Basic Information
Locus ID:
Ag10G01989
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Short Name:
WDR3
Description:
WD repeat-containing protein
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr10 | 210366477 | 210374373 | + | Ag10G01989 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 6.86 | 105,464.76 Da | 45.04 | 90.78 | -0.29 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd00200 | WD40 | 24 | 218 | 1.77958E-42 | - |
| CDD | cd00200 | WD40 | 399 | 692 | 1.46569E-56 | - |
| Pfam | PF00400 | WD domain, G-beta repeat | 97 | 135 | 2.5E-5 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 574 | 607 | 2.7E-5 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 655 | 692 | 8.2E-7 | IPR001680 |
| Pfam | PF04003 | Dip2/Utp12 Family | 795 | 894 | 1.1E-19 | IPR007148 |
| Pfam | PF00400 | WD domain, G-beta repeat | 182 | 218 | 1.3E-4 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 51 | 93 | 1.0E-4 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 613 | 650 | 0.27 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 475 | 512 | 0.13 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 144 | 177 | 1.8E-4 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 399 | 431 | 0.0076 | IPR001680 |
| SUPERFAMILY | SSF50998 | Quinoprotein alcohol dehydrogenase-like | 76 | 696 | 3.53E-64 | IPR011047 |
| Gene3D | G3DSA:2.130.10.10 | - | 566 | 768 | 2.2E-37 | IPR015943 |
| Gene3D | G3DSA:2.130.10.10 | - | 329 | 565 | 1.9E-30 | IPR015943 |
| Gene3D | G3DSA:2.130.10.10 | - | 28 | 316 | 3.3E-52 | IPR015943 |
| SMART | SM00320 | WD40_4 | 653 | 692 | 6.2E-9 | IPR001680 |
| SMART | SM00320 | WD40_4 | 96 | 135 | 3.8E-9 | IPR001680 |
| SMART | SM00320 | WD40_4 | 54 | 93 | 7.0E-7 | IPR001680 |
| SMART | SM00320 | WD40_4 | 611 | 650 | 9.4E-5 | IPR001680 |
| SMART | SM00320 | WD40_4 | 528 | 566 | 0.16 | IPR001680 |
| SMART | SM00320 | WD40_4 | 474 | 513 | 3.2E-5 | IPR001680 |
| SMART | SM00320 | WD40_4 | 180 | 219 | 8.1E-7 | IPR001680 |
| SMART | SM00320 | WD40_4 | 569 | 608 | 1.9E-7 | IPR001680 |
| SMART | SM00320 | WD40_4 | 393 | 431 | 2.1E-4 | IPR001680 |
| SMART | SM00320 | WD40_4 | 138 | 177 | 5.9E-6 | IPR001680 |
| SMART | SM00320 | WD40_4 | 434 | 471 | 56.0 | IPR001680 |
| SMART | SM00320 | WD40_4 | 247 | 290 | 210.0 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 103 | 136 | 14.685726 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 61 | 93 | 9.810144 | - |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 187 | 221 | 9.467419 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 187 | 221 | 11.310488 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 618 | 659 | 11.878597 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 481 | 516 | 9.625601 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 145 | 186 | 15.220417 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 576 | 610 | 10.653776 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 576 | 617 | 13.215325 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 145 | 180 | 12.077406 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 400 | 440 | 11.277069 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 103 | 136 | 12.130133 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 61 | 102 | 12.513543 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 618 | 650 | 9.441055 | - |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 660 | 692 | 11.444681 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 481 | 522 | 11.912015 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 660 | 692 | 13.816853 | IPR001680 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 164 | 178 | - | IPR019775 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 122 | 136 | - | IPR019775 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 80 | 94 | 3.6E-6 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 122 | 136 | 3.6E-6 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 164 | 178 | 3.6E-6 | IPR020472 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 916 | 931 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 312 | 326 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 300 | 333 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 916 | 948 | - | - |
| Coils | Coil | Coil | 292 | 312 | - | - |
Gene Ontology
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT3G21540.1 | transducin family protein / WD-40 repeat family protein. | 0 |
| RefSeq | XP_017258765.1 | PREDICTED: WD repeat-containing protein 3 [Daucus carota subsp. sativus] | 0 |
| Q8BHB4 | WD repeat-containing protein 3 OS=Mus musculus OX=10090 GN=Wdr3 PE=1 SV=1 | 0 | |
| TrEMBL | A0A161ZV22 | Utp12 domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_020803 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 10.853319 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 7.040797 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 5.244663 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 6.597449 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 6.494441 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 6.692333 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 5.813226 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 5.062139 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 19.061695 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 20.562054 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 21.213549 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 20.195181 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 17.481808 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 15.326674 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 2.827462 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 6.283461 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 6.272547 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 7.424354 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 6.852184 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 9.003528 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 8.930705 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 10.829317 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 12.691045 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 11.288883 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 12.116209 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 10.35842 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 8.869759 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 8.804633 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 11.336157 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 1.779177 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 3.900666 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 2.554356 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 4.250493 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 5.790576 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 4.032422 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 2.20948 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 1.947166 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 1.521267 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 8.251247 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 4.79269 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 2.333577 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 7.711504 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 4.846931 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 16.944668 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 13.691769 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 10.093269 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 10.508081 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 10.62572 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 10.018817 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 11.987631 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg3518 |
| Aizoaceae | Mesembryanthemum crystallinum | 2 | gene_1104, gene_20182 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah030622 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg27200, Sbi_jg33331 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg8035 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00005714 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl71296, Sgl74891 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000008406, gene:ENSEOMG00000038751 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.7AG0018460, CQ.Regalona.r1.7BG0021050 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30273730 |
| Apiaceae | Apium graveolens | 1 | Ag10G01989 |
| Arecaceae | Cocos nucifera | 1 | COCNU_07G010480 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103695733 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_09.990.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri16G33505 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT3G21540.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10024329m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp7g13750.v2.2 |
| Brassicaceae | Brassica nigra | 1 | BniB05g020710.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq02G1562 |
| Casuarinaceae | Casuarina glauca | 2 | Cgl02G1614, Cgl02G1630 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno11g06070 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0249s00016.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate06g17820 |
| Malvaceae | Hibiscus hamabo Siebold & Zucc. | 1 | nbisL1-mrna-5980 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG01.1549 |
| Plantaginaceae | Plantago ovata | 2 | Pov_00005009, Pov_00025481 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb4G24696 |
| Poaceae | Echinochloa crus-galli | 2 | BH01.4884, CH01.5486 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_3AG0234020, gene-QOZ80_3BG0293970 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.4HG0411240.1 |
| Poaceae | Lolium multiflorum | 2 | gene-QYE76_070696, gene-QYE76_070719 |
| Poaceae | Oryza coarctata | 2 | Oco05G003130, Oco06G003140 |
| Poaceae | Oryza sativa | 1 | LOC_Os03g05720.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_01G478200 |
| Poaceae | Puccinellia tenuiflora | 2 | Pt_Chr0100050, Pt_Chr0100071 |
| Poaceae | Sporobolus alterniflorus | 2 | Chr01G037100, Chr12G002370 |
| Poaceae | Thinopyrum elongatum | 1 | Tel4E01G524700 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC4AG055020, gene_TRIDC4BG053610 |
| Poaceae | Triticum aestivum | 2 | TraesCS4A02G370000.1, TraesCS4B02G317800.1 |
| Poaceae | Zea mays | 1 | Zm00001eb004160_P003 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-4475 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g4408 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG06.1659, evm.TU.LG11.1012 |
| Posidoniaceae | Posidonia oceanica | 2 | gene.Posoc08g08170, gene.Posoc08g08180 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_2_RagTag.918 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-4286 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-15957 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-10025 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000009l.907 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00005094 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-12605 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-5818 |
| Salicaceae | Populus euphratica | 1 | populus_peu11629 |
| Solanaceae | Lycium barbarum | 2 | gene-LOC132629973, gene-LOC132630654 |
| Solanaceae | Solanum chilense | 1 | SOLCI003887000 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107002644 |
| Tamaricaceae | Reaumuria soongarica | 1 | gene_5583 |
| Tamaricaceae | Tamarix chinensis | 1 | TC02G1968 |
| Zosteraceae | Zostera marina | 1 | Zosma05g33080.v3.1 |