Basic Information
Locus ID:
Ag2G03004
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
RING-type E3 ubiquitin transferase
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr2 | 320588623 | 320594186 | - | Ag2G03004 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.81 | 90,134.90 Da | 46.45 | 104.34 | -0.08 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd16664 | RING-Ubox_PUB | 33 | 78 | 3.1266E-17 | - |
| Pfam | PF04564 | U-box domain | 31 | 105 | 1.0E-13 | IPR003613 |
| SUPERFAMILY | SSF48371 | ARM repeat | 121 | 443 | 1.37E-39 | IPR016024 |
| SUPERFAMILY | SSF57850 | RING/U-box | 22 | 110 | 1.77E-20 | - |
| SUPERFAMILY | SSF48371 | ARM repeat | 408 | 797 | 1.86E-21 | IPR016024 |
| Gene3D | G3DSA:1.25.10.10 | - | 572 | 799 | 1.5E-19 | IPR011989 |
| Gene3D | G3DSA:1.25.10.10 | - | 316 | 485 | 2.7E-20 | IPR011989 |
| Gene3D | G3DSA:1.25.10.10 | - | 115 | 315 | 1.2E-23 | IPR011989 |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 13 | 114 | 2.5E-21 | IPR013083 |
| SMART | SM00185 | arm_5 | 139 | 179 | 1.1 | IPR000225 |
| SMART | SM00185 | arm_5 | 347 | 391 | 15.0 | IPR000225 |
| SMART | SM00185 | arm_5 | 307 | 346 | 370.0 | IPR000225 |
| SMART | SM00504 | Ubox_2 | 32 | 100 | 5.1E-23 | IPR003613 |
| SMART | SM00185 | arm_5 | 181 | 221 | 41.0 | IPR000225 |
| SMART | SM00185 | arm_5 | 671 | 712 | 34.0 | IPR000225 |
| SMART | SM00185 | arm_5 | 266 | 306 | 190.0 | IPR000225 |
| ProSiteProfiles | PS51698 | U-box domain profile. | 28 | 107 | 20.612247 | IPR003613 |
Gene Ontology
Biological Process:
Molecular Function:
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT1G20780.1 | senescence-associated E3 ubiquitin ligase 1. Encodes a protein containing a U-box and an ARM domain. | 0 |
| RefSeq | XP_017253269.1 | PREDICTED: U-box domain-containing protein 44 [Daucus carota subsp. sativus] | 0 |
| Q9LM76 | U-box domain-containing protein 44 OS=Arabidopsis thaliana OX=3702 GN=PUB44 PE=1 SV=1 | 0 | |
| TrEMBL | A0A162A167 | RING-type E3 ubiquitin transferase OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_016785 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 1.396064 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 1.668592 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 1.576905 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 1.604995 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 1.476769 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 1.957014 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 1.933864 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 1.969558 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 1.911907 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 2.157569 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 1.829322 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 0.788568 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 1.790262 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 1.177554 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 4.264802 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 7.407029 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 1.36279 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 9.946533 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 8.853724 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 23.550632 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 13.877324 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 2.738694 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 1.886263 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 1.525125 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 5.197889 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 2.414401 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 1.737267 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 2.929569 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 2.124154 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 6.481345 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 6.362944 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 5.102179 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 7.838586 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 4.599816 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 12.245226 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 10.521732 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 11.594449 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 11.162524 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 1.722073 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 6.643896 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 6.229901 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 24.206018 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 21.337847 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 6.902683 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 6.349768 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 20.860952 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 4.621447 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 2.061017 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 1.251 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 2.594362 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 3 | jg11483, jg22560, jg6038 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_8337 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah035827 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_1g014400 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg39825, Sbi_jg55165 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg14502 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00013034 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl12431, Sgl17698 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000019431, gene:ENSEOMG00000036220 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.1AG0023360, CQ.Regalona.r1.1BG0000890 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30048200 |
| Apiaceae | Apium graveolens | 2 | Ag11G03525, Ag2G03004 |
| Arecaceae | Cocos nucifera | 3 | COCNU_07G014420, COCNU_08G009490, COCNU_10G009070 |
| Arecaceae | Phoenix dactylifera | 5 | gene-LOC103710505, gene-LOC103720109, gene-LOC103723310 ... |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_10.297.V1.1 |
| Asteraceae | Flaveria trinervia | 3 | Ftri18G01279, Ftri1G30940, Ftri8G18286 |
| Brassicaceae | Arabidopsis thaliana | 2 | AT1G20780.1, AT1G76390.1 |
| Brassicaceae | Eutrema salsugineum | 2 | Thhalv10006866m.g.v1.0, Thhalv10018134m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 2 | Sp1g18480.v2.2, Sp5g31540.v2.2 |
| Brassicaceae | Brassica nigra | 3 | BniB03g008770.2N, BniB03g029340.2N, BniB03g055300.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | CeqSG0264 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl03G1252 |
| Cymodoceaceae | Cymodocea nodosa | 4 | gene.Cymno02g10380, gene.Cymno09g00110, gene.Cymno10g08290 ... |
| Hydrocharitaceae | Thalassia testudinum | 5 | gene.Thate01g20640, gene.Thate05g02960, gene.Thate08g17230 ... |
| Malvaceae | Hibiscus hamabo Siebold & Zucc. | 1 | nbisL1-mrna-8967 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG06.63 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00023135 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb1G02794 |
| Poaceae | Echinochloa crus-galli | 9 | AH03.2855, AH05.3217, AH07.4061, BH03.3026, BH05.3253 ... |
| Poaceae | Eleusine coracana subsp. coracana | 5 | gene-QOZ80_2AG0151760, gene-QOZ80_2BG0207130 ... |
| Poaceae | Hordeum vulgare | 2 | HORVU.MOREX.r3.5HG0449730.1, HORVU.MOREX.r3.6HG0634120.1 |
| Poaceae | Lolium multiflorum | 3 | gene-QYE76_009400, gene-QYE76_009520, gene-QYE76_033574 |
| Poaceae | Oryza coarctata | 5 | Oco05G019450, Oco06G020230, Oco23G004820, Oco23G004830 ... |
| Poaceae | Oryza sativa | 3 | LOC_Os03g45420.1, LOC_Os12g17880.1, LOC_Os12g17900.1 |
| Poaceae | Paspalum vaginatum | 3 | gene-BS78_02G266600, gene-BS78_04G331200 ... |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0402551 |
| Poaceae | Sporobolus alterniflorus | 9 | Chr04G020480, Chr06G021970, Chr0G005880, Chr13G000070 ... |
| Poaceae | Thinopyrum elongatum | 2 | Tel5E01G207600, Tel6E01G791700 |
| Poaceae | Triticum dicoccoides | 4 | gene_TRIDC5AG017550, gene_TRIDC5BG019230 ... |
| Poaceae | Triticum aestivum | 6 | TraesCS5A02G111000.3, TraesCS5B02G110000.1 ... |
| Poaceae | Zea mays | 4 | Zm00001eb133350_P001, Zm00001eb190530_P001 ... |
| Poaceae | Zoysia japonica | 3 | nbis-gene-12407, nbis-gene-52803, nbis-gene-8232 |
| Poaceae | Zoysia macrostachya | 4 | Zma_g14770, Zma_g24971, Zma_g25697, Zma_g29930 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG07.475, evm.TU.LG15.467 |
| Posidoniaceae | Posidonia oceanica | 4 | gene.Posoc02g11160, gene.Posoc06g15190, gene.Posoc06g15200 ... |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_15_RagTag.513 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-26670 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-4790 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-15845 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000001l.254 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00002575 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-13865 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-2518 |
| Salicaceae | Populus euphratica | 2 | populus_peu15496, populus_peu33132 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132628229 |
| Solanaceae | Solanum chilense | 1 | SOLCI003211100 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107018115 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.31460_chr11_+ |
| Tamaricaceae | Tamarix chinensis | 1 | TC04G2421 |
| Zosteraceae | Zostera marina | 3 | Zosma01g09610.v3.1, Zosma03g35280.v3.1, Zosma05g23510.v3.1 |