Basic Information
Locus ID:
Ag3G00773
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
WD repeat and HMG-box DNA-binding protein 1
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr3 | 23030265 | 23036560 | + | Ag3G00773 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 6.18 | 106,083.04 Da | 41.10 | 80.50 | -0.34 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd00200 | WD40 | 55 | 345 | 1.7272E-38 | - |
| Pfam | PF00400 | WD domain, G-beta repeat | 55 | 88 | 7.5E-6 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 139 | 162 | 0.018 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 236 | 266 | 1.3E-4 | IPR001680 |
| Pfam | PF12341 | Minichromosome loss protein, Mcl1, middle region | 437 | 719 | 1.4E-91 | IPR022100 |
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 22 | 309 | 2.2E-54 | IPR036322 |
| Gene3D | G3DSA:2.130.10.10 | - | 3 | 193 | 1.0E-31 | IPR015943 |
| Gene3D | G3DSA:2.130.10.10 | - | 194 | 370 | 8.0E-20 | IPR015943 |
| SMART | SM00320 | WD40_4 | 185 | 223 | 63.0 | IPR001680 |
| SMART | SM00320 | WD40_4 | 50 | 89 | 2.1E-8 | IPR001680 |
| SMART | SM00320 | WD40_4 | 134 | 173 | 1.1E-5 | IPR001680 |
| SMART | SM00320 | WD40_4 | 2 | 46 | 430.0 | IPR001680 |
| SMART | SM00320 | WD40_4 | 226 | 266 | 1.1E-6 | IPR001680 |
| SMART | SM00320 | WD40_4 | 92 | 131 | 0.18 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 57 | 98 | 11.510997 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 234 | 268 | 9.862871 | - |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 57 | 89 | 9.388329 | - |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 141 | 174 | 9.467419 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 141 | 182 | 11.64467 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 234 | 275 | 12.580379 | IPR001680 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 253 | 267 | - | IPR019775 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 360 | 443 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 921 | 968 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 380 | 420 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 921 | 959 | - | - |
Gene Ontology
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT3G42660.1 | transducin family protein / WD-40 repeat family protein. | 0 |
| RefSeq | XP_017244439.1 | PREDICTED: WD repeat and HMG-box DNA-binding protein 1 [Daucus carota subsp. sativus] | 0 |
| F4JF14 | Protein ENHANCER OF LHP1 1 OS=Arabidopsis thaliana OX=3702 GN=EOL1 PE=1 SV=1 | 0 | |
| TrEMBL | A0A165XX71 | Mcl1_mid domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_014013 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 1.781882 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 0.874287 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 0.351456 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 0.377466 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 0.317237 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 0.316817 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 0.290811 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 0.085919 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 23.945999 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 26.796137 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 29.75576 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 30.129723 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 20.66118 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 17.008646 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 0 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 0.521021 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 2.467063 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 2.372413 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 0.766475 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 0.975884 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 2.760083 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 6.238388 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 7.467062 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 9.931439 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 7.9845 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 6.006545 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 2.93956 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 3.707586 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 5.135283 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 0 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 0.044167 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 0.008949 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 0.082713 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 8.006256 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 0.160667 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 0.153155 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 0 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 0.132271 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 7.558626 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 0.19706 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 0.171116 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 0.159262 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 0.094406 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 0.356966 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 0 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 0.256022 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 0.102972 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 12.831547 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 8.794329 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 9.826526 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg27374 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_19719 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah001332 |
| Amaranthaceae | Beta vulgaris | 2 | BVRB_5g113660, BVRB_6g145120 |
| Amaranthaceae | Salicornia bigelovii | 4 | Sbi_jg30939, Sbi_jg30942, Sbi_jg45039, Sbi_jg58333 |
| Amaranthaceae | Salicornia europaea | 2 | Seu_jg19547, Seu_jg25936 |
| Amaranthaceae | Suaeda aralocaspica | 2 | GOSA_00004801, GOSA_00004802 |
| Amaranthaceae | Suaeda glauca | 7 | Sgl00282, Sgl04375, Sgl05338, Sgl09444, Sgl12847, Sgl72071 ... |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000007547, gene:ENSEOMG00000022511 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.5AG0018870, CQ.Regalona.r1.5BG0020100 |
| Anacardiaceae | Pistacia vera | 2 | pistato.v30145560, pistato.v30146750 |
| Apiaceae | Apium graveolens | 1 | Ag3G00773 |
| Arecaceae | Cocos nucifera | 1 | COCNU_01G006010 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103712743 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_05.912.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri1G09563 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT3G42660.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10016196m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 2 | Sp5g17930.v2.2, SpUn0079_0020.v2.2 |
| Brassicaceae | Brassica nigra | 1 | BniB08g056420.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq03G2343 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl03G2482 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno05g07400 |
| Dunaliellaceae | Dunaliella salina | 3 | Dusal.0062s00014.v1.0, Dusal.0167s00021.v1.0 ... |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate04g27220 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG10.484 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00011964 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb4G26091 |
| Poaceae | Echinochloa crus-galli | 4 | AH01.490, AH03.1296, BH01.249, CH01.83 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_2AG0131270, gene-QOZ80_2BG0186610 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.5HG0469740.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_004066 |
| Poaceae | Oryza coarctata | 2 | Oco17G001190, Oco18G000730 |
| Poaceae | Oryza sativa | 1 | LOC_Os09g06560.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_02G136500 |
| Poaceae | Puccinellia tenuiflora | 2 | Pt_Chr0705055, Pt_Chr0705079 |
| Poaceae | Sporobolus alterniflorus | 4 | Chr10G001160, Chr11G017590, Chr14G006920, Chr21G005350 |
| Poaceae | Thinopyrum elongatum | 1 | Tel5E01G283200 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC5AG027490, gene_TRIDC5BG028890 |
| Poaceae | Triticum aestivum | 3 | TraesCS5A02G166800.1, TraesCS5B02G163900.1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb308160_P003 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-49980 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g3583 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG02.101, evm.TU.LG09.1335 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc01g16030 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_11_RagTag.205 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-14239 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-10052 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-14374 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000005l.256 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00010026 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-336 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-19027 |
| Salicaceae | Populus euphratica | 2 | populus_peu14493, populus_peu22195 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132632817 |
| Solanaceae | Solanum chilense | 1 | SOLCI000542800 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107012165 |
| Tamaricaceae | Reaumuria soongarica | 1 | gene_11726 |
| Tamaricaceae | Tamarix chinensis | 1 | TC05G0021 |
| Zosteraceae | Zostera marina | 1 | Zosma03g29040.v3.1 |