Basic Information
Locus ID:
Ag8G00921
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
LSD1 zinc finger
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr8 | 89071329 | 89079612 | + | Ag8G00921 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 4.93 | 69,499.89 Da | 72.19 | 62.32 | -0.90 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| Pfam | PF06943 | LSD1 zinc finger | 541 | 565 | 3.5E-9 | IPR005735 |
| Pfam | PF06943 | LSD1 zinc finger | 579 | 603 | 4.8E-9 | IPR005735 |
| TIGRFAM | TIGR01053 | LSD1: zinc finger domain, LSD1 subclass | 538 | 568 | 1.5E-14 | IPR005735 |
| TIGRFAM | TIGR01053 | LSD1: zinc finger domain, LSD1 subclass | 576 | 604 | 3.8E-8 | IPR005735 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 274 | 307 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 376 | 392 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 143 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 13 | 29 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 321 | 454 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 488 | 531 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 337 | 355 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 515 | 531 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 92 | 132 | - | - |
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT4G21610.1 | lsd one like 2. Contains the same novel zinc finger motif with LSD1, a negative regulator of cell death and defense response. Due to differential splicing, it encodes two different proteins, one of which contains an additional, putative DNA binding motif. Northern analysis demonstrated that LOL2 transcripts containing the additional DNA binding motif are predominantly upregulated after treatment with both virulent and avirulent Pseudomonas syringae pv maculicola strains. | 0 |
| RefSeq | XP_017223630.1 | PREDICTED: uncharacterized protein DDB_G0284459-like isoform X1 [Daucus carota subsp. sativus] | 0 |
| O65426 | Protein LOL2 OS=Arabidopsis thaliana OX=3702 GN=LOL2 PE=1 SV=1 | 0 | |
| TrEMBL | A0A175YNV5 | Protein piccolo OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_028076 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 19.794432 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 13.362288 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 16.130199 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 18.106787 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 15.900186 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 21.373734 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 17.036825 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 19.166225 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 24.21101 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 22.338131 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 23.453035 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 23.181208 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 19.161104 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 19.326269 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 7.466214 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 7.425252 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 9.195294 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 7.925802 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 7.074503 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 6.315284 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 8.28744 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 11.477205 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 12.466382 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 13.118329 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 12.38086 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 10.253423 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 7.247999 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 9.318091 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 9.176974 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 3.082887 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 3.164009 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 2.611842 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 5.640239 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 8.384774 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 5.734606 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 4.960542 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 2.840943 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 2.80478 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 12.466262 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 6.996915 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 5.708847 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 5.3764 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 9.776343 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 21.282049 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 18.264616 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 5.857987 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 15.43244 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 23.270247 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 26.594324 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 27.819136 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg24879 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_22243 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah018025 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_8g183230 |
| Amaranthaceae | Salicornia bigelovii | 3 | Sbi_jg26103, Sbi_jg51831, Sbi_jg9944 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg18783 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00017034 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl45921, Sgl50621 |
| Amaranthaceae | Chenopodium album | 2 | gene:ENSEOMG00000011905, gene:ENSEOMG00000032799 |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.8AG0005240, CQ.Regalona.r1.8BG0005350 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30088690 |
| Apiaceae | Apium graveolens | 1 | Ag8G00921 |
| Arecaceae | Cocos nucifera | 1 | COCNU_06G002500 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103696358 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_05.2019.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri15G14234 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT4G21610.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10026412m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp7g19740.v2.2 |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq01G2293 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl01G2597 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno02g13580 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate04g18780 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG12.960 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00005619 |
| Plumbaginaceae | Limonium bicolor | 2 | Lb4G23726, Lb4G24771 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_1AG0024290, gene-QOZ80_1BG0074980 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.3HG0271290.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_053759 |
| Poaceae | Oryza coarctata | 2 | Oco01G014430, Oco02G014710 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_03G193500 |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0603313 |
| Poaceae | Sporobolus alterniflorus | 2 | Chr02G015570, Chr05G018250 |
| Poaceae | Thinopyrum elongatum | 1 | Tel3E01G376800 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC3AG032870, gene_TRIDC3BG037360 |
| Poaceae | Triticum aestivum | 3 | TraesCS3A02G219500.1.cds1, TraesCS3B02G250000.3 ... |
| Poaceae | Zea mays | 1 | Zm00001eb161950_P005 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-29262 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g8206 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc08g11280 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_12_RagTag.850 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-14120 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-21585 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000027l.124 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00006277 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-10632 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-21918 |
| Salicaceae | Populus euphratica | 1 | populus_peu10068 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132621203 |
| Solanaceae | Solanum chilense | 1 | SOLCI005462700 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107008945 |
| Tamaricaceae | Reaumuria soongarica | 1 | gene_16702 |
| Zosteraceae | Zostera marina | 2 | Zosma01g23600.v3.1, Zosma01g30140.v3.1 |