Basic Information
Locus ID:
Ag3G00106
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
WD40 repeats
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr3 | 2369747 | 2376284 | - | Ag3G00106 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 7.82 | 90,071.52 Da | 36.48 | 84.03 | -0.19 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| Pfam | PF00400 | WD domain, G-beta repeat | 201 | 224 | 0.18 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 283 | 314 | 0.085 | IPR001680 |
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 14 | 319 | 3.66E-36 | IPR036322 |
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 245 | 666 | 1.83E-28 | IPR036322 |
| Gene3D | G3DSA:2.130.10.10 | - | 160 | 249 | 1.1E-10 | IPR015943 |
| Gene3D | G3DSA:2.130.10.10 | - | 473 | 705 | 2.6E-13 | IPR015943 |
| Gene3D | G3DSA:2.130.10.10 | - | 250 | 418 | 9.7E-13 | IPR015943 |
| Gene3D | G3DSA:2.130.10.10 | - | 4 | 159 | 1.5E-10 | IPR015943 |
| SMART | SM00320 | WD40_4 | 276 | 315 | 1.1E-4 | IPR001680 |
| SMART | SM00320 | WD40_4 | 623 | 661 | 260.0 | IPR001680 |
| SMART | SM00320 | WD40_4 | 185 | 224 | 0.0011 | IPR001680 |
| SMART | SM00320 | WD40_4 | 530 | 565 | 8.4 | IPR001680 |
| SMART | SM00320 | WD40_4 | 8 | 43 | 26.0 | IPR001680 |
| SMART | SM00320 | WD40_4 | 235 | 273 | 6.3 | IPR001680 |
| SMART | SM00320 | WD40_4 | 50 | 95 | 7.2 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 283 | 324 | 9.372231 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 201 | 233 | 10.675542 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 11 | 42 | 8.770704 | IPR001680 |
| Coils | Coil | Coil | 745 | 765 | - | - |
Gene Ontology
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT4G07410.1 | Transducin family protein / WD-40 repeat family protein. | 0 |
| RefSeq | XP_017247456.1 | PREDICTED: U3 small nucleolar RNA-associated protein 4 homolog [Daucus carota subsp. sativus] | 0 |
| Q8RXU6 | WD repeat-containing protein PCN OS=Arabidopsis thaliana OX=3702 GN=PCN PE=2 SV=1 | 0 | |
| TrEMBL | A0A165ZAU3 | WD_REPEATS_REGION domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_012822 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 15.627297 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 31.898949 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 23.347988 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 24.042368 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 24.803713 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 30.770796 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 13.366606 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 13.8805 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 56.312862 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 49.301437 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 58.797043 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 69.424995 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 64.31414 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 54.492931 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 14.711082 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 18.875744 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 22.813738 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 28.330015 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 26.059448 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 36.714455 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 33.178352 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 47.128086 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 58.171619 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 43.514641 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 43.083572 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 31.734163 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 32.852119 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 35.030281 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 36.834587 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 19.410231 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 35.779572 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 30.419464 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 22.168566 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 23.947628 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 21.990644 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 17.154058 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 12.263227 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 15.399948 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 34.867798 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 21.512512 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 6.244799 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 43.931038 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 50.080204 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 105.416931 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 83.083359 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 42.359409 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 52.809875 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 51.583599 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 51.880348 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 57.202042 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 3 | jg10729, jg10730, jg6198 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_6014 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah036674 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_1g014870 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg39660, Sbi_jg54674 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg14665 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00013194 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl12536, Sgl17809 |
| Amaranthaceae | Chenopodium album | 4 | gene:ENSEOMG00000016372, gene:ENSEOMG00000034312 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.1AG0017340, CQ.Regalona.r1.1BG0005660 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30042950 |
| Apiaceae | Apium graveolens | 4 | Ag10G00567, Ag1G00606, Ag3G00106, Ag4G02178 |
| Arecaceae | Cocos nucifera | 2 | COCNU_08G010260, COCNU_09G007280 |
| Arecaceae | Phoenix dactylifera | 2 | gene-LOC103698302, gene-LOC103721867 |
| Asparagaceae | Asparagus officinalis | 2 | AsparagusV1_01.906.V1.1, AsparagusV1_07.2078.V1.1 |
| Asteraceae | Flaveria trinervia | 3 | Ftri10G01902, Ftri10G02247, Ftri3G23168 |
| Brassicaceae | Arabidopsis thaliana | 2 | AT1G27470.1, AT4G07410.1 |
| Brassicaceae | Eutrema salsugineum | 2 | Thhalv10006817m.g.v1.0, Thhalv10028433m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 2 | Sp1g23720.v2.2, Sp6g10450.v2.2 |
| Brassicaceae | Brassica nigra | 3 | BniB03g017670.2N, BniB04g041860.2N, BniB08g034270.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq03G1274 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl03G1380 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno01g14970 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.1403s00002.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate02g30840 |
| Malvaceae | Hibiscus hamabo Siebold & Zucc. | 1 | nbisL1-mrna-5353 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG06.323 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00037078 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb4G23335 |
| Poaceae | Echinochloa crus-galli | 3 | AH01.690, BH01.834, CH01.845 |
| Poaceae | Eleusine coracana subsp. coracana | 1 | gene-QOZ80_3AG0217280 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.4HG0340180.1 |
| Poaceae | Lolium multiflorum | 2 | gene-QYE76_062061, gene-QYE76_062075 |
| Poaceae | Oryza coarctata | 2 | Oco05G022850, Oco06G023690 |
| Poaceae | Oryza sativa | 1 | LOC_Os03g52470.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_01G090500 |
| Poaceae | Puccinellia tenuiflora | 3 | Pt_Chr0107051, Pt_Chr0107586, Pt_Chr0405319 |
| Poaceae | Sporobolus alterniflorus | 4 | Chr01G005940, Chr04G028050, Chr07G026940, Chr12G031400 |
| Poaceae | Thinopyrum elongatum | 1 | Tel4E01G107800 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC4AG039140, gene_TRIDC4BG010150 |
| Poaceae | Triticum aestivum | 3 | TraesCS4A02G249300.1, TraesCS4B02G065400.1 ... |
| Poaceae | Zea mays | 2 | Zm00001eb056350_P001, Zm00001eb215430_P001 |
| Poaceae | Zoysia japonica | 2 | nbis-gene-14993, nbis-gene-16063 |
| Poaceae | Zoysia macrostachya | 2 | Zma_g2857, Zma_g535 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG03.642, evm.TU.LG12.1012 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc03g27930 |
| Rhizophoraceae | Bruguiera sexangula | 2 | evm.TU.Scaffold_7_RagTag.830, evm.TU.Scaffold_8_RagTag.897 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-9341 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-14464 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-20615 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000018l.270 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00003619 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-11454 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-17112 |
| Salicaceae | Populus euphratica | 1 | populus_peu32069 |
| Solanaceae | Lycium barbarum | 2 | gene-LOC132604057, gene-LOC132627762 |
| Solanaceae | Solanum chilense | 2 | SOLCI005143000, SOLCI007094300 |
| Solanaceae | Solanum pennellii | 2 | gene-LOC107007250, gene-LOC107018225 |
| Tamaricaceae | Reaumuria soongarica | 1 | gene_1783 |
| Tamaricaceae | Tamarix chinensis | 1 | TC04G2685 |
| Zosteraceae | Zostera marina | 2 | Zosma04g07330.v3.1, Zosma05g29090.v3.1 |