Basic Information
Locus ID:
Ag2G00050
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
PHD-finger
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr2 | 654475 | 655629 | + | Ag2G00050 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.56 | 39,964.35 Da | 42.62 | 77.69 | -0.49 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd15492 | PHD_BRPF_JADE_like | 162 | 210 | 3.92657E-19 | - |
| CDD | cd15571 | ePHD | 223 | 331 | 1.77464E-26 | - |
| Pfam | PF13832 | PHD-zinc-finger like domain | 222 | 320 | 1.5E-27 | - |
| Pfam | PF00628 | PHD-finger | 162 | 211 | 6.4E-12 | IPR019787 |
| SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 146 | 214 | 1.51E-14 | IPR011011 |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 219 | 334 | 1.8E-17 | IPR013083 |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 139 | 218 | 1.2E-17 | IPR013083 |
| SMART | SM00249 | PHD_3 | 277 | 332 | 2.6 | IPR001965 |
| SMART | SM00249 | PHD_3 | 162 | 211 | 2.1E-11 | IPR001965 |
| ProSiteProfiles | PS50016 | Zinc finger PHD-type profile. | 160 | 213 | 9.7481 | IPR019787 |
| ProSiteProfiles | PS51805 | Extended PHD (ePHD) domain profile. | 220 | 332 | 19.249025 | IPR034732 |
| ProSitePatterns | PS01359 | Zinc finger PHD-type signature. | 163 | 210 | - | IPR019786 |
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT3G14740.2 | RING/FYVE/PHD zinc finger superfamily protein. | 0 |
| RefSeq | XP_017251547.1 | PREDICTED: nuA3 HAT complex component NTO1 [Daucus carota subsp. sativus] | 0 |
| Q12311 | NuA3 HAT complex component NTO1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=NTO1 PE=1 SV=1 | 0 | |
| TrEMBL | A0A164ZTI8 | Protein Jade-1 OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_019620 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 0.531331 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 0.966522 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 0 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 0 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 0 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 0 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 0 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 1.595273 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 9.101782 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 9.675515 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 11.969069 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 14.073543 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 9.252343 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 10.854771 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 0.531544 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 0.238856 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 1.687826 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 1.3764 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 0.681524 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 0.476815 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 1.012978 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 3.633728 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 4.821762 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 4.431553 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 3.515316 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 2.621754 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 1.551726 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 1.602694 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 2.992102 | 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 | 0.047665 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 0 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 0 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 7.146311 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 0 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 0 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 0 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 0 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 5.767294 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 0.201246 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 0 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 0.058756 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 0 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 0 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 0.168607 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 0 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 0 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 7.721875 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 5.380706 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 9.579926 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg21208 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_12603 |
| Amaranthaceae | Atriplex hortensis | 2 | Ah007527, Ah039183 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg19068, Sbi_jg37499 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg5341 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00012309 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl22165, Sgl27295 |
| Amaranthaceae | Chenopodium album | 2 | gene:ENSEOMG00000011268, gene:ENSEOMG00000041958 |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.4AG0016980, CQ.Regalona.r1.4BG0017360 |
| Anacardiaceae | Pistacia vera | 2 | pistato.v30163170, pistato.v30163260 |
| Apiaceae | Apium graveolens | 1 | Ag2G00050 |
| Arecaceae | Cocos nucifera | 1 | scaffold007600G000040 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103720818 |
| Asteraceae | Flaveria trinervia | 1 | Ftri15G01745 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT3G14740.2 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10021064m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp3g12970.v2.2 |
| Brassicaceae | Brassica nigra | 2 | BniB01g050310.2N, BniB07g054720.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq01G0864 |
| Casuarinaceae | Casuarina glauca | 2 | Cgl01G0990, Cgl01G0994 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno06g02500 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate06g15740 |
| Nitrariaceae | Nitraria sibirica | 2 | evm.TU.LG05.1335, evm.TU.LG05.1339 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00009500 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb7G34943 |
| Poaceae | Echinochloa crus-galli | 3 | AH02.385, BH02.411, CH02.457 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_1AG0012440, gene-QOZ80_1BG0061110 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.3HG0237870.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_050263 |
| Poaceae | Oryza coarctata | 2 | Oco01G003600, Oco02G003620 |
| Poaceae | Oryza sativa | 1 | LOC_Os01g08820.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_03G037900 |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0200070 |
| Poaceae | Sporobolus alterniflorus | 6 | Chr01G009610, Chr02G020290, Chr02G020360, Chr03G005940 ... |
| Poaceae | Thinopyrum elongatum | 1 | Tel3E01G195600 |
| Poaceae | Triticum dicoccoides | 3 | gene_TRIDC3AG014090, gene_TRIDC3BG018650 ... |
| Poaceae | Triticum aestivum | 3 | TraesCS3A02G113700.1, TraesCS3B02G133100.1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb122030_P001 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-13248 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g7755 |
| Portulacaceae | Portulaca oleracea | 1 | evm.TU.LG09.1116 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc03g23780 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_5_RagTag.144 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-11115 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-9789 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000006l.89 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00013345 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-9111 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-15334 |
| Salicaceae | Populus euphratica | 3 | populus_peu00688, populus_peu17748, populus_peu37171 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132618849 |
| Solanaceae | Solanum chilense | 1 | SOLCI000985600 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107024543 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.676_chr01_+ |
| Tamaricaceae | Tamarix chinensis | 1 | TC07G0032 |
| Zosteraceae | Zostera marina | 1 | Zosma06g09010.v3.1 |