Table 1 Summary of FST determination. Lines in italics indicate absence of valid FST

#2.1

3

2

16

304054-303727

Cre16.g649785/Cre16.g649752

no predicted function/ no predicted function

intergenic

not applicable

9

unsure, PCR failed

2

19

810984-811036

Cre19.g757350

NAC domain protein

3' UTR

+

8

A 37 nt fragment of the PCR product is inserted between the active cassette and the flanking DNA; poly-A site not recorded before for the host gene

unsure, PCR failed

#2.2

2

1

1

8429714-8432270 (spliced)

Cre01.g060850

PSBS3, Chloroplast PSII-associated 22 kDa protein

exon 3; FST extends up to exon 10, with splicing

+

0

expression of interrupted gene is not documented by 454 or Illumina data

confirmed

#2.3

2

1

12

589974-589850

Cre12.g488050

FFT5, Fructan fructosyltransferase

intron 2

-

0

confirmed

#2.4

1

1

14

3326333-3326254

Cre14.g630200

no predicted function

3' UTR

+

0

not the endogenous poly-A site; part of the FST is hidden below an early poly-A tail

unsure, PCR failed

#2.5

3

2

12

3269654-3269776 and divergent 3268980-3269003

Cre12.g512250

protein with HRDC domain

intron 4

+

0

two staggered polyadenylation sites

not tested

#2.6

1

1

?

?

?

transposable elements TOC1 and DNA-2-7_CR

not applicable

not applicable

0

UNMAPPED: could be in an unsequenced region, or due to a rearrangement

not tested

#2.7

2

0

-

FAILED: amplifies a sequence from Cre10.g429850 exon 7 but the junction with the cassette cannot be read

not tested

#2.8

1

1

27

75383-75179

Cre27.g774700

SGNH hydrolase

5'-UTR

+

?

poly-A tail at end of cassette masks junction with flanking DNA

confirmed

#2.9

1

1

9

2341565-2341083

Cre09.g400950

Major Facilitator Superfamilly

3’ UTR

+

3

uses endogenous poly-A site

confirmed

#2.11

2

1

17

1621018-1620917

Cre17.g707950/Cre17.g708000

HEP1 escort protein/ PAS domain protein

intergenic

not applicable

0

there are several other good matches, but this is the only perfect one

confirmed

#3.1

3

0

FAILED: no marker DNA in sequence

-

#3.2

2

3

12

9166015-9166885

Cre12.g560350

CNK2, NimA-related protein kinase 2

intron 1 (splits 5'-UTR)

-

0 (filled in)

at least two staggered polyadenylation sites

confirmed by Lynn Quarmby (pers. comm.)

#3.3

1

2

7

1015855:1015936 and 1015996-1016192

Cre07.g319550

FIST C domain protein

intron 1

+

0 (filled in)

two staggered polyadenylation sites

confirmed

#3.4

3

0

0 (filled in)

FAILED : FST too short (1 nt)

-

#3.5

1

1

?

Chr_7:2564723–2565098 and other locations

genes similar to Cre07.g332350

unknown function

usually intron 1

+

9 (incl. overhang)

UNMAPPED: maps equally well in several homologous genes

-

#3.6

2

1

3

2440121-2440156

Cre03.g166950

PGM5, phosphoglycerate mutase

intron 6

+

0 (filled in) + additional G

confirmed

#3.7

2

0

FAILED: amplifies a sequence from Cre14.g632700 exon 20 but the junction with the cassette cannot be read

disproved (gene intact)

#3.8

3

1

?

?

?

0 (uncut)

UNMAPPED: the 35 nt FST maps to several locations

-

#3.11

2

2

17

2083314-2083570

Cre17.g712100

MDAR1

intron 7

+

0 (filled in)

one FST suggests artifactual splicing between end of marker and exon 8

unsure, PCR failed

#3.12

2

1

10

1630598-1630551

Cre10.g429850

protein of unknown function conserved in Chlorophyceae

intron 6

+

0 (uncut)

2 insertions ? underneath the main sequence, you can also read a short FST corresponding to a repeated sequence

unsure, PCR failed

#4.1

1

2

5

377208-377154 and −377020

Cre05.g231500

Zn-finger protein

intron 6

+

0 (uncut)

two staggered polyadenylation sites

confirmed

#4.2

1

1

8

v5:4490830-4491010

Augustus_ 11.2|g9033.t1

unknown function

3' UTR

+

0 (uncut)

a good FST, not found in version 4 genome but found in three unpublished genome assemblies

not tested

#4.3

2

0

FAILED: no good sequence

-

#4.4

2

1

2

9598215-9596562

Cre02.g115000

Ribosome-binding factor A

intron 4

+

0 (uncut)

two staggered polyadenylation sites; intron 5 is retained in the chimeric mRNA, but intron 6 is spliced out

confirmed

#4.5

3

0

FAILED: no good sequence

-

#4.6

2

2

?

?

?

UNMAPPED: a 35 nt FST mapping to several locations, and a long one not mapping at all

-

#4.8

1

2

7

698506-698423 and −698252

Cre07.g317300/ Cre07.g317350

MAPKKKK1 and a protein of unknown function

intergenic

not applicable

0 (uncut)

confirmed

#4.9

1

0

FAILED: polyadenylation starts within the marker

-

#4.10

1

1

7

4591244-4590811

Cre07.g346000

unknown function

end of 3'UTR

+

poly-A site downstream of gene model

confirmed

#4.12

1

0

FAILED: no good sequence

#11.1

1

16

2391524-2391584

Cre16.g666300

protein kinase

upstream, intergenic

not applicable

?

the PCR product cannot be read in the FST (primer too close to end)

disproved (gene intact)

#11.3

1

0

FAILED: no marker DNA in sequence

-

#11.4

1

1

4

704462-705281

Cre04.g215800

no annotation

last exon

+

2

unsure, PCR failed

#11.5

1

0

FAILED: no match to genome

-

#14.1

3

1

14

2909515-2909394 and 2908783- 2908718

Cre14g.627600

Dynein heavy chain

intron 6 and exon 8

+

0

evidence for genome rearrangement or aberrant splicing

disproved (gene intact)

#14.2

1

2

12 and other

> a dozen locations (with splicing)

many

Chlamydomonas- specific kinase family

usually exon 4

+

0

UNMAPPED: too many good hits

-

#14.3

3

1

14

3326333-3326254

Cre14.g630150/ Cre14.g630200

TRAF-type zinc finger protein; protein of unknown function conserved in Volvox only

intergenic

not applicable

0

unsure, PCR failed

#14.4

3

0

FAILED: FST too short (2 nt)

-