Basic Information
Locus ID:
Ag1G00292
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
PHD finger family protein
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr1 | 22477880 | 22487319 | - | Ag1G00292 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 8.89 | 96,136.69 Da | 44.38 | 64.91 | -0.77 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd16448 | RING-H2 | 148 | 201 | 3.48782E-4 | - |
| SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 283 | 341 | 1.93E-8 | IPR011011 |
| SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 192 | 253 | 1.55E-9 | IPR011011 |
| SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 138 | 201 | 1.46E-6 | IPR011011 |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 280 | 342 | 4.1E-18 | IPR013083 |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 140 | 257 | 2.8E-20 | IPR013083 |
| SMART | SM00249 | PHD_3 | 285 | 340 | 2.0E-5 | IPR001965 |
| SMART | SM00249 | PHD_3 | 202 | 248 | 7.0E-4 | IPR001965 |
| SMART | SM00249 | PHD_3 | 147 | 201 | 0.13 | IPR001965 |
| ProSiteProfiles | PS50016 | Zinc finger PHD-type profile. | 145 | 203 | 9.4722 | IPR019787 |
| ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 148 | 201 | 9.199359 | IPR001841 |
| ProSiteProfiles | PS50016 | Zinc finger PHD-type profile. | 283 | 342 | 9.0005 | IPR019787 |
| ProSitePatterns | PS01359 | Zinc finger PHD-type signature. | 148 | 200 | - | IPR019786 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 570 | 601 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 762 | 777 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 524 | 601 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 526 | 543 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 689 | 717 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 738 | 777 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 672 | 687 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 672 | 721 | - | - |
| Coils | Coil | Coil | 87 | 107 | - | - |
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT3G08020.1 | PHD finger family protein. | 0 |
| RefSeq | XP_017226676.1 | PREDICTED: uncharacterized protein LOC108202673 isoform X1 [Daucus carota subsp. sativus] | 0 |
| TrEMBL | A0A175YF67 | PHD-type domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_029680 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 20.056002 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 13.091301 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 15.378823 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 15.671092 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 15.654089 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 17.540682 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 15.999167 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 19.478445 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 34.552917 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 35.368969 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 39.866199 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 35.713505 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 31.67189 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 28.533504 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 14.747237 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 14.74639 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 16.140841 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 17.353657 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 12.949162 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 12.035579 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 14.239161 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 19.287712 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 18.191835 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 19.403568 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 17.348219 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 20.240431 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 18.6852 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 16.183147 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 18.317337 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 7.963187 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 9.602388 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 7.35147 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 10.890663 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 11.67928 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 11.517365 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 5.873143 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 4.90047 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 4.980352 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 18.178587 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 11.401447 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 8.344597 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 17.122532 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 17.091766 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 37.223007 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 30.362616 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 18.030273 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 26.17914 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 19.906628 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 25.356195 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 23.196859 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 3 | jg26669, jg29032, jg29837 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_14563 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah035709 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_2g029230 |
| Amaranthaceae | Salicornia bigelovii | 4 | Sbi_jg21753, Sbi_jg22066, Sbi_jg32577, Sbi_jg9771 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg15992 |
| Amaranthaceae | Suaeda aralocaspica | 2 | GOSA_00008614, GOSA_00024010 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl63009, Sgl67636 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000019312, gene:ENSEOMG00000019759 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.2AG0017040, CQ.Regalona.r1.2BG0018830 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30230180 |
| Apiaceae | Apium graveolens | 1 | Ag1G00292 |
| Arecaceae | Cocos nucifera | 3 | COCNU_05G004410, COCNU_14G012220, scaffold000148G000040 |
| Arecaceae | Phoenix dactylifera | 4 | gene-LOC103703699, gene-LOC103715735, gene-LOC120103723 ... |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_08.947.V1.1 |
| Asteraceae | Flaveria trinervia | 2 | Ftri11G05000, Ftri11G23128 |
| Brassicaceae | Arabidopsis thaliana | 2 | AT3G08020.1, AT3G52100.1 |
| Brassicaceae | Eutrema salsugineum | 2 | Thhalv10010234m.g.v1.0, Thhalv10020119m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 2 | Sp3g06930.v2.2, Sp5g10200.v2.2 |
| Brassicaceae | Brassica nigra | 4 | BniB02g074330.2N, BniB07g058740.2N, BniB08g066360.2N ... |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq05G0456 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl05G0489 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno11g04780 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate09g06470 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG03.73 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00030905 |
| Plumbaginaceae | Limonium bicolor | 2 | Lb2G13289, Lb2G13296 |
| Poaceae | Echinochloa crus-galli | 3 | AH05.3623, BH05.3644, CH05.3822 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_5AG0392440, gene-QOZ80_5BG0440750 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.5HG0447180.1 |
| Poaceae | Oryza coarctata | 2 | Oco23G007590, Oco24G007160 |
| Poaceae | Oryza sativa | 1 | LOC_Os12g34330.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_08G084100 |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0703691 |
| Poaceae | Sporobolus alterniflorus | 4 | Chr04G016160, Chr06G016860, Chr19G009940, Chr27G006490 |
| Poaceae | Thinopyrum elongatum | 1 | Tel5E01G190500 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC5AG014380, gene_TRIDC5BG017340 |
| Poaceae | Triticum aestivum | 3 | TraesCS5A02G099800.1, TraesCS5B02G105000.1 ... |
| Poaceae | Zea mays | 2 | Zm00001eb137800_P001, Zm00001eb410840_P005 |
| Poaceae | Zoysia japonica | 2 | nbis-gene-30221, nbis-gene-48677 |
| Poaceae | Zoysia macrostachya | 2 | Zma_g25133, Zma_g25906 |
| Portulacaceae | Portulaca oleracea | 5 | evm.TU.LG07.910, evm.TU.LG15.1744, evm.TU.LG15.818 ... |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc04g09820 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_8_RagTag.1413 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-9228 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-465 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-15249 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000018l.177 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00002845 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-9518 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-18782 |
| Salicaceae | Populus euphratica | 4 | populus_peu01877, populus_peu01878, populus_peu35939 ... |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132644717 |
| Solanaceae | Solanum chilense | 4 | SOLCI000377600, SOLCI000897300, SOLCI000897700 ... |
| Solanaceae | Solanum pennellii | 5 | gene-LOC107007829, gene-LOC107008120, gene-LOC107008407 ... |
| Tamaricaceae | Reaumuria soongarica | 2 | gene_11736, gene_6989 |
| Tamaricaceae | Tamarix chinensis | 2 | TC01G0050, TC05G1285 |
| Zosteraceae | Zostera marina | 1 | Zosma03g05390.v3.1 |