Basic Information
Locus ID:
AgUnG01343
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 |
|---|---|---|---|---|
| ctg749 | 73064 | 76902 | - | AgUnG01343 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.90 | 34,502.52 Da | 37.87 | 85.27 | -0.08 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd00200 | WD40 | 25 | 319 | 2.63011E-61 | - |
| Pfam | PF12894 | Anaphase-promoting complex subunit 4 WD40 domain | 154 | 204 | 2.1E-6 | IPR024977 |
| Pfam | PF00400 | WD domain, G-beta repeat | 238 | 271 | 1.8E-8 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 52 | 88 | 0.036 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 94 | 131 | 0.11 | IPR001680 |
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 13 | 318 | 2.15E-68 | IPR036322 |
| Gene3D | G3DSA:2.130.10.10 | - | 4 | 321 | 6.0E-85 | IPR015943 |
| SMART | SM00320 | WD40_4 | 49 | 88 | 2.4E-5 | IPR001680 |
| SMART | SM00320 | WD40_4 | 189 | 229 | 1.3E-7 | IPR001680 |
| SMART | SM00320 | WD40_4 | 274 | 319 | 0.11 | IPR001680 |
| SMART | SM00320 | WD40_4 | 2 | 46 | 0.58 | IPR001680 |
| SMART | SM00320 | WD40_4 | 91 | 131 | 0.0018 | IPR001680 |
| SMART | SM00320 | WD40_4 | 147 | 186 | 3.2E-7 | IPR001680 |
| SMART | SM00320 | WD40_4 | 232 | 271 | 1.2E-9 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 56 | 97 | 10.842632 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 239 | 280 | 16.6574 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 10 | 55 | 9.104886 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 239 | 271 | 13.47467 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 154 | 195 | 10.307941 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 154 | 187 | 8.623787 | - |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 196 | 231 | 9.177421 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 196 | 238 | 11.109979 | IPR001680 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 33 | 47 | 3.5E-6 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 258 | 272 | 3.5E-6 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 173 | 187 | 3.5E-6 | IPR020472 |
Gene Ontology
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT4G29830.1 | Transducin/WD40 repeat-like superfamily protein. The protein is composed of repeats of WD motif which is involved in protein complex formation. The gene is involved in flower timing and flower development. This gene is predicted to encode a protein with a DWD motif. It can bind to DDB1a in Y2H assays, and DDB1b in co-IP assays, and may be involved in the formation of a CUL4-based E3 ubiquitin ligase. Loss of gene function leads to a redistribution of H3K4me3 and K3K36me2 modifications within genes but not a change in the overall abundance of these modifications within chromatin. | 0 |
| RefSeq | XP_017215323.1 | PREDICTED: WD repeat-containing protein VIP3 [Daucus carota subsp. sativus] | 0 |
| Q9SZQ5 | WD repeat-containing protein VIP3 OS=Arabidopsis thaliana OX=3702 GN=VIP3 PE=1 SV=1 | 0 | |
| TrEMBL | A0A6L5BC94 | ANAPC4_WD40 domain-containing protein OS=Apium graveolens OX=4045 GN=AG4045_002604 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 59.779858 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 43.208927 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 31.951216 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 34.242573 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 36.024189 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 36.017754 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 29.587473 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 26.057388 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 86.375122 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 86.043159 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 89.552658 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 85.140465 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 78.087288 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 108.416679 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 29.088175 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 35.090321 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 36.14904 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 49.153034 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 52.924595 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 68.684715 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 66.800995 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 60.9016 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 51.330624 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 57.729 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 56.040031 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 49.465557 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 49.256809 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 45.983574 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 45.93251 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 66.868095 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 61.371902 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 58.190811 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 103.586288 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 75.776978 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 85.967453 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 129.540771 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 103.67643 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 119.285713 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 39.172085 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 36.948719 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 22.373774 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 66.736229 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 48.74086 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 96.118118 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 67.691383 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 87.200699 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 58.969368 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 65.776535 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 63.125298 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 64.268723 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg32892 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_25173 |
| Amaranthaceae | Atriplex hortensis | 2 | Ah037057, Ah037058 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_2g042780 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg30160, Sbi_jg43604 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg18298 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00004059 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl66047, Sgl70364 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000019882, gene:ENSEOMG00000034265 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.1AG0018430, CQ.Regalona.r1.1BG0003980 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30259750 |
| Apiaceae | Apium graveolens | 1 | AgUnG01343 |
| Arecaceae | Cocos nucifera | 3 | COCNU_01G000600, COCNU_04G010020, COCNU_14G007390 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103723722 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_07.2088.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri14G20638 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT4G29830.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10027356m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp7g27640.v2.2 |
| Brassicaceae | Brassica nigra | 2 | BniB03g011220.2N, BniB05g007880.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq06G0821 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl06G0845 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno05g09450 |
| Dunaliellaceae | Dunaliella salina | 5 | Dusal.0051s00019.v1.0, Dusal.0103s00026.v1.0 ... |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate04g30150 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG07.1279 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00039599 |
| Poaceae | Echinochloa crus-galli | 3 | AH04.2120, BH04.2203, CH04.2537 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_9AG0691780, gene-QOZ80_9BG0709270 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.4HG0363150.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_065660 |
| Poaceae | Oryza coarctata | 2 | Oco21G009380, Oco22G010780 |
| Poaceae | Oryza sativa | 1 | LOC_Os11g43890.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_05G231600 |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0103410 |
| Poaceae | Sporobolus alterniflorus | 2 | Chr07G014610, Chr31G008020 |
| Poaceae | Thinopyrum elongatum | 1 | Tel4E01G230500 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC4AG026360, gene_TRIDC4BG024920 |
| Poaceae | Triticum aestivum | 3 | TraesCS4A02G165700.1, TraesCS4B02G144300.1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb165440_P001 |
| Poaceae | Zoysia japonica | 3 | nbis-gene-37626, nbis-gene-37627, nbis-gene-46011 |
| Poaceae | Zoysia macrostachya | 4 | Zma_g18256, Zma_g18257, Zma_g18267, Zma_g19125 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG03.2518, evm.TU.LG17.1561 |
| Posidoniaceae | Posidonia oceanica | 2 | gene.Posoc01g20940, gene.Posoc05g10640 |
| Rhizophoraceae | Bruguiera sexangula | 2 | evm.TU.60383.4, evm.TU.60384.4 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-12976 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-12790 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-16932 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000033l.381 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00014747 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-4001 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-8161 |
| Salicaceae | Populus euphratica | 1 | populus_peu11887 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132636898 |
| Solanaceae | Solanum chilense | 1 | SOLCI006027900 |
| Solanaceae | Solanum pennellii | 2 | gene-LOC107005340, gene-LOC107023996 |
| Tamaricaceae | Reaumuria soongarica | 2 | STRG.5088_chr03_+, gene_18202 |
| Tamaricaceae | Tamarix chinensis | 1 | TC02G0490 |
| Zosteraceae | Zostera marina | 1 | Zosma03g19170.v3.1 |