Basic Information
Locus ID:
Ag11G03444
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
Belongs to the histone deacetylase family. HD Type 1 subfamily
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr11 | 20117765 | 20123701 | + | Ag11G03444 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.11 | 55,565.85 Da | 36.94 | 72.39 | -0.49 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| Pfam | PF00850 | Histone deacetylase domain | 36 | 324 | 5.4E-85 | IPR023801 |
| SUPERFAMILY | SSF52768 | Arginase/deacetylase | 17 | 381 | 6.23E-125 | IPR023696 |
| Gene3D | G3DSA:3.40.800.20 | Histone deacetylase domain | 15 | 388 | 4.9E-141 | IPR037138 |
| PIRSF | PIRSF037913 | HDAC_I_euk | 3 | 490 | 2.0E-212 | IPR003084 |
| PRINTS | PR01271 | Histone deacetylase signature | 223 | 236 | 3.0E-65 | IPR003084 |
| PRINTS | PR01270 | Histone deacetylase superfamily signature | 145 | 168 | 1.4E-23 | IPR000286 |
| PRINTS | PR01270 | Histone deacetylase superfamily signature | 177 | 192 | 1.4E-23 | IPR000286 |
| PRINTS | PR01271 | Histone deacetylase signature | 240 | 258 | 3.0E-65 | IPR003084 |
| PRINTS | PR01271 | Histone deacetylase signature | 38 | 55 | 3.0E-65 | IPR003084 |
| PRINTS | PR01271 | Histone deacetylase signature | 123 | 143 | 3.0E-65 | IPR003084 |
| PRINTS | PR01271 | Histone deacetylase signature | 164 | 180 | 3.0E-65 | IPR003084 |
| PRINTS | PR01271 | Histone deacetylase signature | 71 | 89 | 3.0E-65 | IPR003084 |
| PRINTS | PR01271 | Histone deacetylase signature | 102 | 119 | 3.0E-65 | IPR003084 |
| PRINTS | PR01270 | Histone deacetylase superfamily signature | 262 | 272 | 1.4E-23 | IPR000286 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 461 | 494 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 468 | 494 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 383 | 417 | - | - |
Gene Ontology
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT4G38130.2 | histone deacetylase 1. Encodes a histone deacetylase that enhances AtERF7-mediated transcriptional repression. Binds SIM3 and ERF7. Expressed in the nucleus in most tissues examined and throughout the life of the plant. Involved in jasmonic acid and ethylene dependent pathogen resistance. The sequence in GenBank has 17 AG dinucleotide repeats missing, which is also missing in Ler shotgun sequence from Cereon. Although it is annotated to be in Columbia, the GB sequence is probably not of Columbia origin. Plays a role in embryogenesis as mutants grown at higher temperatures display abnormalities in the organization of the root and shoot. Plant lines expressing an RNAi construct targeted against HDA19 shows some resistance to agrobacterium-mediated root transformation. | 0 |
| RefSeq | XP_017243742.1 | PREDICTED: histone deacetylase 19-like [Daucus carota subsp. sativus] | 0 |
| O22446 | Histone deacetylase 19 OS=Arabidopsis thaliana OX=3702 GN=HDA19 PE=1 SV=2 | 0 | |
| TrEMBL | A0A165YVC9 | Histone deacetylase OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_013349 PE=3 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 50.339108 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 33.319054 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 33.527023 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 39.094746 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 34.212086 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 37.014503 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 31.89736 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 31.907997 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 59.889191 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 66.198235 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 70.290825 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 65.534126 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 62.833218 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 57.51952 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 24.790373 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 30.410395 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 29.273422 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 35.900875 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 26.353502 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 32.752174 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 37.423637 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 37.962296 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 39.102932 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 37.987198 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 33.741241 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 35.91394 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 30.911703 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 33.740936 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 38.178608 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 33.912457 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 37.923435 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 31.535942 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 49.208275 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 32.344543 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 34.366535 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 35.974964 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 28.303463 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 34.946983 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 40.499069 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 29.043619 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 27.292234 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 32.553459 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 46.805656 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 64.180412 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 62.208847 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 40.129604 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 47.846199 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 47.411976 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 41.475925 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 41.081688 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology