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:
(1) Reference genome view: Assembly v.9 with BACs/QTL/SNPs aligned in GBrowse:
http://www.animalgenome.org/cgi-bin/gbrowse/pig/;
(2) Information for user setups to use Otterlace
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: |
|
|
|
| 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 |
|
| 1700028N11Rikb |
|
location ⇒ |
6:33557577-33557617 |
|
FP102369,CH242-128M4,6:33522006-33560344
(Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
|
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).
