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. 2018 Aug 3;7:1189. [Version 1] doi: 10.12688/f1000research.15604.1

Table 1. Details of the 73 androgen regulated mRNA isoforms identified in prostate cancer cells.

Isoform 1 Isoform 2 TCGA PRAD
Gene Event type Position (hg19) RefSeq Position (hg19) RefSeq Change with
androgens		 PCR
Validation		 Predicted
to change
protein?		 Isoform 1 ID Isoform 2 ID Comparable?
LIG4 Alternative
promoter 		chr13:108859792-
108870716 		NM_001098268.1 chr13:108859792-
108867130 		NM_002312.3 Induction of
promoter 2		 Yes (Qiaxel) No (5'
UTR)		 uc001vqp.2 uc001vqn.2 Yes
TACC2 Alternative
promoter 		chr10:123748689-
124014060 		NM_206862.3 chr10:123872554-
124014060 		NM_001291879.1 Repression of promoter 1 Yes (Qiaxel) Yes uc001lfv.2 uc001lfx.2 Yes
TPD52 Alternative
promoter 		chr8:80947103-
81083894 		NM_001287144.1 chr8:80947103-
80993066 		NM_001025252.2 Induction of
promoter 2		 Yes (Qiaxel) Yes uc003ybs.1 uc003ybr.1 Yes
NUP93 Alternative
promoter 		chr16:56764017-
56878861 		NM_014669.4 chr16:56815704-
56878861 		NM_001242795.1 Induction of
promoter 1		 Yes (SYBR) Yes uc002eka.2 uc002ekb.2 Yes
RLN1 Alternative
promoter 		chr9:5334932-
5339873 		NM_006911.3 chr9:5335270-
5339396 		Not annotated Repression of
promoter 2 		Yes (Qiaxel) Yes
(change
from non-
coding)		 uc003zjb.1 Not
annotated 		No
AP2S1 Alternative
promoter 		chr19:47341415-
47354252 		NM_001301078.1 chr19:47341415-
47353547 		NM_001301076.1 Induction of
promoter 2		 Yes (SYBR) Yes uc002pft.1 Not
annotated 		No
RLN2 Alternative
promoter 		chr9:5299866-
5304611 		NM_005059.3 chr9:5299890-
5304222 		Not annotated Induction of
promoter 1		 Yes (Qiaxel) Yes
(change
from non-
coding)		 uc003ziz.1 Not
annotated 		No
PIK3R1 Alternative
promoter 		chr5:67511584-
67597649 		NM_181523.2 chr5:67584252-
67597649 		NM_181524.1 Repression of
promoter 2 		Yes (SYBR) Yes uc003jva.2 uc003jvc.2 Yes
MAPRE2 Alternative
promoter 		chr18:32556892-
32723432 		NM_001143826.2 chr18:32621324-
32723432 		NM_014268.3 Switch to
promoter 2		 Yes (Qiaxel) Yes uc010xcb.1 uc002kyf.2 Yes
NDUFAF4 Alternative
promoter 		chr6:97337187-
97345767 		NM_014165.3 chr6:97337227-
97345368 		Not annotated Repression of
promoter 2 		Yes (Qiaxel) Yes
(change
from non-
coding)		 uc003pov.2 Not
annotated 		No
DCXR Alternative
promoter 		chr17:79993757-
79995573 		NM_016286.3 chr17:79993765-
79995217 		Not annotated Repression of
promoter 2 		Yes (Qiaxel) Yes uc002kdg.2 Not
annotated 		No
PEX10 Alternative
promoter 		chr1:2336241-
2344010 		NM_002617.3 Not annotated Switch to
promoter 2		 Yes (Qiaxel) Yes uc001ajh.2 Not
annotated 		No
SNAPC2 Alternative
promoter 		chr19:7985194-
7988136 		NM_003083.3 chr19:7985867-
7988136 		NR_030717.1 Switch to
promoter 2		 Yes (SYBR) Yes
(change
to non-
coding)		 uc002miw.1 uc002mix.1 Yes
ATP6V0D1 Alternative
promoter 		chr16:67471917-
67515089 		NM_004691.4 chr16:67471931-
67475338 		Not annotated Repression of
promoter 2 		Yes uc002ete.1 Not
annotated 		No
ARRDC1 Alternative
promoter 		chr9:140500092-
140509812 		NM_001317968.1 chr9:140506874-
140509793 		Not annotated Induction of
promoter 2		 Yes
(change
to non-
coding)		 uc004cnp.1 Not
annotated 		No
DENND1A Alternative
promoter 		chr9:126141933-
126692417 		NM_020946.1 chr9:126143408-
126586780 		Not annotated Repression of
promoter 2 		Yes uc004bnz.1 Not
annotated 		No
KLHL36 Alternative
promoter 		chr16:84682117-
84701292 		NM_024731.3 chr16:84684274-
84701134 		Not annotated Induction of
promoter 2		 Yes uc002fig.2 Not
annotated 		No
RAB3IL1 Alternative
promoter 		chr11:61664768-
61687741 		NM_001271686.1 chr11:61664768-
61685081 		NM_013401.3 Repression of
promoter 2 		Yes uc001nsp.2 uc001nso.2 Yes
ACER3 Alternative
promoter 		chr11:76571917-
76737841 		NM_018367.6 chr11:76631206-
76737818 		Not annotated Repression of
promoter 2 		Yes uc009yum.1 Not
annotated 		No
OSBPL1A Alternative
promoter 		chr18:21742011-
21977833 		NM_080597.3 chr18:21742011-
21852196 		NM_018030.4 Induction of
promoter 2		 Yes uc002kve.2 uc002kvd.2 Yes
TRIM16 Alternative
promoter 		chr17:15531280-
15586193 		NM_006470.3 chr17:15530970-
15555735 		Not annotated Induction of
promoter 2		 Yes uc002gow.2 Not
annotated 		No
VSIG10L Alternative
promoter 		chr19:51834795-
51845378 		NM_001163922.1 chr19:51834795-
51843009 		Not annotated Induction of
promoter 1		 Yes uc002pwf.2 Not
annotated 		No
SEPT5 Alternative
promoter 		chr22:19701987-
19710845 		NM_002688.5 chr22:19705958-
19710845 		NM_001009939.2 Repression of
promoter 2 		Yes uc002zpv.1 uc002zpw.1 Yes
HMGCR Alternative
promoter 		chr5:74632154-
74657926 		NM_000859 chr5:74632993-
74657926 		NM_000859.2 Repression of
promoter 1 		Yes uc011cst.1 uc003kdp.2 Yes
RDH13 Alternative
promoter 		chr19:55555692-
55580914 		NM_138412.3 chr19:55555692-
55574585 		NM_001145971.1 Induction of
promoter 1		 Yes uc002qip.2 uc010esr.1 Yes
GPRIN2 Alternative
promoter 		chr10:46993001-
47000677 		Not annotated chr10:46993546-
47000568 		NM_014696.3 Repression of
promoter 2 		No (5' UTR) Not annotated uc001jec.2 No
CLK3 Alternative
promoter 		chr15:74900713-
74922542 		NM_003992.4 chr15:74,908,246-
74,922,542 		NM_003992 Repression of
promoter 1 		Yes uc002ayg.3 uc002ayj.3 Yes
RNH1 Alternative
promoter 		chr11:494512-
507283 		NM_203387.2 chr11:494512-
506821 		NM_002939.3 Induction of
promoter 1		 No (5' UTR) uc001lpp.1 uc001lpl.1 Yes
ZFAND6 Alternative
promoter 		chr15:80351910-
80430735 		NM_001242911.1 chr15:80364903-
80430735 		NM_001242916.1 Repression of
promoter 2 		No (5' UTR) uc002bff.1 uc002bfh.1 Yes
CDIP1 Alternative
promoter 		chr16:4560677-
4588816 		NM_013399.2 chr16:4560677-
4588471 		NM_001199054.1 Repression of
promoter 2 		No (5' UTR) uc002cwu.2 uc002cwv.2 Yes
YIF1B Alternative
promoter 		chr19:38794200-
38806606 		NM_001039672.2 chr19:38794200-
38806445 		NM_001145461.1 Switch to
promoter 2		 Yes uc002ohz.2 uc002ohx.2 Yes
LIMK2 Alternative
promoter 		chr22:31608250-
31676066 		NM_005569.3 chr22:31644348-
31676066 		NM_016733.2 Switch to
promoter 2		 Yes uc003akh.2 uc003aki.2 Yes
TSC22D3 Alternative
promoter 		chrX:106956452-
106959711 		NM_001015881.1 chrX:106956452-
106960291 		NM_004089.3 Repression of
promoter 1 		Yes uc004enf.2 uc004eng.2 Yes
ALDH1A3 Alternative
promoter 		chr15:101419897-
101456830 		NM_000693.3 chr15:101438281-
101457072 		Not annotated Repression of
promoter 1 		Yes uc002bwn.3 Not
annotated 		No
TRABD Alternative
promoter 		chr22:50624341-
50638028 		NM_001320485.1 chr22:50628979-
50638028 		NM_001320487.1 Switch to
promoter 2		 No (5' UTR) uc003bjq.1 uc003bjs.1 Yes
LIMCH1 Alternative
promoter 		chr4:41361624-
41702061 		NM_001289124.1 chr4:41362648-
41702061 		NM_001289122.2 Repression of
promoter 2 		Yes uc003gvu.3 Not
annotated 		No
GMFB Alternative
promoter 		chr14:54941209-
54955744 		NM_004124.2 chr14:54941314-
54955637 		Not annotated Induction of
promoter 2		 Yes
(change
to non-
coding)		 uc010tqz.1 Not
annotated 		No
MLST8 Alternative
promoter 		chr16:2255178-
2259418 		NM_022372.4 chr16:2255732-
2259418 		NM_001199174.1 Switch to
promoter 1		 No (5' UTR) uc010uvy.1 uc002cpf.2 Yes
TLE3 Alternative
promoter 		chr15:70340130-
70390256 		NM_020908.2 chr15:70340130-
70387124 		NM_001282982.1 Induction of
promoter 2		 Yes uc002asn.2 uc002ask.2 Yes
UBA1 Alternative
promoter 		chrX:47050199-
47074527 		NM_153280.2 chrX:47053201-
47074527 		NM_003334.3 Repression of
promoter 1 		No (5' UTR) uc004dhj.3 uc004dhk.3 Yes
TNRC6B Alternative
promoter 		chr22:40440821-
40731812 		NM_001024843.1 chr22:40573929-
40731812 		NM_001162501.1 Repression of
promoter 2 		Yes uc003aym.2 uc011aor.1 Yes
FDFT1 Alternative
promoter 		chr8:11660120-
11696818 		NM_004462.4 chr8:11665926-
11696818 		NM_001287750.1 Repression of
promoter 2 		Yes uc003wui.2 uc010lsb.2 Yes
GREB1 Alternative
promoter 		chr2:11674242-
11782912 		NM_014668.3 chr2:11680080-
11728355 		NM_148903.2 Induction of
promoter 2		 Yes uc002rbo.1 uc002rbl.2 Yes
NCAPD3 Alternative
promoter 		chr11:134022337-
134094426 		NM_015261.2 chr11:134022772-
134093593 		Not annotated Induction of
promoter 2		 Yes uc001qhd.1 Not
annotated 		No
SLC36A4 Alternative
promoter 		chr11:92877337-
92931141 		NM_152313.3 chr11:92877337-
92930621 		NM_001286139.1 Induction of
promoter 2		 Yes uc001pdn.2 Not
annotated 		No
KLC2 Alternative
promoter 		chr11:66024765-
66035331 		NM_001134775.1 chr11:66025174-
66035331 		NM_022822.2 Repression of
promoter 1 		No (5' UTR) uc010rov.1 uc001ohb.2 Yes
RAP1GAP Alternative
promoter 		chr1:21922708-
21978348 		NM_001145658.1 chr1:21922533-
21946950 		Not annotated Repression of
promoter 1 		Yes uc001bez.1 Not
annotated 		No
TMEM79 Alternative
promoter 		chr1:156252704-
156262234 		NR_026678.1 chr1:156254070-
156262234 		NM_032323.2 Repression of
promoter 1 		No (5' UTR) uc001fod.2 uc010phi.1 Yes
NR4A1 Alternative
promoter 		chr12:52416616-
52453291 		NM_001202233.1 chr12:52445186-
52453291 		NM_173157.2 Induction of
promoter 2		 Yes uc010sno.1 uc001rzr.2 Yes
ZNF32 Alternative
promoter 		chr10:44139307-
44144326 		NM_001324166.1 chr10:44139307-
44144326 		NM_001324167.1 Repression of
promoter 2 		No (5' UTR) uc001jbc.2 uc001jbb.2 Yes
C1QTNF3 Alternative
promoter 		chr5:34017963-
34043371 		NM_181435.5 chr5:34018571-
34035881 		Not annotated Induction of
promoter 1		 Yes uc003jio.2 Not
annotated 		No
UBE2D3 Alternative
promoter 		chr4:103715540-
103748710 		NM_181887.2 chr4:103715540-
103749105 		NM_181886.3 Switch to
promoter 2		 No (5' UTR) uc003hwk.2 uc011cet.1 Yes
KRT8 Alternative
promoter 		chr12:53290971-
53343650 		NM_001256293.1 chr12:53,290,971-
53,298,868 		NM_002273 Repression of
promoter 1 		No (5' UTR) uc009zml.1 uc001sbd.2 Yes
ELOVL1 Alternative
promoter 		chr1:43829068-
43833745 		NM_022821.3 chr1:43829093-
43832057 		Not annotated Induction of
promoter 2		 Yes
(change
to non-
coding)		 uc001cjb.2 Not
annotated 		No
RCAN1 Alternative
promoter 		chr21:35888740-
35987441 		NM_004414.6 chr21:35888740-
35899308 		NM_203418.2 Induction of
promoter 2		 Yes uc002yue.2 uc002yub.2 Yes
SORBS3 Alternative
promoter 		chr8:22409251-
22433008 		NM_005775.4 chr8:22422332-
22433100 		Not annotated Induction of
promoter 2		 Yes uc003xbv.2 Not
annotated 		No
MAT2A Alternative
3' end 		chr2:85766101-
85772403 		NM_005911.5 chr2:85,766,101-
85,770,775 		NM_005911 Repression of
isoform 2 		Yes (Qiaxel) Yes uc002spr.2 uc010ysr.1 Yes
CNNM2 Alternative
3' end 		chr10:104678075-
104687375 		NM_199077.2 chr10:104678075-
104838344 		NM_017649.4 Induction of
isoform 1		 Yes (SYBR) Yes uc001kwl.2 uc001kwm.2 Yes
TMEM125 Alternative
3' end 		chr1:43735698-
43736343 		Not annotated chr1:43735665-
43739673 		NM_144626.2 Induction of
isoform 1		 Yes
(change
to non-
coding)		 Not
annotated 		uc001cir.2 No
CBWD2 Alternative
3' end 		chr2:114195268-
114253781 		NM_172003.3 chr2:114195169-
114199073 		Not annotated Induction of
isoform 2		 Yes uc002tju.2 Not
annotated 		No
NDUFV3 Alternative
exon 		chr21:44313378-
44329773 		NM_021075.3 chr21:44313378-
44329773 		NM_001001503.1 Switch to isoform 2 (exon
excluded)		 Yes uc002zcm.2 uc002zcn.2 Yes
ZNF678 Alternative
exon 		chr1:227751220-
227850164 		NM_178549.3 Not annotated Switch to isoform 2 (exon
excluded)		 Yes
(change
to non-
coding)		 uc009xet.1 Not
annotated 		No
ZNF121 Alternative
exon 		chr19:9676404-
9695209 		NM_001308269.1 chr19:9676404-
9695209 		NM_001008727.3 Switch to isoform 2 (exon
excluded)		 Yes uc010xkq.1 uc010xkp.1 Yes
SPATC1L Alternative
exon 		chr21:47581062-
47604373 		NM_032261.4 Not annotated Induction of isoform 2 (exon
included)		 Yes uc002zii.2 Not
annotated 		No
MOCOS Alternative
exon 		chr18:33767480-
33848685 		NM_017947.2 Not annotated Switch to isoform 2 (exon
excluded)		 Yes uc002kzq.3 Not
annotated 		No
RBM45 Alternative
exon 		chr2:178977151-
178994382 		NM_152945.3 Not annotated Switch to isoform 2 (exon
included)		 Yes uc002ulv.2 Not
annotated 		No
MIPEP Alternative
exon 		chr13:24304328-
24463587 		NM_005932.3 Not annotated Repression of isoform 2 (exon
excluded)		 Yes uc001uox.3 Not
annotated 		No
BBS4 Alternative
exon 		chr15:72978520-
73030817 		NM_001320665.1 Not annotated Induction of isoform 2 (exon
included)		 Yes uc002avb.2 Not
annotated 		No
FAM195A Alternative
exon 		chr16:691804-
698474 		NM_138418.3 chr16:691804-
698474 		NR_138607.1 Switch to isoform 1 (exon
exluded)		 Yes
(change
from non-
coding)		 uc002cic.1 uc002cie.2 Yes
LINC01133 Alternative
exon 		chr1:159931008-
159948851 		ENST00000443364.6 chr1:159931014-
159948876 		NR_038849.1 Induction of isoform 1 (exon
excluded)		 Both non-coding Not
annotated 		uc001fuu.2 No
SS18 Alternative
exon 		chr18:23596217-
23670611 		NM_001007559.2 chr18:23596217-
23670611 		NM_005637.3 Switch to isoform 2 (exon
excluded)		 Yes uc002kvm.2 uc002kvn.2 Yes
RHOC Alternative
exon 		chr1:113243897-
113249757 		ENST00000369638.6 chr1:113243947-
113249742 		ENST00000369636.6 Switch to isoform 2 (exon
excluded)		 No (5' UTR) uc009wgk.1 uc001ecr.1 Yes
ZNF226 Retained
intron 		chr19:44669215-
44681838 		NM_001319088.1 chr19:44669249-
44679582 		NM_015919.3 Switch to isoform 1 (intron
included)		 Yes uc002oyo.2 uc002oyn.2 Yes