Basic Information
Locus ID:
Ag1G00849
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
histone deacetylase
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr1 | 140647717 | 140650622 | + | Ag1G00849 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.77 | 15,976.74 Da | 56.58 | 70.28 | -0.32 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| Pfam | PF02148 | Zn-finger in ubiquitin-hydrolases and other protein | 54 | 112 | 8.1E-16 | IPR001607 |
| SUPERFAMILY | SSF57850 | RING/U-box | 32 | 123 | 4.47E-21 | - |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 28 | 135 | 5.1E-27 | IPR013083 |
| SMART | SM00290 | Zf_UBP_1 | 53 | 102 | 5.3E-4 | IPR001607 |
| ProSiteProfiles | PS50271 | Zinc finger UBP-type profile. | 52 | 113 | 16.582327 | IPR001607 |
Gene Ontology
Molecular Function:
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT2G14825.1 | - | 0 |
| RefSeq | XP_017224232.1 | PREDICTED: histone deacetylase 6 [Daucus carota subsp. sativus] | 0 |
| A0A8I6GM68 | Protein deacetylase HDAC6 OS=Rattus norvegicus OX=10116 GN=Hdac6 PE=3 SV=1 | 0 | |
| TrEMBL | A0A175YFB0 | UBP-type domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_029115 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 17.128426 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 23.750841 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 26.854506 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 22.47463 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 24.80385 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 24.746864 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 19.384823 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 13.726217 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 28.249596 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 21.25672 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 26.109554 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 27.145895 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 28.955059 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 24.677191 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 22.91165 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 19.146372 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 22.341705 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 19.27578 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 16.640848 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 17.321634 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 22.703051 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 27.597424 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 20.573404 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 21.754881 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 26.052216 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 15.666703 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 20.493217 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 16.520046 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 16.803286 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 15.197399 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 12.832917 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 13.741668 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 18.221743 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 24.869532 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 22.543442 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 26.795565 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 25.343924 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 20.670328 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 19.212904 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 13.445309 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 12.778687 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 38.697063 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 40.475693 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 54.811707 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 55.31649 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 47.530315 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 49.017044 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 43.955795 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 43.404972 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 44.799614 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg30213 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_9494 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah015819 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_8g190350 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg25312, Sbi_jg9162 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg19427 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00011187 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl42949, Sgl47782 |
| Amaranthaceae | Chenopodium album | 2 | gene:ENSEOMG00000034159, gene:ENSEOMG00000048384 |
| Amaranthaceae | Chenopodium quinoa | 1 | CQ.Regalona.r1.8AG0011600 |
| Anacardiaceae | Pistacia vera | 4 | pistato.v30106020, pistato.v30106030, pistato.v30106240 ... |
| Apiaceae | Apium graveolens | 2 | Ag1G00849, Ag5G01453 |
| Arecaceae | Cocos nucifera | 1 | COCNU_13G006640 |
| Arecaceae | Phoenix dactylifera | 2 | gene-LOC103695865, gene-LOC120113229 |
| Asteraceae | Flaveria trinervia | 1 | Ftri14G05249 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10022899m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp3g28020.v2.2 |
| Brassicaceae | Brassica nigra | 1 | BniB06g037630.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq09G0285 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl09G0321 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno01g09340 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate02g21920 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG08.586 |
| Plantaginaceae | Plantago ovata | 2 | Pov_00012013, Pov_00022435 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb3G16654 |
| Poaceae | Echinochloa crus-galli | 2 | AH05.3576, CH05.3760 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_5AG0391890, gene-QOZ80_5BG0439320 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.5HG0448420.1 |
| Poaceae | Oryza coarctata | 2 | Oco23G007250, Oco24G006860 |
| Poaceae | Oryza sativa | 1 | LOC_Os12g32374.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_08G080800 |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0703574 |
| Poaceae | Sporobolus alterniflorus | 4 | Chr04G015830, Chr06G016540, Chr19G010180, Chr27G006220 |
| Poaceae | Thinopyrum elongatum | 1 | Tel5E01G197300 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC5AG016090, gene_TRIDC5BG017910 |
| Poaceae | Triticum aestivum | 3 | TraesCS5A02G105700.1, TraesCS5B02G107800.1 ... |
| Poaceae | Zea mays | 3 | Zm00001eb137960_P003, Zm00001eb264700_P001 ... |
| Poaceae | Zoysia japonica | 1 | nbis-gene-48639 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g25108 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG04.2636, evm.TU.LG08.233 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc03g20740 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_2_RagTag.399 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-4796 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-9514 |
| Rhizophoraceae | Ceriops zippeliana | 2 | nbisL1-mrna-9755, nbisL1-mrna-9756 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000009l.721 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00005114 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-2544 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-16488 |
| Salicaceae | Populus euphratica | 1 | populus_peu36229 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132606483 |
| Solanaceae | Solanum chilense | 1 | SOLCI003702700 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107032407 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.14562_chr08_- |
| Zosteraceae | Zostera marina | 1 | Zosma05g22570.v3.1 |