supporting online material - regulation of splicing factors by...
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Supporting online material - Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible
sp
ecie
sg
en
eg
en
om
e s
ou
rce
locu
srep
resen
tati
ve
gen
e m
od
el o
r m
RN
A
alt
sp
licin
g?
intr
on
rete
nti
on
?
up
str
eam
jun
cti
on
ES
Ts
do
wn
str
eam
jun
cti
on
ES
Ts
exo
n
skip
ped
ES
Ts
up
str
eam
jun
cti
on
intr
on
rete
nti
on
do
wn
str
eam
jun
cti
on
intr
on
rete
nti
on
full in
tro
n
rete
nti
on
early
po
lyA
H. sap
ien
sSR
SF5
UC
SC h
g19
chr1
4:70
2338
34-7
0238
721
NM
_006
925
yy
205
5287
685
0
M. m
uscu
lus
SRSF
5U
CSC
mm
9ch
r12:
8204
6491
-820
5149
4N
M_0
0915
9y
y2
156
4533
40
R. n
org
evic
us
SRSF
5U
CSC
rn4
chr6
:104
7282
76-1
0473
2985
NM
_019
257
yy
111
3556
271
0
C. fa
milia
ris
SRSF
5U
CSC
can
Fam
2ch
r8:4
6549
512-
4655
4334
ENSC
AFT0
0000
0262
76y
00
54
20
0
G. g
allu
sSR
SF5
UC
SC g
alG
al3
chr5
:301
6379
6-30
1684
33N
M_0
0103
1197
yy
10
514
31
0
SRSF
5aU
CSC
gal
Gal
3ch
r5:3
0595
571-
3061
2641
NM
_001
0064
76y
y1
022
37
00
X. tr
op
icalis
SRSF
5U
CSC
xen
Tro2
scaf
fold
_246
:146
3821
-146
7713
NM
_001
0047
83y
y71
4028
712
985
01
krt5
.1U
CSC
xen
Tro2
scaf
fold
_145
:676
974-
6899
26N
M_0
0100
5638
yy
10
301
20
0
F. ru
brip
es
SRSF
5bU
CSC
fr2
chrU
n:16
6973
539-
1669
7638
8EN
STR
UT0
0000
0458
080
01
00
00
SRSF
5aU
CSC
fr2
chrU
n:27
0261
895-
2702
6547
8EN
STR
UT0
0000
0272
050
00
00
00
D. rerio
SRSF
5bU
CSC
dan
Rer
5ch
r20:
3862
2161
-386
3698
8N
M_0
0100
2610
yy
51
1810
30
1
SRSF
5aU
CSC
dan
Rer
5ch
r13:
3824
6638
-382
5147
5N
M_2
0086
7y
y11
417
643
91
0
SR A
UC
SC b
raFl
o1 /
JGI v
1.0
chrU
n: 2
5461
5939
-254
6243
58ES
T cl
uste
r 260
1579
:13
y1
1?76
10
00
SR B
UC
SC b
raFl
o1 /
JGI v
1.0
chrU
n:30
9654
001-
3096
5717
4es
tExt
_fge
nesh
2_pg
.C_9
2002
7
SR C
UC
SC b
raFl
o1 /
JGI v
1.0
chrU
n: 2
5482
6591
-254
8350
12es
tExt
_fge
nesh
2_pm
.C_6
9001
4y
11?
761
00
0
S. p
urp
uratu
sSR
CU
CSC
strP
ur2
Scaf
fold
8089
2:72
4-98
31C
X551
350,
CX5
5765
1y
11
260
10
0
D. m
ela
no
gaste
rB5
2U
CSC
dm
3ch
r3R
:948
7022
-949
2613
NM
_176
488
yy
107
829
21
0
C. ele
gan
srs
p-1
UC
SC c
e6ch
rII:1
1453
896-
1145
5723
NM
_064
041
yy
20
101
30
0
rsp-
2U
CSC
ce6
chrII
:114
5136
0-11
4528
71N
M_0
6404
0y
00
151
11
0
N.v
ecte
nsis
NV
1JG
I v1.
0sc
affo
ld_1
1:47
2975
-477
003
estE
xt_f
gene
sh1_
pg.C
_110
055
y3
418
00
00
NV
2JG
I v1.
0sc
affo
ld_1
03:5
6740
5-57
0642
2667
685_
5y
11
521
00
0
NV
3JG
I v1.
0sc
affo
ld_3
18:1
4436
5-14
8353
estE
xt_f
gene
sh1_
pg.C
_318
0016
y0
011
01
00
NV
4JG
I v1.
0sc
affo
ld_1
3:13
3190
1-13
3473
3es
tExt
_fge
nesh
1_pg
.C_1
3016
9y
y3
10
02
00
NV
5JG
I v1.
0sc
affo
ld_3
79:9
4033
-945
96es
tExt
_fge
nesh
1_pg
.C_3
7900
06
NV
6JG
I v1.
0sc
affo
ld_9
3:61
4755
-619
479
estE
xt_f
gene
sh1_
pg.C
_930
062
yy
32
200
10
0
N. crassa
NC
U07
069
Entre
z G
ene
NW
_001
8497
96.1
:c26
7293
-265
451
XM_9
5524
1y
A. n
iger
An16
g038
90En
trez
Gen
eN
T_16
6531
.1:c
8741
59-8
7192
2XM
_001
3976
63y
S. p
om
be
srp2
Entre
z G
ene
NC
_003
424.
3:c4
4269
65-4
4252
50N
M_0
0101
9999
Tabl
e S1
– S
RSF
5 or
thol
ogs i
nclu
ded
in a
naly
sis. C
ount
s of E
STs a
nd m
RNA
s sho
win
g al
tern
ativ
e sp
licin
g ar
e no
ted
in th
e la
st co
lum
ns
(incl
udin
g pa
rtial
evi
denc
e of
intro
n re
tent
ion,
such
as E
STs e
xten
ding
into
the
intro
n). W
e as
signe
d te
mpo
rary
nam
es to
gen
es in
C. i
ntes
tinal
is,
B. fl
orid
ae, S
. pur
pura
tus,
and
N. v
ecte
nsis
befo
re p
hylo
gene
tic c
lass
ifica
tion
-
sp
ecie
sg
en
eg
en
om
e
so
urce
locu
srep
resen
tati
ve
gen
e m
od
el o
r m
RN
A
alt
sp
licin
g?
intr
on
rete
nti
on
?
sp
licin
g in
2n
d in
tro
n -
up
str
eam
jun
cti
on
ES
Ts
sp
licin
g in
2n
d in
tro
n -
do
wn
str
eam
jun
cti
on
ES
Ts
sp
licin
g in
2n
d in
tro
n -
exo
n
skip
ped
ES
Ts
sp
licin
g in
2n
d
intr
on
-
up
str
eam
jun
cti
on
in
tro
n
rete
nti
on
sp
licin
g in
2n
d
intr
on
-
do
wn
str
eam
jun
cti
on
in
tro
n
rete
nti
on
sp
licin
g in
2n
d in
tro
n -
full in
tro
n
rete
nti
on
early
po
lyA
sp
licin
g in
1st
intr
on
-
up
str
eam
jun
cti
on
ES
Ts
sp
licin
g in
1st
intr
on
-
do
wn
str
eam
jun
cti
on
ES
Ts
sp
licin
g in
1st
intr
on
-
exo
n
skip
ped
ES
Ts
sp
licin
g in
1st
intr
on
-
up
str
eam
jun
cti
on
in
tro
n
rete
nti
on
sp
licin
g in
1st
intr
on
-
do
wn
str
eam
jun
cti
on
in
tro
n
rete
nti
on
sp
licin
g in
1st
intr
on
-
full in
tro
n
rete
nti
on
early
po
lyA
H. sap
ien
sS
RS
F4
UC
SC
hg19
chr1
:29474251-2
9508637
NM
_005626
y (
i1, i2
)y (
i2)
43
157
47
10
68
159
00
01
SR
SF
6U
CS
C h
g19
chr2
0:4
2086504-4
2092242
NM
_006275
yy
58
6132
10
90
0
M. m
uscu
lus
SR
SF
4U
CS
C m
m9
chr4
:131429554-1
31457640
NM
_020587
y (
i1)
y (
i1)
00
00
00
03
835
00
00
SR
SF
6U
CS
C m
m9
chr2
:162757244-1
62762854
NM
_026499
yy
219
94
319
10
R. n
org
evic
us
SR
SF
4U
CS
C r
n4
chr5
:150731169-1
50758938
NM
_001108685
y (
i1)
00
00
00
01
13
00
00
SR
SF
6U
CS
C r
n4
chr3
:153795474-1
53800796
NM
_001014185
yy
13
23
014
00
C. fa
milia
ris
SR
SF
4U
CS
C c
anF
am
2chr2
:74298034-7
4323762
BU
751463, D
N425514 (
gap in 1
st in
tron)
00
00
00
0
SR
SF
6U
CS
C c
anF
am
2chr2
4:3
4189662-3
4192538
EN
SC
AF
T00000014759, D
N355700
yy
11
20
10
0
G. g
allu
sS
RS
F4
UC
SC
galG
al3
chr2
3:3
043852-3
048526
BX
936077, B
X931065
00
00
00
0
SR
SF
6U
CS
C g
alG
al3
chr2
0:6
9285-7
4296
NM
_001030843 (
gap in intr
on)
yy
03
13
03
00
X. tr
op
icalis
SR
SF
4U
CS
C x
enT
ro2
scaffold
_492:4
34541-4
41727
CX
803859
y (
i2)
y (
i2)
01
93
10
10
SR
SF
6U
CS
C x
enT
ro2
scaffold
_38:8
05274-8
14512
NM
_001001248
yy
613
72
30
70
0
F. ru
brip
es
SR
SF
4U
CS
C fr2
chrU
n:1
39894565-1
39897692
EN
ST
RU
T00000030178
SR
SF
6U
CS
C fr2
chrU
n:3
55227627-3
55231373
EN
ST
RU
T00000007652
y0
10
00
00
D. rerio
SR
SF
4U
CS
C d
anR
er5
chr1
9:2
3988960-2
3998507
NM
_199574
y (
i2)
00
84
11
30
1
SR
SF
6a
UC
SC
danR
er5
chr2
3:3
858771-3
870268
NM
_213466
00
70
30
0
SR
SF
6b
UC
SC
danR
er5
chr1
1:3
91396-4
00063
NM
_001008732
yy
12
11
43
00
C. in
testi
nalis
SR
AU
CS
C c
i2chr0
1q:6
846290-6
849708
AK
116209
y*
SR
BU
CS
C c
i2chr0
1q:6
888465-6
893171
BW
305692, B
W324472
y*
SR
CU
CS
C c
i2chr0
2q:6
965692-6
967083
AK
114189
SR
DU
CS
C c
i2chr0
5q:4
307321-4
308319
ES
Ts (
unspliced in O
RF
)
SR
EU
CS
C c
i2chr0
5q:4
319181-4
321175
AK
112385
Tabl
e S2
– S
RSF
4 an
d SR
SF6
orth
olog
s inc
lude
d in
ana
lysi
s. A
s in
tabl
e S1
. “i1
” in
dica
tes a
ltern
ativ
e sp
licin
g or
intro
n re
tent
ion
in th
e fir
st in
tron
of S
RSF
4 or
thol
ogs,
and
“i2”
indi
cate
s the
seco
nd in
tron.
All
alte
rnat
ive
splic
ing
even
ts in
SR
SF6
are
in th
e se
cond
intro
n, a
nd
first
-intro
n al
tern
ativ
e sp
licin
g in
SR
SF4
was
onl
y ob
serv
ed in
hum
an, m
ouse
, and
rat,
so m
any
cells
are
not
app
licab
le a
nd a
re le
ft em
pty.
A
ltern
ativ
e sp
licin
g in
C. i
ntes
tinal
is S
R A
and
B w
as n
ot h
omol
ogou
s to
alte
rnat
ive
splic
ing
in o
ther
spec
ies.
-
anemone 5
S. pombe srp2
N. crassa srp2
A. niger srp2
anemone 6
anemone 4
fly b52
lancelet b
sea squirt c
worm rsp1
worm rsp2
lancelet c
lancelet a
urchin c
fugu srsf4
zebrafish srsf4
frog srsf6
dog srsf6
rat srsf6
mouse srsf6
human srsf6
chicken srsf6
zebrafish srsf6a
fugu srsf6
zebrafish srsf6b
frog srsf4
chicken srsf4
rat srsf4
dog srsf4
human srsf4
mouse srsf4
sea squirt b
sea squirt a
sea squirt d
sea squirt e
chicken srsf5a
frog krt5.1
zebrafish srsf5a
fugu srsf5a
zebrafish srsf5b
fugu srsf5b
dog srsf5
rat srsf5
human srsf5
mouse srsf5
frog srsf5
chicken srsf5
anemone 3
anemone 2
anemone 1
At 31
81
4
1
332
3
1
47
39 73
22
32
63
69
68
95
4
1
0
0
0
100
100
96
88
34
98
23
95
95
92
31
5442
7184
87
87
70
7163
28
anem
one
5
S. p
ombe
srp
2
N. c
rass
a sr
p2A
. nig
er s
rp2
anem
one
6an
emon
e 4
fly b
52
lanc
elet
b
sea
squi
rt c
wor
m rs
p1w
orm
rsp2
lanc
elet
cla
ncel
et a
urch
in c
fugu
srs
f4ze
braf
ish
srsf
4
frog
srs
f4
dog
srsf
4ra
t srs
f4m
ouse
srs
f4hu
man
srs
f4
chic
ken
srsf
4
zebr
afis
h sr
sf4a
fugu
srs
f4ze
braf
ish
srsf
4b
frog
srs
f4ch
icke
n sr
sf4
rat s
rsf4
dog
srsf
4
hum
an s
rsf4
mou
se s
rsf4
sea
squi
rt b
sea
squi
rt a
sea
squi
rt d
sea
squi
rt e
chic
ken
srsf
5afr
og k
rt5.
1ze
braf
ish
srsf
5afu
gu s
rsf5
a
zebr
afis
h sr
sf5b
fugu
srs
f5b
dog
srsf
5ra
t srs
f5
hum
an s
rsf5
mou
se s
rsf5
frog
srs
f5ch
icke
n sr
sf5
anem
one
3an
emon
e 2
anem
one
1
A B
Figure S1 – A. Maximum likelihood tree of all animal and fungi SRSF4/5/6 genes, with bootstrap values. Vertebrate SRSF4/6 (blue) and SRSF5 (green) orthologs are grouped. Red indicates genes with no introns. B. Alignment of all SRSF4/5/6 protein sequences indicating exon positions. Colors denote exons. Sequences were trimmed after the second RRM domain before alignment. Black bars indicate the positions of alternative exons in human SRSF4, SRSF5, and SRSF6.
-
human
mouse
rat
chicken(SRSF5)
chicken(SRSF5)
frog(SRSF5)
zebrafish(SRSF5b)
zebrafish(SRSF5a)
lancelet(A)
urchin(C)
fly
worm(rsp-1)
anemone(1)
3 4
18
20 5
52
87 68
2 1
56
45 33
11 1
35
56 27
1
5
14 3
1
22
3 7
11 4
176
43 9
1 1
76
1
1 1
26
1
10 7
83
9 2
2
10
1
AAA
5 1
18
10 31
71 40
287
85AAA1129
Figure S2 – Transcript evidence for alternative splicing of SRSF5. Alternative regions of each gene are shown with the upstream and downstream constitutive exons in blue and alternative exon in orange (to scale). Counts of ESTs and mRNAs showing alternative splicing are noted (including partial evidence of intron retention, such as ESTs extending into the intron) and splice junction lines are scaled to this count.
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