Skip to main content

Table 1 A summary of the 40 observed exceptions

From: Intronization, de-intronization and intron sliding are rare in Cryptococcus

  

Non-

Alternative

JEC21/alt boundary

  
 

Int

conserved

In Frame

Presence/Absence

Frame

 

Gene

#

Boundary

Boundaries

JEC21

H99

R265

WM276

shift

Comments

Conserved alternative boundary

CNA00590

1

5'

-6 (GTGAGT)

+/+

+/+

-/+

-/+

Yes

cDNA supporting alternative boundary

CNA03150

3

3'

-9 (CAG)

+/+

-/+

-/+

-/+

Yes

 

CNC00370

9

5'

+3 (GTGAGT)

+/+

-/+

-/+

-/+

Yes

cDNA supporting intron ret.

CNC01260

8

3'

+6 (TAG)

+/+

+/+

-/+

-/+

Yes

cDNA supporting alt boundary, intron ret.

CND02500

1

3'

+6 (TAG)

+/+

+/+

-/+

-/+

Yes

cDNA supporting out-of-frame boundary

CND03170

8

5'

+6 (GTAAGT)

+/+

+/+

-/+

+/+

Yes

 

CND03550

1

3'

+6 (CAG)

+/+

-/+

+/+

+/+

Yes

Fig 2A

CND03880

7

3'

-3 (CAG)

+/+

+/+

-/+

-/+

Yes

 

CND04350

1

3'

+9 (C/TAG)

+/+

-/+

-/+

-/+

Yes

 

CNE00380

3

3'

+3 (C/AAG)

+/+

-/+

-/+

-/+

No

cDNA supporting alternative boundary

CNE01370

3

3'

+9 (CAG)

+/+

+/+

+/+

-/+

Yes

 

CNF02810

9

3'

+9 (C/TAG)

+/+

+/+

-/+

-/+

Yes

 

CNH03260

8

3'

+6 (TAG)

+/+

-/+

-/+

-/+

Yes

 

CNK01580

2

3'

+6 (C/TAG)

+/+

+/+

-/+

-/+

No

cDNAs supporting alternative boundary

Non-conserved alternative boundaries

CNA01650

1

3'

-3 (TAG)

+/-

-/+

-/+

-/+

Yes

 

CNB04950

6

5'

+3 (GTTCAC)

+/-

+/-

-/+

-/+

No

 

CNC04760

1

3'

+3 (TAG)

+/-

+/-

+/+

-/+

Yes

Fig 2B

CND00770

1

3'

-3 (CAG)

+/-

+/-

+/-

-/+

Yes

 

CNH03490

7

3'

-12 (CAG)

+/-

+/-

-/+

-/+

Yes

 

CNI02860

6

5'

+3 (GTTCAT)

+/-

+/-

+/-

-/+

Yes

 

CNK00690

2

3'

+6 (CAG)

+/+

-/+

+/-

+/+

Yes

 

CNL04670

4

3'

+9 (C/TAG)

+/-

+/+

-/+

-/+

Yes

 

CNL06040

1

3'

-3 (GAG)

+/-

+/-

+/+

-/+

Yes

 

CNM02250

2

3'

-9 (AAG)

+/-

+/-

-/+

-/+

No

 

Intronization/de-intronization

CND01950

3

3'

No

+/

-/

-/

-/

No

Intronization Fig 3B (1/0 cDNAs spliced/unspliced)

CNF02770

6

Both

No

+/

-/

-/

-/

No

Intronization Fig 3E (1/7 cDNAs spliced/unspliced)

CNG00990

3

Both

No

+/

-/

-/

-/

No

Intronization Fig 3A (1/4 cDNAs spliced/unspliced)

CNL03830

4

3'

No

+/

-/

-/

-/

No

Intronization Fig 3D (1/7 cDNAs spliced/unspliced)

CNI02050

4

Both

No

+/

-/

-/

-/

No

Intronization Fig 3C (2/4 cDNAs spliced/unspliced)

CNL04380

1

3'

No

+/

+/

-/

-/

Yes

Direction unclear Fig 4A (1/0 cDNAs spliced/unspliced)

CND00470

1

5'

No

+/

-/

-/

+/

No

Convergent Fig 4B (2/0 cDNAs spliced/unspliced)

More complex cases

CNB05120

2

5'

No

+/

+/

-/

+/

Yes

Unclear (53 bp)

CNF04220

1

Both

No

+/

+/

-/

-/

Yes

Unclear (58 bp)

CNI04240

1

3'

No

+/

-/

+/

+/

Yes

Unclear (64 bp)

CNJ02980

2

5'

No

+/

+/

-/

-/

Yes

Unclear (52/53 bp)

CNK02560

2

3'

No

+/

-/

-/

-/

Yes

Unclear (136/137/143 bp)

CNK02690

2

3'

No

+/

+/

-/

-/

Yes

Unclear (57/58 bp)

CNL06330

4

3'

No

+/

-/

+/

+/

Yes

Unclear (62 bp)

CNM00170

5

Both

No

+/

-/

-/

-/

Yes

Unclear (Fig 4C), unspliced cDNA (61/64 bp)

CNN00940

2

3'

No

+/

-/

+/

+/

Yes

Unclear (84 bp, inframe stop)