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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].
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BMC Genomics

ISSN: 1471-2164

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