Basic Information
Locus ID:
Ag1G00145
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
WD repeat-containing protein
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr1 | 9753356 | 9766492 | + | Ag1G00145 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 6.86 | 83,607.08 Da | 37.96 | 82.53 | -0.36 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd00200 | WD40 | 34 | 367 | 7.25416E-51 | - |
| CDD | cd17041 | Ubl_WDR48 | 633 | 759 | 1.04737E-36 | - |
| Pfam | PF00400 | WD domain, G-beta repeat | 251 | 287 | 3.3E-4 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 34 | 66 | 0.085 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 115 | 154 | 3.7E-4 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 214 | 245 | 0.0013 | IPR001680 |
| Pfam | PF11816 | Domain of unknown function (DUF3337) | 612 | 759 | 5.5E-31 | IPR021772 |
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 33 | 450 | 1.46E-60 | IPR036322 |
| Gene3D | G3DSA:2.130.10.10 | - | 187 | 474 | 2.7E-37 | IPR015943 |
| Gene3D | G3DSA:2.130.10.10 | - | 13 | 173 | 1.4E-25 | IPR015943 |
| SMART | SM00320 | WD40_4 | 248 | 287 | 2.8E-7 | IPR001680 |
| SMART | SM00320 | WD40_4 | 114 | 154 | 1.8E-6 | IPR001680 |
| SMART | SM00320 | WD40_4 | 332 | 368 | 390.0 | IPR001680 |
| SMART | SM00320 | WD40_4 | 19 | 67 | 2.0 | IPR001680 |
| SMART | SM00320 | WD40_4 | 290 | 329 | 0.0014 | IPR001680 |
| SMART | SM00320 | WD40_4 | 206 | 245 | 9.4E-6 | IPR001680 |
| SMART | SM00320 | WD40_4 | 72 | 110 | 0.0078 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 255 | 288 | 11.497408 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 255 | 296 | 14.719144 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 213 | 254 | 14.886235 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 213 | 245 | 11.523771 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 49 | 76 | 8.570195 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 121 | 156 | 9.873505 | IPR001680 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 274 | 288 | - | IPR019775 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 97 | 111 | 1.3E-5 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 274 | 288 | 1.3E-5 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 54 | 68 | 1.3E-5 | IPR020472 |
Gene Ontology
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT3G05090.1 | Transducin/WD40 repeat-like superfamily protein. Encodes a DCAF protein. Mutants are defective in lateral root development and suggest roles for DDB1Cul4mediated protein degradation in regulating auxin accumulation during lateral root primordium development and lateral root meristem emergence. | 0 |
| RefSeq | XP_017226724.1 | PREDICTED: WD repeat-containing protein 48 [Daucus carota subsp. sativus] | 0 |
| Q05B17 | WD repeat-containing protein 48 OS=Xenopus tropicalis OX=8364 GN=wdr48 PE=2 SV=1 | 0 | |
| TrEMBL | A0A175YEU5 | WPP domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_029743 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 24.327063 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 18.466623 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 18.483088 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 19.296785 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 19.512112 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 17.647457 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 17.734865 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 15.975973 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 31.065384 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 31.801121 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 34.548985 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 32.847782 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 31.367434 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 28.971315 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 18.006136 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 18.587599 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 15.110752 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 24.834621 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 17.766014 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 28.579576 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 33.740765 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 16.705914 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 19.373232 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 18.361347 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 16.570086 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 21.792496 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 21.309322 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 18.305376 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 22.926291 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 6.267763 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 7.287495 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 7.829515 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 20.111053 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 13.753506 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 15.155052 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 10.446835 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 5.618792 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 9.507915 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 14.919875 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 10.941668 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 9.696757 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 35.313862 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 31.945236 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 23.399363 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 20.897514 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 37.070259 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 25.264435 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 15.973729 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 20.225298 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 19.816725 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 2 | jg19691, jg30652 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_10061 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_4g082610 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg16873, Sbi_jg61407 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg167 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00008250 |
| Amaranthaceae | Suaeda glauca | 4 | Sgl24776, Sgl24779, Sgl29923, Sgl29924 |
| Amaranthaceae | Chenopodium album | 5 | gene:ENSEOMG00000009205, gene:ENSEOMG00000030942 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.4AG0009920, CQ.Regalona.r1.4BG0010080 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30091950 |
| Apiaceae | Apium graveolens | 1 | Ag1G00145 |
| Arecaceae | Cocos nucifera | 2 | COCNU_07G012090, COCNU_10G008250 |
| Arecaceae | Phoenix dactylifera | 3 | gene-LOC103696637, gene-LOC103710558, gene-LOC120109777 |
| Asparagaceae | Asparagus officinalis | 2 | AsparagusV1_02.2061.V1.1, AsparagusV1_08.3107.V1.1 |
| Asteraceae | Flaveria trinervia | 2 | Ftri17G08808, Ftri9G06990 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT3G05090.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10020130m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 2 | Sp2g20380.v2.2, Sp3g03910.v2.2 |
| Brassicaceae | Brassica nigra | 2 | BniB01g058470.2N, BniB07g033100.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq06G2332 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl06G2448 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno14g03160 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0521s00016.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate03g07210 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG03.2331 |
| Plantaginaceae | Plantago ovata | 2 | Pov_00023942, Pov_00029263 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb1G01097 |
| Poaceae | Echinochloa crus-galli | 4 | AH05.279, BH05.321, CH05.147, CH05.373 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_5AG0382600, gene-QOZ80_5BG0429490 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.5HG0457370.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_002839 |
| Poaceae | Oryza coarctata | 2 | Oco23G002490, Oco24G002010 |
| Poaceae | Oryza sativa | 1 | LOC_Os12g06810.1 |
| Poaceae | Paspalum vaginatum | 2 | gene-BS78_08G035800, gene-BS78_K274200 |
| Poaceae | Sporobolus alterniflorus | 4 | Chr04G022780, Chr06G024570, Chr19G012550, Chr27G003380 |
| Poaceae | Thinopyrum elongatum | 1 | Tel5E01G225600 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC5AG020840, gene_TRIDC5BG021650 |
| Poaceae | Triticum aestivum | 3 | TraesCS5A02G122900.2, TraesCS5B02G122700.1 ... |
| Poaceae | Zea mays | 3 | Zm00001eb139400_P003, Zm00001eb333910_P001 ... |
| Poaceae | Zoysia japonica | 1 | nbis-gene-25564 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g24792 |
| Portulacaceae | Portulaca oleracea | 3 | evm.TU.LG16.1231, evm.TU.LG20.1220, evm.TU.LG20.1221 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc06g02090 |
| Rhizophoraceae | Bruguiera sexangula | 2 | evm.TU.Scaffold_1_RagTag.221, evm.TU.Scaffold_2_RagTag.1979 |
| Rhizophoraceae | Carallia pectinifolia | 2 | nbisL1-mrna-3396, nbisL1-mrna-7999 |
| Rhizophoraceae | Ceriops tagal | 2 | nbisL1-mrna-18491, nbisL1-mrna-38 |
| Rhizophoraceae | Ceriops zippeliana | 3 | nbisL1-mrna-13748, nbisL1-mrna-5274, nbisL1-mrna-5275 |
| Rhizophoraceae | Kandelia candel | 2 | evm.TU.utg000009l.103, evm.TU.utg000012l.151 |
| Rhizophoraceae | Kandelia obovata | 2 | Maker00005674, Maker00010920 |
| Rhizophoraceae | Rhizophora apiculata | 2 | nbisL1-mrna-12935, nbisL1-mrna-7809 |
| Rhizophoraceae | Rhizophora mangle | 2 | nbisL1-mrna-16216, nbisL1-mrna-201 |
| Salicaceae | Populus euphratica | 2 | populus_peu13509, populus_peu15845 |
| Solanaceae | Lycium barbarum | 2 | gene-LOC132612343, gene-LOC132645226 |
| Solanaceae | Solanum chilense | 3 | SOLCI005635600, SOLCI005635700, SOLCI006484600 |
| Solanaceae | Solanum pennellii | 2 | gene-LOC107006682, gene-LOC107028575 |
| Tamaricaceae | Reaumuria soongarica | 2 | STRG.32032_chr09_-, gene_12009 |
| Tamaricaceae | Tamarix chinensis | 2 | TC05G2311, TC06G0818 |
| Zosteraceae | Zostera marina | 1 | Zosma01g34730.v3.1 |