Basic Information
Locus ID:
Ag6G01764
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
lysine-specific demethylase
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr6 | 111474397 | 111502606 | + | Ag6G01764 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 6.95 | 209,954.97 Da | 47.33 | 87.04 | -0.32 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd15543 | PHD_RSF1 | 240 | 284 | 5.70666E-20 | - |
| CDD | cd16100 | ARID | 100 | 188 | 2.65881E-17 | - |
| Pfam | PF02375 | jmjN domain | 32 | 65 | 3.9E-15 | IPR003349 |
| Pfam | PF00628 | PHD-finger | 1703 | 1745 | 1.1E-7 | IPR019787 |
| Pfam | PF02373 | JmjC domain, hydroxylase | 410 | 526 | 9.7E-43 | IPR003347 |
| Pfam | PF01388 | ARID/BRIGHT DNA binding domain | 103 | 188 | 2.8E-10 | IPR001606 |
| Pfam | PF00628 | PHD-finger | 239 | 286 | 3.1E-9 | IPR019787 |
| Pfam | PF08429 | PLU-1-like protein | 889 | 1183 | 1.1E-24 | IPR013637 |
| Pfam | PF02928 | C5HC2 zinc finger | 619 | 671 | 3.2E-14 | IPR004198 |
| SUPERFAMILY | SSF51197 | Clavaminate synthase-like | 363 | 561 | 3.02E-31 | - |
| SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 226 | 286 | 1.2E-14 | IPR011011 |
| SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 1696 | 1750 | 3.1E-15 | IPR011011 |
| SUPERFAMILY | SSF46774 | ARID-like | 81 | 195 | 1.57E-21 | IPR036431 |
| Gene3D | G3DSA:2.60.120.650 | Cupin | 267 | 548 | 2.1E-107 | - |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 1685 | 1746 | 1.1E-16 | IPR013083 |
| Gene3D | G3DSA:2.60.120.650 | Cupin | 15 | 127 | 2.6E-25 | - |
| SMART | SM00501 | bright_3 | 99 | 193 | 1.1E-23 | IPR001606 |
| SMART | SM00545 | JmjN_1 | 30 | 71 | 6.7E-21 | IPR003349 |
| SMART | SM00558 | cupin_9 | 377 | 543 | 1.6E-60 | IPR003347 |
| SMART | SM00249 | PHD_3 | 1447 | 1492 | 0.0019 | IPR001965 |
| SMART | SM01014 | ARID_2 | 95 | 188 | 5.2E-6 | - |
| SMART | SM00249 | PHD_3 | 239 | 285 | 6.3E-10 | IPR001965 |
| SMART | SM00249 | PHD_3 | 1703 | 1745 | 5.0E-10 | IPR001965 |
| ProSiteProfiles | PS51184 | JmjC domain profile. | 377 | 543 | 38.096573 | IPR003347 |
| ProSiteProfiles | PS50016 | Zinc finger PHD-type profile. | 237 | 287 | 9.6502 | IPR019787 |
| ProSiteProfiles | PS51183 | JmjN domain profile. | 31 | 72 | 18.040232 | IPR003349 |
| ProSiteProfiles | PS51011 | ARID domain profile. | 98 | 192 | 18.99753 | IPR001606 |
| ProSitePatterns | PS01359 | Zinc finger PHD-type signature. | 1704 | 1744 | - | IPR019786 |
| ProSitePatterns | PS01359 | Zinc finger PHD-type signature. | 240 | 284 | - | IPR019786 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1752 | 1796 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1779 | 1796 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1752 | 1778 | - | - |
| Coils | Coil | Coil | 1011 | 1038 | - | - |
Gene Ontology
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT1G63490.4 | - | 0 |
| RefSeq | XP_017234993.1 | PREDICTED: lysine-specific demethylase lid [Daucus carota subsp. sativus] | 0 |
| F4I240 | Lysine-specific demethylase JMJ17 OS=Arabidopsis thaliana OX=3702 GN=JMJ17 PE=1 SV=1 | 0 | |
| TrEMBL | A0A166E065 | JmjC domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_006743 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 21.012676 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 22.620714 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 28.754337 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 27.305786 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 29.07682 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 37.937885 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 32.212639 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 36.599892 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 32.339809 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 32.624603 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 33.801319 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 31.423714 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 32.090904 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 28.135645 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 7.002047 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 8.78219 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 8.626707 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 14.884079 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 10.244697 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 14.066502 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 20.982904 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 10.088752 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 11.552538 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 11.061483 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 10.803898 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 16.709366 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 10.3887 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 12.003716 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 14.51927 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 2.051275 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 3.557673 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 2.420706 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 4.733025 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 3.04211 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 4.884264 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 2.897637 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 1.382235 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 1.858594 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 15.188576 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 12.398461 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 9.407517 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 16.669449 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 19.821775 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 28.465395 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 23.468725 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 13.976208 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 25.374043 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 14.906956 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 17.399927 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 15.076243 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg7628 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_14746 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah004642 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg23843, Sbi_jg7673 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg12348 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00001211 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl51980, Sgl57283 |
| Amaranthaceae | Chenopodium album | 4 | gene:ENSEOMG00000008167, gene:ENSEOMG00000022133 ... |
| Amaranthaceae | Chenopodium quinoa | 4 | CQ.Regalona.r1.2BG0010030, CQ.Regalona.r1.5AG0007490 ... |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30137140 |
| Apiaceae | Apium graveolens | 1 | Ag6G01764 |
| Arecaceae | Cocos nucifera | 1 | COCNU_09G007690 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103705556 |
| Asparagaceae | Asparagus officinalis | 2 | AsparagusV1_07.2188.V1.1, AsparagusV1_07.2189.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri13G25995 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT1G63490.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10023217m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp2g01130.v2.2 |
| Brassicaceae | Brassica nigra | 1 | BniB04g024190.2N |
| Casuarinaceae | Casuarina equisetifolia | 2 | Ceq03G0366, Ceq03G0370 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl03G0462 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG10.1379 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00030419 |
| Plumbaginaceae | Limonium bicolor | 5 | Lb2G10687, Lb2G10688, Lb2G10689, Lb2G10690, Lb2G10861 |
| Poaceae | Echinochloa crus-galli | 3 | AH06.3076, BH06.2875, CH06.989 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_6AG0551750, gene-QOZ80_6BG0505330 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.7HG0752360.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_037051 |
| Poaceae | Oryza coarctata | 2 | Oco11G017830, Oco12G018160 |
| Poaceae | Oryza sativa | 1 | LOC_Os06g51490.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_10G267700 |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0404194 |
| Poaceae | Sporobolus alterniflorus | 1 | Chr10G022770 |
| Poaceae | Thinopyrum elongatum | 1 | Tel7E01G1015100 |
| Poaceae | Triticum dicoccoides | 1 | gene_TRIDC7AG078290 |
| Poaceae | Triticum aestivum | 3 | TraesCS7A02G566000.1, TraesCS7B02G492100.1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb229050_P001 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG18.600, evm.TU.LG26.431 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc06g05360 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_16_RagTag.185 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-22424 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-6279 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-20315 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000022l.382 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00014317 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-3525 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-6682 |
| Salicaceae | Populus euphratica | 1 | populus_peu34394 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132634893 |
| Solanaceae | Solanum chilense | 1 | SOLCI004164700 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107028578 |
| Tamaricaceae | Reaumuria soongarica | 1 | gene_11321 |
| Tamaricaceae | Tamarix chinensis | 1 | TC06G0230 |