCG00000016675	18:40664309-40683406
CRF		ENSSSCG00000014093	2:74714448-74728351		CU928290,CH242-426G6,2:74690550-74761260 (Clone quality: bE426G6 on chr=2; Num_of_Contigs=2; )
CRF		location ⇒	12:16272710-16273017		CU463967,CH242-394M10,12:16272693-16301628 (Clone quality: bE394M10 on chr=12; Num_of_Contigs=5; )
CRF		location ⇒	12:16278803-16278985		CU463967,CH242-394M10,12:16272693-16301628 (Clone quality: bE394M10 on chr=12; Num_of_Contigs=5; )
CRH		ENSSSCG00000016675	18:40664309-40683406
CRH		ENSSSCG00000006215	4:71073497-71075565		CU550675,CH242-329I16,4:71045167-71242427 (Clone quality: bE329I16 on chr=4; Num_of_Contigs=1; )
CRH		ENSSSCG00000014093	2:74714448-74728351		CU928290,CH242-426G6,2:74690550-74761260 (Clone quality: bE426G6 on chr=2; Num_of_Contigs=2; )
CRH		location ⇒	12:15086494-15086651		CU693465,CH242-266I14,12:15085716-15108218 (Clone quality: bE266I14 on chr=12; Num_of_Contigs=9; )
CRH		location ⇒	12:15086938-15086991		CU693465,CH242-266I14,12:15085716-15108218 (Clone quality: bE266I14 on chr=12; Num_of_Contigs=9; )
CRH		location ⇒	12:15270141-15270298		CU929493,CH242-263L7,12:15220972-15314231 (Clone quality: bE263L7 on chr=12; Num_of_Contigs=5; )
CRH		location ⇒	12:15270585-15270638		CU929493,CH242-263L7,12:15220972-15314231 (Clone quality: bE263L7 on chr=12; Num_of_Contigs=5; )
CRHBP		ENSSSCG00000014093	2:74714448-74728351		CU928290,CH242-426G6,2:74690550-74761260 (Clone quality: bE426G6 on chr=2; Num_of_Contigs=2; )

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, 1851-1900, 1901-1950, 1951-2000, 2001-2050, 2051-2100, 2101-2150, 2151-2200, 2201-2250, 2251-2300, 2301-2350, 2351-2400, 2401-2450, 2451-2500, 2501-2550, 2551-2600, 2601-2650, 2651-2700, 2701-2750, 2751-2800, 2801-2850, 2851-2900, 2901-2950, 2951-3000, 3001-3050, 3051-3100, 3101-3150, 3151-3200, 3201-3250, 3251-3300, 3301-3350, 3351-3400, 3401-3450, 3451-3500, 3501-3550, 3551-3600, 3601-3650, 3651-3700, 3701-3750, 3751-3800, 3801-3850, 3851-3900, 3901-12

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).