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)

CCDC135		ENSSSCG00000002817	6:20022778-20034724		CU467555,CH242-299M23,6:20022123-20035456 (Clone quality: bE299M23 on chr=6; Num_of_Contigs=20; )
CCDC136		ENSSSCG00000016579	18:18019674-18050395
CCDC138		ENSSSCG00000008135	3:42743805-42792929
CCDC141		ENSSSCG00000016002	15:79539873-79672587
CCDC142		ENSSSCG00000008279	3:63106355-63118650
CCDC146		ENSSSCG00000015412	9:95683152-95711811		CU595290,CH242-102O8,9:95662713-95713618 (Clone quality: bE102O8 on chr=9; Num_of_Contigs=11; )
CCDC147		ENSSSCG00000010614	14:120414318-120436593
CCDC148		ENSSSCG00000015876	15:60708315-60871986
CCDC15		ENSSSCG00000015206	9:50604910-50673207
CCDC150		ENSSSCG00000016071	15:94383376-94407408
CCDC151		ENSSSCG00000013626	2:52389052-52397517		CU855518,CH242-272A5,2:52374247-52417356 (Clone quality: bE272A5 on chr=2; Num_of_Contigs=10; )
CCDC152		ENSSSCG00000016867	16:24824416-24890984		CU972496,CH242-40I2,16:24766459-24926535 (Clone quality: bE40I2 on chr=16; Num_of_Contigs=1; )
CCDC153		ENSSSCG00000015109	9:44888680-45024114
CCDC155		ENSSSCG00000003172	6:38042735-38066751
CCDC157		ENSSSCG00000010003	14:48150445-48158791		CT956025,CH242-69C12,14:48142322-48239134 (Clone quality: bE69C12 on chr=14; Num_of_Contigs=15; )
CCDC158		ENSSSCG00000008983	8:61425051-61541461
CCDC159		ENSSSCG00000013621	2:52301019-52308092
CCDC160		ENSSSCG00000012681	X:108268025-108268990	FP015951,CH242-54G11,X:108183838-108371118 (Clone quality: bE54G11 on chr=X; Num_of_Contigs=1; )
CCDC163P		ENSSSCG00000003916	6:118790362-118794033		CU442720,CH242-94F19,6:118759178-118889484 (Clone quality: bE94F19 on chr=6; Num_of_Contigs=3; )
CCDC18		ENSSSCG00000006897	4:128224549-128320897
CCDC19		ENSSSCG00000006394	4:93902473-93922607		CU856127,CH242-86L20,4:93898168-93927205 (Clone quality: bE86L20 on chr=4; Num_of_Contigs=6; )
CCDC22		ENSSSCG00000012297	X:42740625-42759236		FP067430,CH242-266D21,X:42733839-42767607 (Clone quality: bE266D21 on chr=X; Num_of_Contigs=12; )
CCDC23		ENSSSCG00000006772	4:112022351-112022551		CU463248,CH242-400P6,4:112002441-112085502 (Clone quality: bE400P6 on chr=4; Num_of_Contigs=4; )
CCDC25		ENSSSCG00000009669	14:11514449-11523936		CU656007,CH242-32D13,14:11512232-11583414 (Clone quality: bE32D13 on chr=14; Num_of_Contigs=2; )
CCDC28A		ENSSSCG00000004148	1:26978663-26995104		CU633664,CH242-223F5,1:26965246-27006535 (Clone quality: bE223F5 on chr=1; Num_of_Contigs=6; )
CCDC28A		location ⇒	1:26979367-26978805		CU633664,CH242-223F5,1:26965246-27006535 (Clone quality: bE223F5 on chr=1; Num_of_Contigs=6; )
CCDC28A		location ⇒	1:26985745-26985590		CU633664,CH242-223F5,1:26965246-27006535 (Clone quality: bE223F5 on chr=1; Num_of_Contigs=6; )
CCDC28A		location ⇒	1:26990861-26990695		CU633664,CH242-223F5,1:26965246-27006535 (Clone quality: bE223F5 on chr=1; Num_of_Contigs=6; )
CCDC28A		location ⇒	1:26992794-26992587		CU633664,CH242-223F5,1:26965246-27006535 (Clone quality: bE223F5 on chr=1; Num_of_Contigs=6; )
CCDC28B		ENSSSCG00000003618	6:60933562-61020268
CCDC3		ENSSSCG00000011110	10:56028725-56115898
CCDC30		ENSSSCG00000003965	6:120956915-121039983
CCDC33		ENSSSCG00000001908	7:64681680-64712933	CT797479,CH242-196N13,7:64639731-64852331 (Clone quality: bE196N13 on chr=7; Num_of_Contigs=2; )
CCDC34		ENSSSCG00000013336	2:31019014-31056128	CU466955,CH242-220A17,2:30959779-31177028 (Clone quality: bE220A17 on chr=2; Num_of_Contigs=6; )
CCDC36		ENSSSCG00000011376	13:26707792-26741224		CU856115,CH242-45E6,13:26688217-26742695 (Clone quality: bE45E6 on chr=13; Num_of_Contigs=7; )
CCDC37		ENSSSCG00000001826	7:59256149-59285824		CU571146,CH242-69O5,7:59247143-59315417 (Clone quality: bE69O5 on chr=7; Num_of_Contigs=5; )
CCDC38		ENSSSCG00000000894	5:82616816-82631628
CCDC39		ENSSSCG00000011768	13:90272182-90327141
CCDC40		ENSSSCG00000017158	12:1452610-1493415	CU464073,CH242-396G1,12:1427255-1662757 (Clone quality: bE396G1 on chr=3; Num_of_Contigs=9; )
CCDC42		ENSSSCG00000017988	12:50885065-50899353
CCDC42B		ENSSSCG00000009875	14:38997324-39004361
CCDC46		ENSSSCG00000017266	12:10478921-10636923
CCDC50		ENSSSCG00000011817	13:96875924-96941480
CCDC51		ENSSSCG00000011350	13:26066164-26076189
CCDC54		ENSSSCG00000014200	2:104527850-104528173		CU972447,CH242-66J20,2:104518479-104533746 (Clone quality: bE66J20 on chr=2; Num_of_Contigs=7; )
CCDC55		ENSSSCG00000017795	12:44150212-44217911
CCDC56		ENSSSCG00000017388	12:17663493-17664611		CU928483,CH242-17I6,12:17641484-17682744 (Clone quality: bE17I6 on chr=12; Num_of_Contigs=8; )
CCDC58		location ⇒	9:10816748-10817173		CU694783,CH242-251G19,9:10816040-10904306 (Clone quality: bE251G19 on chr=9; Num_of_Contigs=8; )
CCDC58		location ⇒	9:10817202-10817377		CU694783,CH242-251G19,9:10816040-10904306 (Clone quality: bE251G19 on chr=9; Num_of_Contigs=8; )
CCDC59		ENSSSCG00000000942	5:95521452-95526833		FP103100,CH242-512N7,5:95516384-95534712 (Clone quality: bE512N7 on chr=5; Num_of_Contigs=7; )

Go to records:
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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).