Basic Information
Locus ID:
Ag6G00551
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
Modified RING finger domain
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr6 | 18644588 | 18647557 | + | Ag6G00551 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 7.80 | 70,071.79 Da | 42.91 | 100.12 | -0.09 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd16664 | RING-Ubox_PUB | 267 | 309 | 8.76959E-27 | - |
| Pfam | PF04564 | U-box domain | 264 | 333 | 4.2E-19 | IPR003613 |
| Pfam | PF00514 | Armadillo/beta-catenin-like repeat | 393 | 431 | 1.9E-8 | IPR000225 |
| Pfam | PF00514 | Armadillo/beta-catenin-like repeat | 475 | 513 | 2.8E-8 | IPR000225 |
| SUPERFAMILY | SSF48371 | ARM repeat | 362 | 636 | 1.12E-42 | IPR016024 |
| SUPERFAMILY | SSF57850 | RING/U-box | 255 | 336 | 6.6E-31 | - |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 242 | 342 | 6.3E-30 | IPR013083 |
| Gene3D | G3DSA:1.25.10.10 | - | 349 | 443 | 2.1E-16 | IPR011989 |
| Gene3D | G3DSA:1.25.10.10 | - | 444 | 640 | 7.9E-32 | IPR011989 |
| SMART | SM00185 | arm_5 | 474 | 514 | 3.3E-4 | IPR000225 |
| SMART | SM00185 | arm_5 | 433 | 473 | 0.46 | IPR000225 |
| SMART | SM00185 | arm_5 | 515 | 555 | 340.0 | IPR000225 |
| SMART | SM00185 | arm_5 | 392 | 432 | 0.012 | IPR000225 |
| SMART | SM00504 | Ubox_2 | 266 | 329 | 2.7E-32 | IPR003613 |
| ProSiteProfiles | PS50176 | Armadillo/plakoglobin ARM repeat profile. | 444 | 486 | 8.7674 | IPR000225 |
| ProSiteProfiles | PS50176 | Armadillo/plakoglobin ARM repeat profile. | 403 | 445 | 11.1124 | IPR000225 |
| ProSiteProfiles | PS50176 | Armadillo/plakoglobin ARM repeat profile. | 485 | 527 | 9.1174 | IPR000225 |
| ProSiteProfiles | PS51698 | U-box domain profile. | 262 | 336 | 41.567711 | IPR003613 |
| Coils | Coil | Coil | 138 | 158 | - | - |
Gene Ontology
Biological Process:
Molecular Function:
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT1G23030.1 | ARM repeat superfamily protein. | 0 |
| RefSeq | XP_017232057.1 | PREDICTED: U-box domain-containing protein 10-like [Daucus carota subsp. sativus] | 0 |
| Q8GUG9 | U-box domain-containing protein 11 OS=Arabidopsis thaliana OX=3702 GN=PUB11 PE=2 SV=2 | 0 | |
| TrEMBL | A0A166EEF4 | RING-type E3 ubiquitin transferase OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_007288 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 1.330323 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 0.672378 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 0.387324 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 0.982423 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 0.925413 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 0.893289 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 0.444139 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 0 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 4.352437 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 4.964311 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 5.92602 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 3.321846 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 4.254051 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 5.048742 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 1.939649 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 0.94247 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 1.909801 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 5.575284 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 4.093335 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 4.385545 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 5.562973 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 1.93756 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 2.819512 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 3.022285 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 3.330267 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 4.146536 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 4.887538 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 4.566961 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 4.518911 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 1.157591 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 2.756157 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 1.654961 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 1.467882 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 1.36871 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 2.050239 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 1.647033 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 1.413914 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 1.800649 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 6.960186 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 11.451839 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 7.871047 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 0.945325 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 0.435643 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 0.372881 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 0.463269 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 0.416595 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 0.310869 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 8.409045 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 9.043069 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 7.443655 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 3 | jg35008, jg5192, jg7314 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_18581 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah025332 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_6g144830 |
| Amaranthaceae | Salicornia bigelovii | 3 | Sbi_jg12914, Sbi_jg52950, Sbi_jg52951 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg8905 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00009008 |
| Amaranthaceae | Suaeda glauca | 7 | Sgl31132, Sgl32514, Sgl32515, Sgl36486, Sgl37776, Sgl37777 ... |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000002705, gene:ENSEOMG00000003094 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.6AG0012350, CQ.Regalona.r1.6BG0012950 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30217060 |
| Apiaceae | Apium graveolens | 4 | Ag11G03910, Ag5G01966, Ag6G00551, Ag8G01841 |
| Arecaceae | Cocos nucifera | 1 | COCNU_03G010220 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103695610 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_06.500.V1.1 |
| Asteraceae | Flaveria trinervia | 2 | Ftri13G03791, Ftri8G13159 |
| Brassicaceae | Arabidopsis thaliana | 2 | AT1G23030.1, AT1G71020.1 |
| Brassicaceae | Eutrema salsugineum | 2 | Thhalv10007104m.g.v1.0, Thhalv10018269m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 2 | Sp1g20480.v2.2, Sp5g26190.v2.2 |
| Brassicaceae | Brassica nigra | 3 | BniB03g030610.2N, BniB03g048920.2N, BniB04g038270.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq09G0910 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl09G0986 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno11g08420 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG03.1412 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00021569 |
| Plumbaginaceae | Limonium bicolor | 2 | Lb1G01465, Lb2G13229 |
| Poaceae | Echinochloa crus-galli | 3 | AH07.3353, BH07.3179, CH07.3239 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_2AG0144450, gene-QOZ80_2BG0199920 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.6HG0612510.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_025079 |
| Poaceae | Oryza coarctata | 2 | Oco03G020820, Oco04G021440 |
| Poaceae | Oryza sativa | 1 | LOC_Os02g49950.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_04G267000 |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0203429 |
| Poaceae | Sporobolus alterniflorus | 2 | Chr09G020900, Chr13G005150 |
| Poaceae | Thinopyrum elongatum | 1 | Tel6E01G533800 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC6AG044730, gene_TRIDC6BG052360 |
| Poaceae | Triticum aestivum | 3 | TraesCS6A02G293600.1, TraesCS6B02G324000.1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb190130_P001 |
| Poaceae | Zoysia japonica | 2 | nbis-gene-21941, nbis-gene-21942 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g17081 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG13.827, evm.TU.LG21.485 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc08g00600 |
| Rhizophoraceae | Bruguiera sexangula | 2 | evm.TU.Scaffold_15_RagTag.162, evm.TU.Scaffold_17_RagTag.829 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-23543 |
| Rhizophoraceae | Ceriops tagal | 2 | nbisL1-mrna-11779, nbisL1-mrna-16846 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-17499 |
| Rhizophoraceae | Kandelia candel | 2 | evm.TU.utg000001l.104, evm.TU.utg000013l.465 |
| Rhizophoraceae | Kandelia obovata | 2 | Maker00004452, Maker00004586 |
| Rhizophoraceae | Rhizophora apiculata | 2 | nbisL1-mrna-10858, nbisL1-mrna-11620 |
| Rhizophoraceae | Rhizophora mangle | 2 | nbisL1-mrna-14209, nbisL1-mrna-2766 |
| Salicaceae | Populus euphratica | 2 | populus_peu07148, populus_peu21130 |
| Solanaceae | Lycium barbarum | 2 | gene-LOC132613646, gene-LOC132641621 |
| Solanaceae | Solanum chilense | 2 | SOLCI005517900, SOLCI005631600 |
| Solanaceae | Solanum pennellii | 2 | gene-LOC107017697, gene-LOC107020839 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.9235_chr03_+ |
| Tamaricaceae | Tamarix chinensis | 2 | TC04G1243, TC11G1005 |