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Table 1 Characteristics of 22 confirmed read-throughs in RCC

From: Functional characterization of BC039389-GATM and KLK4-KRSP1 chimeric read-through transcripts which are up-regulated in renal cell cancer

Read-through Type Transcript isoforms Exon junction Exclusion terminal/initial exons Modification/Introduction exon Retention intergenic sequence GT-AG splice site Supporting EST Coding consequence TaqMan
MIA2-CTAGE5 classical 1 M6middle-C4   x   y N 1 x
WRB-SH3BGR classical 2 W4-S3 x    y Y 1 x
W4-S3 (S6-7 out) x    y   1 x
FAM175A-HELQ classical 1 F8-H3 x    y Y 1 x
TCEA NC-RAB9A classical 2 T4-R2 x    y N 2 x
T4-R2 x    y   2 x
FXYD2-DSCAML1 classical 5 F3e-D2 x    y N 2 x
(F3c out) F3e-D2 x    y N 2 x
F3e-D2 (D2 intra-spliced)   x   y N 2 x
(F3c out) F3e-D2 (D2 intra-spliced)   x   y N 2 x
F3e-intergenic seq-D2    x n N 2 x
SLC12A4-LCAT classical 1 S26middle-L2   x   y N 2  
CD81-TSSC4 classical 1 C8middle-T1   x   y N 2  
VAMP8-VAMP5 classical 3 V3middle-V2   x   n Y 2 x
(V3 intra-spliced) V3middle-V2   x   n Y 1 x
V3middle2-V2   x   n Y 2 x
STX16-NPEPL1 classical 4 S8-N2a (N3 out) x    y Y 1 x
S8-intergenic ex on 2-N2a (N3 out)   x   y Y 3; fsX42  
S8-intergenic ex ons 1,2-N2b (N3 out)   x   y Y 3; fsX92  
S8-N2b (N3 out) x    y Y 3; fsX42  
TMED6-COG8 * classical 3 T1-C2 x    y Y 3; fsX17 x
T2-C2 x    y Y 3; fsX4 x
T3-C2 x    y Y 3; fsX17  
TMEM27-ACE2 classical 4 T5-A2 x    y N 3; fsX9  
T5-A2middle   x   y N 3; fsX16  
T4-A2 x    y N 3; fsX9  
T4-A2middle   x   y N 3; fsX16  
METTL21B-TSFM classical 1 M2-T2 (T5 out) x    y Y 3; fsX105  
GLYCTK-DNAH1 classical 3 (G2 out) G3-D1middle   x   y N 3; fsX14  
G3-intergenic seq-D1middle(D1c in)   x x y N 3; fsX1  
G3-D1middle   x   y N 3; fsX14  
AKO97351-SLC6A 16 classical 5 A1-S2 x    y N 3; fsX23  
A2-S2 x    y N 3; fsX22  
A3middle-S2   x   y N 2  
A1-S8 x    y N 3; fsX7  
A1-S9 x    y N 3; fsX2  
KLK4-KRSP1 not classical 5 KKv1 K3-K4 x    y Y 4; fsX56 x
KKv2 K5middle-K4   x   n Y 4; fsX3 x
KKv3 K5middle2-K4   x   y Y 4; fsX56  
KKv4 K1-K4 x    y Y 4; fsX56  
KKv5 K1-K3 x    y Y 4; fsX72  
BC039389-GA TM not classical 2 BGv1 B3-G2 x    n Y 4 x
BGv2 B3-G3 x    y Y 4 x
AK311380-MVB12A not classical 2 A2-M2 x    y Y 4  
(A1 intra-spliced) A2-M2 x    y Y 4  
BC041984-TMEM135 not classical 1 B2-T2 x    y N 4  
RNPEP-ELF3 not classical 1 Ri6middlie-E1middle   x   y Y 5 x
ACSM2A-AX747287 extended 3′ UTR 2 A 15-intergenic seq-A    x   N 2 x
A 15middle-Amiddle   x   n N 2  
TAGLN-AK126420 extended 3′ UTR 1 T5-intergenic seq-A    x   Y 2 x
STXBP5-BC043173 extended 3′ UTR 1 S 28-intergenic seq-B    x   y 2 x
TOTAL: 22   51   27 (53%) 20 (39%) 5 (10%)     
  1. Read-throughs are sorted in three types: classical, if the parent genes’ structure and ORF are well defined; non-classical, if at least one parent gene is incompletely defined non-coding RNA or pseudogene or the read-through being an antisense transcript; extended 3′UTR, if the 3′ parent likely represents a longer 3′UTR sequence to complement the 5′ parent with. The number of isoforms per read-through is given in the third column, together with the names of KLK4-KRSP1 and BC039389-GATM isoforms specifically featured in this publication (labeled red). The exon junction is given between 5′ parent and 3′ parent gene according to their NCBI entries and hg19 assembly, as exemplified with WRB-SH3BGR: WRB exon 4 (W4) is spliced to SH3BGR exon 3 (S3). A second isoform with same exon junction exists where SH3BGR exons 6 and 7 are spliced out (S6-7 out). Some exons were shortened at previously unknown positions (termed middle, or middle2 if different positions were used) before they were connected to the other parent gene. Some exons were spliced to lose a short part of the sequence inside the exon (intra-spliced). Some isoforms retained the entire or partial intergenic sequence (seq) between the parent genes or spliced elements of it (exons). An exon junction with intronic sequence is indicated as “i” (for example, Ri6middle = shortened intron 6 of RNPEP)). The second to last column shows the coding consequence of the exon junction further described in Table 2. The last column “TaqMan” indicates the isoforms that were targeted in the expression screening depicted in Figure 1C. *TMED6-COG8 has been identified as part of this study but evaluated in detail elsewhere [30].