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Table 3 Identification and analysis of EXT genes in Populus trichocarpa

From: Bioinformatic Identification and Analysis of Hydroxyproline-Rich Glycoproteins in Populus trichocarpa

Locus Identifier 3.0 (ID 2.0)a

Name

Class

SP3/SP4/SP5/YXY Repeats

Amino Acids

Pfamb

SPc

GPI

Organ/issue-specific Expression11

Arabidopsis HRGP BLAST Hits

Poplar HRGP BLAST Hitse

Potri.018G050100 (POPTR 0018 s05480)

PtEXT1

Classical EXT

1/6/4/5

190

PF04554.11

Y

N

Young leaf

AtEXT22, AtEXT21

Potri.001G201800

Potri.001G019700 (POPTR 0001 s05720)

PtEXT2

Classical EXT

1/21/0/11

213

 

Y

N

 

AtEXT3/5

PtEXT8

Potri.001G122100 (POPTR_0001 s00420)

PtEXT3

Classical EXT

2/5/6/0

238

PF14547.4

Y

N

Male catkins

AtPRP16, AtPRP15, AtPRP14, AtHAE4

Potri.013G128800, Potri.002G200100, Potri.018G025900, Potri.001G158400, Potri.014G059800

Potri.001G259600 (POPTR 0001 s26690)

PtEXT4

Classical EXT

2/8/2/0

500

 

Y

N

 

AtAGP51C

PtEXT7, AGP6C, AGP43P

Potri.001G020100 (POPTR 0001 s05740)

PtEXT5

Classical EXT

1/22/0/13

257

 

Y

N

 

None

PtEXT6, PtEXT8

Potri.001G019900

PtEXT6

Classical EXT

1/25/0/14

259

 

Y*

N

 

None

PtEXT8, PtEXT5

Potri.001G260200 (POPTR_0001 s26680)

PtEXT7

Classical EXT

4/6/1/0

222

 

Y

N

 

None

AGP43P, AGP6C, PtEXT4, Potri.003G074200

Potri.001G020000

PtEXT8

Classical EXT

1/23/0/16

267

 

Y*

N

 

AtEXT3/5

PtEXT6, PtEXT5

Potri.010G001200 (POPTR_0010s003 50)

PtEXT9

Short EXT

1/6/0/3

174

 

Y

Y

 

AtEXT37, AtEXT41

PtEXT24, Potri.008G129200, Potri.010G128900, Potri.008G117500, FLA21

Potri.010G113300 (POPTR_0010s12360)

PtEXT10

Short EXT

0/2/0/0

131

 

Y

N

 

AtEXT31, AtEXT33

PtEXT23, Potri.006G106800, Potri.005G033000, Potri.001G371600, PossiblePtEXT5

Potri.T091000

PtEXT11

Short EXT

1/1/0/0

106

 

Y

N

 

None

PtEXT12, PtEXT19, Potri.005G079400

Potri.013G045700 (POPTR 0013 s04290)

PtEXT12

Short EXT

1/1/0/0

111

 

Y

N

 

None

PtEXT11, PtEXT19

Potri.003G064900 (POPTR_0003 s063 50)

PtEXT13

Short EXT

1/1/3/0

167

 

Y

N

 

AtEXT32, AtAGP57C, AtPERK5

PtEXT26, Potri.009G013500, Potri.006G276200

Potri.006G225400 (POPTR_0006s24190)

PtEXT14

Short EXT

2/0/1/3

186

 

Y

Y

Male catkins, roots

AtEXT38, AtEXT7

Potri.015G147200, Potri.008G168300, Potri.010G094700, Potri.012G144400, PtFH2

Potri.002G070100

PtEXT15

Short EXT

0/1/2/2

102

 

Y

N

 

AtEXT3/5, AtEXT1/4, AtEXT22

PtEXT20, Potri.017G110900, PtEXT1, PtLRX3

Potri.019G015900 (POPTR_0019s03210)

PtEXT16

Short EXT

0/2/0/0

108

 

Y

N

 

None

PtEXT18, PtEXT33, PtEXT17, Potri.019G015700, Potri.T139100

Potri.019G015800 (POPTR_0019s03200)

PtEXT17

Short EXT

0/2/0/0

107

 

Y

N

Male catkins

None

PtEXT33, PtEXT18, PtEXT16, Potri.T139100, Potri.019G015700

Potri.019G016000

PtEXT18

Short EXT

0/2/0/0

116

 

Y

N

 

None

PtEXT16, PtEXT33, PtEXT17, Potri.019G015700, Potri.T139100

Potri.019G017300 (POPTR_0019s03400)

PtEXT19

Short EXT

0/2/0/0

110

 

Y*

N

Dark etiolated seedlings

AtPERK6, AtAGP45P

PtEXT11, PtEXT12, Potri.005G257000, Potri.010G244800, Potri.006G136900

Potri.005G190100

PtEXT20

Short EXT

1/2/0/2

115

 

Y

N

 

AtEXT3/5, AtEXT1/4, AtPRP3, AtPRP1

Potri.019G083200, Potri.013G112500, PtLRX3, Potri.007G090300, Potri.005G077700

Potri.014G124700

PtEXT21

Short EXT

0/2/0/0

168

 

Y

N

 

AtEXT34, AtEXT41, AtPERK3, AtPERK5

Potri.015G147200, Potri.012G144400, Potri.001G371600, Potri.004G143700, PtFH2

Potri.T082000

PtEXT22

Short EXT

1/1/1/0

177

 

Y*

N

 

None

PtAEH4, PtEXT28, PtEXT27, Potri.001G042100, Potri.008G043900

Potri.008G129100 (POPTR_0008s12800)

PtEXT23

Short EXT

0/3/0/0

155

 

Y

Y

Female catkins, xylem

AtEXT31, AtEXT33, AtPAG10

PtEXT10, Potri.010G094700, Potri.015G147200, Potri.006G163700, Potri.018G086100

Potri.008G213600 (POPTR_0008s22980)

PtEXT24

Short EXT

0/1/1/2

172

 

Y

Y

Male catkins

AtEXT37, AtPERK6, AtEXT41

PtEXT9, Potri.008G129200, PossiblePtEXT15, Potri.010G094700, Potri.004G143700

Potri.008G125400 (POPTR_0008s12430)

PtEXT25

Short EXT

2/0/0/0

80

 

Y*

N

 

None

Potri.005G239200, Potri.010G094700, Potri.010G006800, Potri.002G189300, Potri .005G239200

Potri.001G169200 (POPTR 0001 s16930)

PtEXT26

Short EXT

0/0/2/0

147

 

Y

N

 

None

PtEXT13, Potri.010G006800

Potri.001G042200 (POPTR 0001 s03370)

PtEXT27

Short EXT

2/2/0/1

177

 

Y

N

 

None

PtEXT28, PtEXT22, PtAEH4, Potri.001G042100, Potri.001G316500

Potri.T179500 (POPTR_0523s00220)

PtEXT28

Short EXT

1/0/1/0

176

 

Y*

N

 

None

PtAEH4, PtEXT22, PtEXT27, Potri.001G042100, Potri.005G030300

Potri.T101300 (POPTR_0017 s06820)

PtEXT29

Short EXT

0/2/0/0

151

 

Y*

N

 

AtAGP56C

Potri.007G120100, Potri.002G054100, Potri.001G371600, Potri.015G147200, Potri.002G235500

Potri.T139000

PtEXT33

Short EXT

0/1/0/0

107

 

Y

N

 

None

PtEXT17, PtEXT18, PtEXT16, Potri.019G015700, Potri.T139100

Potri.009G108100 (POPTR_0009s 11130)

PtLRX1

Chimeric

5/16/6/1

982

PF13855.4

Y

N

Female catkins

AtPEX3, AtPEX1, AtPEX4, AtPEX2, AtLRX4

PtLRX2, PtLRX10, PtLRX3, PtLRX6, PtLRX7

Potri.004G146400 (POPTR_0004s15360)

PtLRX2

Chimeric

2/19/1/1

603

PF13855.4

Y

N

Male catkins

AtPEX3, AtPEX4, AtPEX1, AtPEX2, AtLRX4

PtLRX1, PtLRX10, PtLRX3, PtLRX4, PtLRX7

Potri.006G081200

PtLRX3

Chimeric

2/1/3/0

584

PF13855.4 PF08263.10

Y*

N

 

AtLRX2, AtLRX1, AtLRX4, AtLRX3, AtLRX5

PtLRX7, PtLRX6, PtLRX4, PtLRX2, PtLRX10

Potri.006G245600 (POPTR_0006s26190)

PtLRX4

Chimeric

2/2/5/1

549

PF08263.10

Y

N

Xylem

AtLRX4, AtLRX3, AtLRX5, AtLRX7, AtLRX6

PtLRX8, PtLRX5, PtLRX9, PtLRX6, PtLRX3

Potri.006G162300 (POPTR_0024s00730)

PtLRX5

Chimeric

2/3/3/0

569

PF13855.4

Y

N

Male catkins

AtLRX4, AtLRX3, AtLRX2, AtLRX1, AtPEX4

PtLRX9, PtLRX6, PtLRX4, PtLRX8, PtLRX3

Potri.018G075900 (POPTR_0018s06150)

PtLRX6

Chimeric

1/2/5/0

509

PF13855.4

Y

N

Male catkins, young leaf, xylem

AtLRX3, AtLRX5, AtLRX2, AtLRX7, AtLRX1

PtLRX5, PtLRX9, PtLRX4, PtLRX8, PtLRX3

Potri.018G151000 (POPTR_0018s14790)

PtLRX7

Chimeric

1/6/1/0

481

PF08263.10 PF13855.4

Y

N

Male catkins

AtLRX2, AtLRX1, AtLRX4, AtLRX3, AtLRX5

PtLRX3, PtLRX6, PtLRX5, PtLRX9, PtLRX4

Potri.018G035100 (POPTR_0018s01010)

PtLRX8

Chimeric

0/3/2/1

496

PF08263.10

Y

N

Male catkins

AtLRX4, AtLRX3, AtLRX5, AtLRX7, AtLRX6

PtLRX4, PtLRX6, Potri.010G083000, PtLRX3, PtLRX7

Potri.T016600 (POPTR_0028s00200)

PtLRX9

Chimeric

2/3/4/0

573

PF13855.4

Y

N

Male catkins

AtLRX4, AtLRX3, AtLRX2, AtLRX1, AtPEX4

PtLRX5, PtLRX6, PtLRX8, PtLRX3, PtLRX7

Potri.014G036700 (POPTR_0014s03600)

PtLRX10

Chimeric

1/5/1/1

474

PF13855.4

Y

N

Male catkins

AtPEX3, AtPEX1, AtPEX4, AtPEX2, AtLRX4

PtLRX2, PtLRX1, PtLRX3, PtLRX7, Potri.007G139200

Potri.010G041400 (POPTR_0010s05110)

PtPERK1

Chimeric

5/0/2/1

700

PF07714.15

N

N

 

AtPERK13, AtPERK12, AtPERK11, AtPERK10, AtPERK8

PtPERK11,PtPERK3, PtPERK6, PtPERK3, PtPERK12

Potri.010G132900 (POPTR_0010s14290)

PtPERK2

Chimeric

5/4/2/1

765

PF00069.23

N

N

 

AtPERK8, AtPERK13, AtPERK1, AtPERK15, AtPERK4

PtPERK12, PtPERK11, PtPERK1, PtPERK8, PtPERK10

Potri.017G110400 (POPTR_0017s14140)

PtPERK3

Chimeric

5/5/0/1

724

PF07714.15

N

N

Dark etiolated and light-grown seedlings

AtPERK8, AtPERK10, AtPERK13, AtPERK12, AtPERK3

PtPERK6, PtPERK12, PtPERK2, PtPERK1, PtPERK11

Potri.009G115200 (POPTR_0009s 11810)

PtPERK4

Chimeric

1/6/2/1

649

PF07714.15

N

N

Male catkins

AtPERK5, AtPERK4, AtPERK15, AtPERK3, AtPERK13

PtPERK10, PtPERK9, PtPERK8, Potri.001G183000, Potri.T140000

Potri.004G153600 (POPTR_0004s16100)

PtPERK5

Chimeric

3/3/3/1

656

PF07714.15

N

N

 

AtPERK5, AtPERK7, AtPERK4, AtPERK6, AtPERK15

PtPERK4, PtPERK10, PtPERK9, PtPERK8, Potri.001G183000

Potri.004G105200 (POPTR_0004s10490)

PtPERK6

Chimeric

6/4/0/2

724

PF07714.15

N

N

Dark etiolated seedlings

AtPERK10, AtPERK12, AtPERK13, AtPERK3, AtPERK15

PtPERK3, PtPERK2, PtPERK1, PtPERK11, PtPERK10

Potri.006G242800

PtPERK7

Chimeric

2/0/0/1

706

PF07714.15

N

N

 

AtPERK1, AtPERK5, AtPERK14, AtPERK15, AtPERK3

PtPERK10, PtPERK9, Potri.001G183000, Potri.003G053300, Potri.T140000

Potri.018G081300 (POPTR_0018s08800)

PtPERK8

Chimeric

0/2/2/0

672

PF07714.15

N

N

Xylem

AtPERK1, AtPERK4, AtPERK5, AtPERK15, AtPERK6

Potri.001G183000, PtPERK10, PtPERK9, Potri.003G053300, PtPERK5

Potri.007G027000 (POPTR_0007s12680)

PtPERK9

Chimeric

2/3/5/1

639

PF07714.15

N

N

 

AtPERK5, AtPERK7, AtPERK6, AtPERK15, AtPERK13

PtPERK10, PtPERK8, PtPERK5, Potri.003G053300, Potri.T140000

Potri.005G124400 (POPTR_0005s12590)

PtPERK10

Chimeric

2/1/5/0

592

PF07714.15

N

N

Female catkins, male catkins

AtPERK4, AtPERK5, AtPERK7, AtPERK6, AtPERK1

PtPERK9, PtPERK8, PtPERK5, PtPERK4, Potri.001G183000

Potri.008G189700 (POPTR_0008s19400)

PtPERK11

Chimeric

5/3/1/1

733

PF07714.15

N

N

Male catkins

AtPERK13, AtPERK11, AtPERK8, AtPERK10, AtPERK15

PtPERK1, PtPERK3, PtPERK6, PtPERK12, PtPERK2

Potri.008G111600 (POPTR_0008s11080)

PtPERK12

Chimeric

0/6/2/1

728

PF07714.15

N

N

 

AtPERK13, AtPERK1, AtPERK5, AtPERK15, AtPERK3

PtPERK2, PtPERK1, PtPERK8, PtPERK11, Potri.001G183000

Potri.003G103800 (POPTR_0003 s10280)

PtFH1

Chimeric

1/0/2/0

1226

PF02181.21 PF10409.7

N

N

Female catkins, male catkins

None

Potri.018G019600, PtFH5, Potri.018G108000, Potri.006G263700, Potri.015G061000

Potri.011G131700 (POPTR 0011 s13510)

PtFH2

Chimeric

1/0/2/0

987

PF02181.21

Y

N

Roots

None

Potri.001G416100, Potri.007G119900, Potri.007G054900, PtFH4, Potri.017G009900

Potri.002G240200 (POPTR_0002s24130)

PtFH3

Chimeric

1/0/1/0

1066

PF02181.21

Y

N

Young leaf, male catkins

None

PtFH4, Potri.007G140200, Potri.017G009900, Potri.007G054900, Potri.013G017900

Potri.014G174700 (POPTR_0014s17310)

PtFH4

Chimeric

0/0/2/0

1071

PF02181.21

Y

N

Roots, light-grown seedling

AtPERK5

PtFH3, Potri.007G140200, Potri.017G009900, Potri.007G054900, Potri.013G017900

Potri.012G067900 (POPTR_0012s06980)

PtFH5

Chimeric

0/0/2/0

1400

PF10409.7 PF02181.21

N

N

Xylem, male catkins

None

Potri.015G061000, Potri.018G019600, Potri.006G185500, Potri.018G108000, PtFH1

Potri.009G145700 (POPTR_0009s14810)

PtEXT30

Chimeric

5/0/0/0

467

PF06830.9

Y

N

Male catkins, roots

AtEXT51

Potri.009G097400, Potri.012G145400, Potri.011G127900, Potri.009G012600, Potri.009G012500

Potri.014G115700 (POPTR_0014s11110)

PtEXT31

Chimeric

8/0/0/0

526

PF00295.15

Y*

N

Roots

None

Potri.002G190600, Potri.005G005500, Potri.013G005000, Potri.010G152000, Potri.008G100500

Potri.011G066900 (POPTR_0011s07300)

PtEXT32

Chimeric

0/1/2/2

498

PF00112.21 PF00396.16 PF08246.10

Y

N

Female catkins, male catkins

AtAGP4C

Potri.011G066800, Potri.004G057700, Potri.005G232900, Potri.014G024100, Potri.001G302100

Potri.004G024500

PtAEH1

AGP EXT Hybrid

0/1/1/1

673

PF01657.15 PF07714.15

Y

N

 

None

Potri.004G024600, PtAEH2, Potri.004G025800, Potri.011G028400, Potri.004G025900

Potri.004G024800

PtAEH2

AGP EXT Hybrid

0/1/1/1

678

PF01657.15 PF07714.15

Y

N

 

None

Potri.004G024600, Potri.004G025800, PtAEH1, Potri.011G028400, Potri.004G025900

Potri.003G082300 (POPTR_0003 s08030)

PtAEH3

AGP EXT Hybrid

2/0/0/0

188

 

Y*

Y

Dark and light-grown seedlings, young leaf

AtPRP1

Potri.005G191900, Potri.016G025300, Potri.004G162500, PossibleHybrid2, Potri.015G147200

Potri.003G184500

PtAEH4

AGP EXT Hybrid

1/1/1/0

177

 

Y*

N

 

None

PtEXT22, PtEXT28, PtEXT27, Potri.001G042100, Potri.019G047600

  1. a Protein identifiers of the version 2.0 are shown in the parenthesis. Italics indicates a protein that was identified only by a BLAST search
  2. b The domains indicated by the Pfam number are: PF04554.11, Extensin_2 domain (Extensin-like region); PF14547.4, Hydrophob_seed domain (Hydrophobic seed protein); PF13855.4, LRR_8 domain (Leucine rich repeat); PF08263.10, LRRNT_2 domain (Leucine rich repeat N-terminal domain); PF07714.15, Pkinase_Tyr domain (Protein tyrosine kinase); PF00069.23, Pkinase domain (Protein kinase domain); PF02181.21, FH2 domain (Formin Homology 2 Domain); PF10409.7, PTEN_C2 domain (C2 domain of PTEN tumour-suppressor protein); PF06830.9, Root_cap domain (Root cap); PF00295.15, Glyco_hydro_28 domain (Glycoside hydrolase family 28); PF00112.21, Peptidase_C1 domain (Papain family cysteine protease); PF00396.16, Granulin domain (Granulin); PF08246.10, Inhibitor_I29 domain (Cathepsin propeptide inhibitor domain); PF01657.15, Stress-antifung domain (Salt stress response/antifungal); PF07714.15, Pkinase_Tyr domain (Protein tyrosine kinase)
  3. c Asterisk indicates a protein that is predicted to have a signal peptide either using the sensitive mode in the SignalP website or only if amino acids at the N terminus are discarded
  4. d Expression data are shown only when available at http://bar.utoronto.ca/efppop/cgi-bin/efpWeb.cgi
  5. e A locus ID indicates that it is not identified as an HRGP
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BMC Plant Biology

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