Basic Information
Locus ID:
AgUnG00089
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
DDB1- and CUL4-associated factor
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| ctg1477 | 153752 | 162650 | - | AgUnG00089 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 9.50 | 51,586.61 Da | 43.27 | 70.38 | -0.68 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd00200 | WD40 | 59 | 361 | 2.02525E-46 | - |
| Pfam | PF00400 | WD domain, G-beta repeat | 102 | 137 | 1.2E-5 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 283 | 318 | 1.4E-4 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 61 | 95 | 5.2E-5 | IPR001680 |
| Pfam | PF04158 | Sof1-like domain | 362 | 448 | 4.0E-32 | IPR007287 |
| Pfam | PF00400 | WD domain, G-beta repeat | 332 | 361 | 1.8E-5 | IPR001680 |
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 55 | 361 | 7.51E-60 | IPR036322 |
| Gene3D | G3DSA:2.130.10.10 | - | 42 | 165 | 4.9E-25 | IPR015943 |
| Gene3D | G3DSA:2.130.10.10 | - | 166 | 432 | 4.9E-37 | IPR015943 |
| SMART | SM00320 | WD40_4 | 153 | 190 | 320.0 | IPR001680 |
| SMART | SM00320 | WD40_4 | 55 | 95 | 2.4E-6 | IPR001680 |
| SMART | SM00320 | WD40_4 | 193 | 233 | 0.0041 | IPR001680 |
| SMART | SM00320 | WD40_4 | 320 | 361 | 6.5E-4 | IPR001680 |
| SMART | SM00320 | WD40_4 | 98 | 137 | 1.1E-8 | IPR001680 |
| SMART | SM00320 | WD40_4 | 236 | 275 | 240.0 | IPR001680 |
| SMART | SM00320 | WD40_4 | 279 | 318 | 6.2E-6 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 62 | 98 | 10.996502 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 286 | 327 | 11.544415 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 329 | 370 | 11.477578 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 105 | 146 | 14.518635 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 62 | 104 | 13.917108 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 286 | 318 | 9.282875 | - |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 329 | 361 | 8.940149 | - |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 105 | 138 | 11.418318 | - |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 82 | 96 | - | IPR019775 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 82 | 96 | 5.4E-7 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 348 | 362 | 5.4E-7 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 124 | 138 | 5.4E-7 | IPR020472 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 415 | 453 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 416 | 453 | - | - |
| Coils | Coil | Coil | 411 | 431 | - | - |
Gene Ontology
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT4G28450.1 | nucleotide binding;protein binding. This gene is predicted to encode a protein with a DWD motif. It can bind to DDB1a in Y2H assays and may be involved in the formation of a CUL4-based E3 ubiquitin ligase | 0 |
| RefSeq | XP_017243861.1 | PREDICTED: DDB1- and CUL4-associated factor 13 [Daucus carota subsp. sativus] | 0 |
| Q7ZYQ6 | DDB1- and CUL4-associated factor 13 OS=Xenopus laevis OX=8355 GN=dcaf13 PE=2 SV=1 | 0 | |
| TrEMBL | A0A6L5BBL6 | DDB1- and CUL4-associated factor 13 OS=Apium graveolens OX=4045 GN=AG4045_030416 PE=3 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 57.443523 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 28.055767 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 46.379299 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 46.849739 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 46.126846 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 52.576618 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 43.416454 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 30.971661 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 33.020374 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 31.89526 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 30.632088 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 36.551395 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 41.459282 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 36.189957 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 12.400179 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 14.291089 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 15.19187 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 20.218954 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 17.189266 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 26.71463 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 26.833496 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 21.688633 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 34.10413 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 26.486441 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 25.478506 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 24.893858 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 18.265282 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 22.671377 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 25.552725 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 3.886016 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 7.824147 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 8.095504 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 13.819655 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 11.861489 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 14.769765 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 6.856145 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 5.50679 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 4.205275 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 11.727702 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 3.515992 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 3.253752 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 31.858019 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 24.365286 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 82.469238 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 66.78405 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 40.917187 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 46.407234 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 32.328487 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 36.037098 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 36.064415 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg19353 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_25909 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah029207 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_9g209700 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg11749, Sbi_jg46661 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg20986 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00029039 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl79894, Sgl82354 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000007589, gene:ENSEOMG00000036398 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.7AG0011870, CQ.Regalona.r1.7BG0013940 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30020300 |
| Apiaceae | Apium graveolens | 1 | AgUnG00089 |
| Arecaceae | Cocos nucifera | 1 | COCNU_11G002350 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103715202 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_06.1096.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri4G13478 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT4G28450.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10025176m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp7g26430.v2.2 |
| Brassicaceae | Brassica nigra | 1 | BniB02g083540.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq02G2691 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl02G2787 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno12g03520 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0025s00044.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 3 | gene.Thate09g08450, gene.Thate09g08480, gene.Thate09g08580 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG04.1790 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00004582 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb3G20086 |
| Poaceae | Echinochloa crus-galli | 2 | AH02.45, CH02.39 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_1AG0000300, gene-QOZ80_1BG0048750 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.3HG0250210.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_051675 |
| Poaceae | Oryza coarctata | 2 | Oco01G006280, Oco02G006380 |
| Poaceae | Oryza sativa | 1 | LOC_Os01g13730.1 |
| Poaceae | Paspalum vaginatum | 2 | gene-BS78_03G002300, gene-BS78_K047000 |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0204803 |
| Poaceae | Sporobolus alterniflorus | 2 | Chr23G000840, Chr26G018440 |
| Poaceae | Thinopyrum elongatum | 1 | Tel3E01G286400 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC3AG021970, gene_TRIDC3BG025980 |
| Poaceae | Triticum aestivum | 3 | TraesCS3A02G160900.1, TraesCS3B02G191500.1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb064830_P001 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-32750 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g7161 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG10.350, evm.TU.LG17.346 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc09g04530 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_18_RagTag.444 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-28066 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-2647 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-7875 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000023l.187 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00018788 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-7292 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-21220 |
| Salicaceae | Populus euphratica | 2 | populus_peu22520, populus_peu23921 |
| Solanaceae | Lycium barbarum | 2 | gene-LOC132618660, gene-LOC132633202 |
| Solanaceae | Solanum chilense | 1 | SOLCI005019500 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107024119 |
| Tamaricaceae | Reaumuria soongarica | 1 | gene_6808 |
| Tamaricaceae | Tamarix chinensis | 1 | TC07G0503 |
| Zosteraceae | Zostera marina | 1 | Zosma03g02810.v3.1 |