Basic Information
Locus ID:
Ag2G01034
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
histone deacetylase
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr2 | 53868042 | 53871086 | + | Ag2G01034 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 4.85 | 30,479.93 Da | 48.90 | 52.28 | -0.97 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| Pfam | PF17800 | Nucleoplasmin-like domain | 3 | 93 | 7.7E-11 | IPR041232 |
| Gene3D | G3DSA:2.60.120.340 | Nucleoplasmin core domain | 1 | 101 | 1.6E-16 | - |
| ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 259 | 285 | 11.177467 | IPR013087 |
| ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 261 | 282 | - | IPR013087 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 98 | 285 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 252 | 271 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 102 | 120 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 166 | 192 | - | - |
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT5G22650.2 | histone deacetylase 2B. Encodes a member of a plant-specific class of histone deacetylases. Controls the development of adaxial/abaxial leaf polarity. Its mRNA is widely expressed in stems, leaves, flowers and young siliques. Plant lines expressing RNAi constructs directed against this gene showed a marked reduction in agrobacterium-mediated root transformation. | 0 |
| RefSeq | XP_017248719.1 | PREDICTED: histone deacetylase HDT1-like [Daucus carota subsp. sativus] | 0 |
| Q8LJS2 | Histone deacetylase HDT1 OS=Glycine max OX=3847 GN=HDT1 PE=2 SV=1 | 0 | |
| TrEMBL | A0A162A538 | C2H2-type domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_018742 PE=3 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 341.681 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 212.305328 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 201.032013 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 205.187714 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 229.403488 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 216.305481 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 168.880203 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 107.635529 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 297.213562 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 294.110535 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 309.407562 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 336.397278 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 301.257263 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 259.244659 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 100.659744 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 157.897415 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 184.704605 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 145.889069 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 129.687439 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 187.086426 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 164.48732 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 236.648849 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 270.661469 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 247.20076 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 261.945709 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 145.803802 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 158.507233 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 150.20874 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 178.744583 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 210.740067 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 260.27475 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 274.814697 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 368.263947 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 342.246796 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 313.009094 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 285.233917 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 269.37616 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 268.916901 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 209.255859 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 76.98671 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 29.92421 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 149.821838 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 190.658737 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 515.774719 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 295.295807 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 199.663452 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 226.552505 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 428.609009 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 359.873474 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 433.010773 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 5 | jg15041, jg31978, jg32670, jg35967, jg8181 |
| Aizoaceae | Mesembryanthemum crystallinum | 2 | gene_14409, gene_21238 |
| Amaranthaceae | Atriplex hortensis | 2 | Ah011449, Ah030881 |
| Amaranthaceae | Beta vulgaris | 3 | BVRB_7g160340, BVRB_9g211080, BVRB_9g211090 |
| Amaranthaceae | Salicornia bigelovii | 4 | Sbi_jg11888, Sbi_jg27463, Sbi_jg33193, Sbi_jg46829 |
| Amaranthaceae | Salicornia europaea | 2 | Seu_jg21129, Seu_jg7924 |
| Amaranthaceae | Suaeda aralocaspica | 2 | GOSA_00009448, GOSA_00012280 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl36042, Sgl71386 |
| Amaranthaceae | Chenopodium album | 6 | gene:ENSEOMG00000008477, gene:ENSEOMG00000016783 ... |
| Amaranthaceae | Chenopodium quinoa | 3 | CQ.Regalona.r1.7AG0019570, CQ.Regalona.r1.9AG0010760 ... |
| Anacardiaceae | Pistacia vera | 3 | pistato.v30057190, pistato.v30064670, pistato.v30274690 |
| Apiaceae | Apium graveolens | 3 | Ag10G00664, Ag10G02017, Ag2G01034 |
| Arecaceae | Cocos nucifera | 1 | scaffold007076G000010 |
| Arecaceae | Phoenix dactylifera | 3 | gene-LOC103698848, gene-LOC103717262, gene-LOC103717689 |
| Asparagaceae | Asparagus officinalis | 4 | AsparagusV1_01.14.V1.1, AsparagusV1_02.1127.V1.1 ... |
| Asteraceae | Flaveria trinervia | 3 | Ftri11G23030, Ftri12G31108, Ftri2G22122 |
| Brassicaceae | Arabidopsis thaliana | 4 | AT2G27840.1, AT3G44750.1, AT5G03740.1, AT5G22650.1 |
| Brassicaceae | Eutrema salsugineum | 4 | Thhalv10002782m.g.v1.0, Thhalv10014245m.g.v1.0 ... |
| Brassicaceae | Schrenkiella parvula | 4 | Sp4g10680.v2.2, Sp5g16430.v2.2, Sp6g22690.v2.2 ... |
| Brassicaceae | Brassica nigra | 8 | BniB01g016040.2N, BniB02g040970.2N, BniB02g056800.2N ... |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq02G1501 |
| Casuarinaceae | Casuarina glauca | 2 | Cgl02G1555, Cgl05G1725 |
| Cymodoceaceae | Cymodocea nodosa | 2 | gene.Cymno07g00040, gene.Cymno07g00060 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0022s00013.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate02g16430 |
| Malvaceae | Hibiscus hamabo Siebold & Zucc. | 1 | nbisL1-mrna-478 |
| Nitrariaceae | Nitraria sibirica | 2 | evm.TU.LG01.2139, evm.TU.LG09.766 |
| Plantaginaceae | Plantago ovata | 2 | Pov_00004917, Pov_00026501 |
| Plumbaginaceae | Limonium bicolor | 3 | Lb1G02469, Lb3G17555, Lb3G19840 |
| Poaceae | Echinochloa crus-galli | 4 | AH02.4251, BH05.1244, CH01.2743, CH05.1459 |
| Poaceae | Eleusine coracana subsp. coracana | 1 | gene-QOZ80_5AG0361410 |
| Poaceae | Hordeum vulgare | 2 | HORVU.MOREX.r3.1HG0095390.1, HORVU.MOREX.r3.3HG0308540.1 |
| Poaceae | Lolium multiflorum | 5 | gene-QYE76_007791, gene-QYE76_015652, gene-QYE76_023278 ... |
| Poaceae | Oryza coarctata | 4 | Oco02G029000, Oco08G000010, Oco09G018640, Oco10G018600 |
| Poaceae | Oryza sativa | 1 | LOC_Os05g51830.1 |
| Poaceae | Paspalum vaginatum | 2 | gene-BS78_03G374700, gene-BS78_08G083800 |
| Poaceae | Puccinellia tenuiflora | 2 | Pt_Chr0505954, Pt_Chr0600409 |
| Poaceae | Sporobolus alterniflorus | 7 | Chr01G016630, Chr02G016680, Chr0G020500, Chr0G024550 ... |
| Poaceae | Thinopyrum elongatum | 3 | Tel1E01G753900, Tel3E01G660300, Tel3E01G710000 |
| Poaceae | Triticum dicoccoides | 4 | gene_TRIDC1AG065380, gene_TRIDC1BG074690 ... |
| Poaceae | Triticum aestivum | 4 | TraesCS1A02G445700.4, TraesCS1D02G454400.2 ... |
| Poaceae | Zea mays | 6 | Zm00001eb143960_P001, Zm00001eb294030_P002 ... |
| Poaceae | Zoysia japonica | 2 | nbis-gene-24679, nbis-gene-28412 |
| Poaceae | Zoysia macrostachya | 2 | Zma_g11769, Zma_g28941 |
| Portulacaceae | Portulaca oleracea | 8 | evm.TU.LG06.1065, evm.TU.LG07.1009, evm.TU.LG09.1877 ... |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc05g22980 |
| Rhizophoraceae | Bruguiera sexangula | 2 | evm.TU.Scaffold_12_RagTag.591, evm.TU.Scaffold_1_RagTag.1458 |
| Rhizophoraceae | Carallia pectinifolia | 3 | nbisL1-mrna-24138, nbisL1-mrna-30671, nbisL1-mrna-6134 |
| Rhizophoraceae | Ceriops tagal | 3 | nbisL1-mrna-16366, nbisL1-mrna-3076, nbisL1-mrna-4524 |
| Rhizophoraceae | Ceriops zippeliana | 2 | nbisL1-mrna-19829, nbisL1-mrna-3996 |
| Rhizophoraceae | Kandelia candel | 2 | evm.TU.utg000016l.483, evm.TU.utg000027l.205 |
| Rhizophoraceae | Kandelia obovata | 2 | Maker00016977, Maker00017857 |
| Rhizophoraceae | Rhizophora apiculata | 2 | nbisL1-mrna-5774, nbisL1-mrna-7657 |
| Rhizophoraceae | Rhizophora mangle | 3 | nbisL1-mrna-12065, nbisL1-mrna-427, nbisL1-mrna-5775 |
| Salicaceae | Populus euphratica | 3 | populus_peu08558, populus_peu11588, populus_peu36779 |
| Solanaceae | Lycium barbarum | 3 | gene-LOC132600522, gene-LOC132606966, gene-LOC132629913 |
| Solanaceae | Solanum chilense | 3 | SOLCI003023900, SOLCI003411500, SOLCI006579300 |
| Solanaceae | Solanum pennellii | 3 | gene-LOC107004842, gene-LOC107031726, gene-LOC107031948 |
| Tamaricaceae | Reaumuria soongarica | 4 | MSTRG.3824_chr02_-, gene_5669, gene_8084, gene_8085 |
| Tamaricaceae | Tamarix chinensis | 3 | TC00000018, TC02G2533, TC03G1856 |
| Zosteraceae | Zostera marina | 3 | Zosma01g01830.v3.1, Zosma03g05130.v3.1, Zosma06g10160.v3.1 |