This short talk introduces ProtAnnot, a tool for visualizing effects of alternative splicing on protein and gene function using a genome browser.

1. ProtAnnot - visualizing
effects
of
alterna2ve
splicing
and
transcrip2on
on
protein
sequence
and
func2on
in
a
genome
browser
An Integrated Genome Browser
plug-in App
available from BioViz.org
Ann Loraine, UNC Charlotte
North Carolina Research Campus, Kannapolis

2. Download
BioViz
.org

3. Click
to
open
Arabidopsis
Click
to
open
Arabidopsis
genome

4. Araport
and
TAIR
10
gene
models
available
datasets

5. Zoomed-­‐in
view
SR45a
-­‐
splicing
regulator
alternaBve
splicing
5'UTR
3'UTR
Full-­‐length

6. Open
App
Manager
click
to
install

7. ProtAnnot
installed
Filled
circles
are
installed
Apps

8. Select
gene
models

9. Select
Tools
>
Start
ProtAnnot

10. ProtAnnot
window
opens
exon
summary
change
in
height
signals
alterna2vely
spliced
region
5'
UTR
in
black
3'
UTR
in
black
coding
exons
colored
by
frame

11. Select
ProtAnnot
>
Run
InterproScan

12. Select
InterPro
signature
databases
• HMMSmart
-­‐
domains
• SignalPHMM
-­‐
signal
pep2des
• TMM-­‐HMM
-­‐
membrane
• or
others...
select
Run
enter
email

13. Search
is
running…in
background
Can
keep
using
ProtAnnot
and
IGB
while
search
runs
separate
from
GUI
event
loop.

14. Search
finished,
results
added
Can
click
links
to
see
Interpro
XML-­‐format
results
hosted
for
a
short
2me
on
EBI
Web
site

15. Click
domain
to
select
it
Click
link
to
visit
Web
page
for
RRM
domain
Both
variants
contain
RNA-­‐binding
domain
Exon-­‐included
form
lacks
RS
repeat
region
–
splicing
ac2va2on,
PP
interac2on
RS
repeat
region

16. mutant
fused
stems
abnormal
floral
structures
ragged
cauline
leaves
Expression
and
rela2ve
abundance
of
splice
variants
disrupted.
Allele
is
dominant.
SR45a
dominant
negaBve

17. Live
Demo:
Wed,
Jan.
13
12:15
-­‐
12:30
PM
Nowlan
Freese