Table 1

Amphioxus GFP genes.

Gene

JGI Gene Model

Baumann et al. 2008

Scaffold

Position

Correction of Gene Prediction

Gene Product

EST Count


Clade a


GFPa1

fgenesh2_pg.scaffold_1000062

Lan1

1

1116500–1118933

None

EST/PCR

204

GFPa2

fgenesh2_pg.scaffold_264000004

Lan3

264

58192–60413

Trimmed N-term

EST

27

GFPa3

fgenesh2_pg.scaffold_549000016

Lan9

549

352398–358639

None

No

GFPa4

fgenesh2_pg.scaffold_549000017

549

364853–368343

Trimmed C-term

No

GFPa5

fgenesh2_pg.scaffold_1000068

Lan12

1

1208185–1211151

Trimmed C-term

No


Clade b


GFPb1

fgenesh2_pg.scaffold_408000038

Lan13

408

704470–709647

Trimmed N-term

No

GFPb1a

fgenesh2_pg.scaffold_58000035

58

532019–534945

Trimmed N-term (7AA + ATG)

No

GFPb2

fgenesh2_pg. scaffold_408000037

408

691033–694888

Extended N, C term

No

GFPb2a

fgenesh2_pg. scaffold_58000034

Lan19

58

518572–521504

Trimmed start (48AA)

No

GFPb3

estExt_fgenesh2_pg.C_4080036

Lan5-Nterm

408

656826–660682

Extended N-term, trimmed C-term.

EST

1

GFPb3a

fgenesh2_pg.scaffold_58000032

58

485880–488855

Trimmmed N-term, added ATG

No

GFPb4

estExt_fgenesh2_pg.C_4080036

Lan5-Cterm

408

674499–680280

Trimmed N-term.

EST

1

GFPb4a

fgenesh2_pg.scaffold_58000033

58

507562–508283

Two-exon fragment. Trimmed and extended both ends

No


Clade c


GFPc1

fgenesh2_pg.scaffold_722000001

Lan11

722

186–3347

Trimmed N-term, added ATG

No

GFPc1a

fgenesh2_pg.scaffold_58000036

58

555111–557942

None

PCR


Clade d


GFPd1

fgenesh2_pg.scaffold_149000048

150

209871–211956

Trimmed N-term

EST/PCR

13

GFPd1a

fgenesh2_pg.scaffold_150000025

149

908671–910787

None

No

GFPd2

fgenesh2_pg.scaffold_771000005

771

43072–45512

None

EST/PCR

5

GFPd2a

estExt_fgenesh2_pg.C_2370020

Lan7

237

340592–343047

Trimmed N-term

No


Clade e


GFPe1

fgenesh2_pg.scaffold_1000063

1

1141692–1143777

Filled internal deletion

EST/PCR

194

GFPe2

fgenesh2_pg.scaffold_1000066

Lan4

1

1168253–1170596

None

EST

26

GFPe2a

fgenesh2_pg.scaffold_13000140

13

3112741–3113363

Extended N-term

No

GFPe3

fgenesh2_pg.scaffold_1000064

Lan2

1

1150911–1152721

None

EST

125

GFPe3a

fgenesh2_pg.scaffold_264000003

264

31164–32864

Extended C-term

No


Clade f


GFPf1

fgenesh2_pg.scaffold_1000065

Lan6

1

1159351–1162889

None

EST

3

GFPf1a

fgenesh2_pg.scaffold_264000002

264

14129–18055

Trimmed internal insert

EST (truncated)


List of amphioxus GFP gene sequences with genomic mapping, errors in original gene predictions, evidence of gene product, and EST count. Secondary alleles have an "a" suffix. EST count refers to the number of GFP sequences in library of 334,502 B. floridae ESTs.

Bomati et al. BMC Evolutionary Biology 2009 9:77   doi:10.1186/1471-2148-9-77

Open Data