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)

C5A		ENSSSCG00000003113	6:36871363-36872376		FP102420,CH242-118A10,6:36863968-36881618 (Clone quality: bE118A10 on chr=6; Num_of_Contigs=13; )
C5A		ENSSSCG00000005512	1:274568890-274654777
C5A		ENSSSCG00000009947	14:42651169-42652260		CU468889,CH242-242A7,14:42643147-42658415 (Clone quality: bE242A7 on chr=14; Num_of_Contigs=11; )
C5A		ENSSSCG00000013106	2:9254314-9255531		CU861565,CH242-480L10,2:9238313-9266378 (Clone quality: bE480L10 on chr=2; Num_of_Contigs=15; )
C5AR1		location ⇒	6:36929199-36928781		FP102420,CH242-118A10,6:36926859-36929245 (Clone quality: bE118A10 on chr=6; Num_of_Contigs=13; )
C5orf13		ENSSSCG00000014210	2:106598575-106603964		CU695210,CH242-273C5,2:106579550-106633457 (Clone quality: bE273C5 on chr=2; Num_of_Contigs=10; )
C5orf15		ENSSSCG00000014295	2:124085846-124097499		CU928302,CH242-266O13,2:124032962-124185534 (Clone quality: bE266O13 on chr=2; Num_of_Contigs=2; )
C5orf20		location ⇒	2:20274-20339		CU928976,CH242-144M19,2:1-32533 (Clone quality: bE144M19 on chr=2; Num_of_Contigs=17; )
C5orf20		location ⇒	2:20337-20272		CU928976,CH242-144M19,2:1-32533 (Clone quality: bE144M19 on chr=2; Num_of_Contigs=17; )
C5orf20		location ⇒	2:28411-28532		CU928976,CH242-144M19,2:1-32533 (Clone quality: bE144M19 on chr=2; Num_of_Contigs=17; )
C5orf20		location ⇒	2:47015-46922		CU928976,CH242-144M19,2:43742-170991 (Clone quality: bE144M19 on chr=2; Num_of_Contigs=17; )
C5orf22		ENSSSCG00000016808	16:15635095-15654277
C5orf25		ENSSSCG00000014062	2:70734020-70778550
C5orf28		ENSSSCG00000016875	16:25337570-25337932		CU655933,CH242-366J11,16:25334116-25338459 (Clone quality: bE366J11 on chr=16; Num_of_Contigs=13; )
C5orf32		ENSSSCG00000014361	2:128973298-129017574
C5orf33		ENSSSCG00000016836	16:18914228-18962392	CU856110,CH242-36H10,16:18824515-19007053 (Clone quality: bE36H10 on chr=16; Num_of_Contigs=2; )
C5orf34		ENSSSCG00000016876	16:25369752-25390146		CU655933,CH242-366J11,16:25369404-25390362 (Clone quality: bE366J11 on chr=16; Num_of_Contigs=13; )
C5orf35		ENSSSCG00000016919	16:33565683-33572586	CU407158,CH242-211N24,16:33443912-33621708 (Clone quality: bE211N24 on chr=16; Num_of_Contigs=7; )
C5orf36		ENSSSCG00000014160	2:90313341-90399942
C5orf37		ENSSSCG00000014084	2:73546194-73586812		CU466984,CH242-83I14,2:73524244-73593212 (Clone quality: bE83I14 on chr=2; Num_of_Contigs=10; )
C5orf39		ENSSSCG00000016868	16:24952491-24953030		FP089569,CH242-86B7,16:24948452-24954570 (Clone quality: bE86B7 on chr=16; Num_of_Contigs=10; )
C5orf4		ENSSSCG00000017068	16:65710816-65746524
C5orf40		ENSSSCG00000017055	16:63593789-63594487		CU896613,CH242-137H14,16:63575816-63634355 (Clone quality: bE137H14 on chr=16; Num_of_Contigs=5; )
C5orf42		ENSSSCG00000016843	16:19887888-19945642
C5orf43		ENSSSCG00000016935	16:38049853-38050077		CU571116,CH242-207L19,16:38019238-38186472 (Clone quality: bE207L19 on chr=16; Num_of_Contigs=2; )
C5orf45		ENSSSCG00000014015	2:68079198-68101333	CU639394,CH242-198P20,2:67907486-68117033 (Clone quality: bE198P20 on chr=2; Num_of_Contigs=3; )
C5orf46		ENSSSCG00000014421	2:134749745-134759273
C5orf47		ENSSSCG00000016980	16:47677171-47678862		FP085449,CH242-277G7,16:47652819-47685190 (Clone quality: bE277G7 on chr=16; Num_of_Contigs=6; )
C5orf48		ENSSSCG00000014245	2:117321341-117325667		CU929657,CH242-507N1,2:117296080-117327134 (Clone quality: bE507N1 on chr=2; Num_of_Contigs=11; )
C5orf49		ENSSSCG00000017098	16:71406220-71420611
C5orf51		ENSSSCG00000016864	16:24044751-24061445
C5orf52		ENSSSCG00000010014	14:48349175-48354755
C5orf53		ENSSSCG00000014360	2:128952333-128952491		CU693462,CH242-200N5,2:128937308-128956225 (Clone quality: bE200N5 on chr=2; Num_of_Contigs=6; )
C5orf58		ENSSSCG00000017007	16:51033553-51038891		CU915300,CH242-100L14,16:51005846-51108426 (Clone quality: bE100L14 on chr=16; Num_of_Contigs=2; )
C6		ENSSSCG00000007095	17:27462320-27479733		CU914246,CH242-1M4,17:27449366-27480603 (Clone quality: bE1M4 on chr=17; Num_of_Contigs=3; )
C6		ENSSSCG00000002044	7:82568725-82569811		CT737318,CH242-17H24,7:82408265-82613937 (Clone quality: bE17H24 on chr=7; Num_of_Contigs=1; )
C6		ENSSSCG00000012813	X:123482741-123535969	CU861979,CH242-305A15,X:123389549-123544360 (Clone quality: bE305A15 on chr=X; Num_of_Contigs=11; )
C6		ENSSSCG00000016861	16:23348601-23399764
C6		location ⇒	16:23271859-23272103		CU861949,CH242-227N6,16:23265633-23315280 (Clone quality: bE227N6 on chr=16; Num_of_Contigs=5; )
C6		location ⇒	16:23277742-23278266		CU861949,CH242-227N6,16:23265633-23315280 (Clone quality: bE227N6 on chr=16; Num_of_Contigs=5; )
C6		location ⇒	16:23356775-23356548		CU570701,CH242-122M17,16:23345596-23357862 (Clone quality: bE122M17 on chr=16; Num_of_Contigs=9; )
C6		location ⇒	16:23370227-23369981		CU570701,CH242-122M17,16:23357963-23390983 (Clone quality: bE122M17 on chr=16; Num_of_Contigs=9; )
C6orf103		ENSSSCG00000004115	1:19778619-19805498
C6orf105		ENSSSCG00000001048	7:8528123-8587765		CU467708,CH242-246M4,7:8526918-8626401 (Clone quality: bE246M4 on chr=7; Num_of_Contigs=2; )
C6orf106		ENSSSCG00000001527	7:34872608-35055423
C6orf115		ENSSSCG00000004145	1:26766962-26782312		CU076042,CH242-113G19,1:26758824-26810704 (Clone quality: bE113G19 on chr=1; Num_of_Contigs=6; )
C6orf118		ENSSSCG00000004028	1:4194028-4211691		CU074299,CH242-142F6,1:4143602-4241828 (Clone quality: bE142F6 on chr=1; Num_of_Contigs=2; )
C6orf120		ENSSSCG00000004007	1:390645-391199		CU582832,CH242-136I21,1:370231-438180 (Clone quality: bE136I21 on chr=1; Num_of_Contigs=15; )
C6orf125		ENSSSCG00000001519	7:34309712-34337481	CU481857,CH242-122A6,7:34237512-34415946 (Clone quality: bE122A6 on chr=7; Num_of_Contigs=5; )
C6orf126		ENSSSCG00000001551	7:36226581-36228645		CT868716,CH242-516I1,7:36091251-36290487 (Clone quality: bE516I1 on chr=7; Num_of_Contigs=1; )

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).