Basic Information
Locus ID:
Ag5G00312
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 |
|---|---|---|---|---|
| chr5 | 5998432 | 6004677 | + | Ag5G00312 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.71 | 89,319.96 Da | 43.90 | 91.75 | -0.27 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd16664 | RING-Ubox_PUB | 240 | 282 | 1.69454E-24 | - |
| Pfam | PF00514 | Armadillo/beta-catenin-like repeat | 571 | 608 | 1.1E-10 | IPR000225 |
| Pfam | PF04564 | U-box domain | 236 | 306 | 1.6E-21 | IPR003613 |
| Pfam | PF00514 | Armadillo/beta-catenin-like repeat | 653 | 690 | 1.0E-6 | IPR000225 |
| SUPERFAMILY | SSF48371 | ARM repeat | 540 | 812 | 8.13E-47 | IPR016024 |
| SUPERFAMILY | SSF57850 | RING/U-box | 224 | 313 | 9.08E-29 | - |
| Gene3D | G3DSA:1.25.10.10 | - | 523 | 817 | 3.2E-62 | IPR011989 |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 235 | 309 | 8.6E-26 | IPR013083 |
| SMART | SM00185 | arm_5 | 692 | 731 | 0.0023 | IPR000225 |
| SMART | SM00185 | arm_5 | 651 | 691 | 0.14 | IPR000225 |
| SMART | SM00185 | arm_5 | 610 | 650 | 11.0 | IPR000225 |
| SMART | SM00185 | arm_5 | 569 | 609 | 1.8E-7 | IPR000225 |
| SMART | SM00185 | arm_5 | 732 | 772 | 3.5 | IPR000225 |
| SMART | SM00504 | Ubox_2 | 239 | 302 | 9.4E-32 | IPR003613 |
| ProSiteProfiles | PS50176 | Armadillo/plakoglobin ARM repeat profile. | 703 | 744 | 10.9024 | IPR000225 |
| ProSiteProfiles | PS50176 | Armadillo/plakoglobin ARM repeat profile. | 580 | 622 | 13.212399 | IPR000225 |
| ProSiteProfiles | PS51698 | U-box domain profile. | 235 | 309 | 41.107735 | IPR003613 |
| ProSiteProfiles | PS50176 | Armadillo/plakoglobin ARM repeat profile. | 662 | 704 | 10.377399 | IPR000225 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 458 | 495 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 340 | 425 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 405 | 425 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 458 | 508 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 342 | 373 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 374 | 404 | - | - |
| Coils | Coil | Coil | 179 | 202 | - | - |
Gene Ontology
Biological Process:
Molecular Function:
KEGG Pathway
KO Term:
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT2G23140.1 | RING/U-box superfamily protein with ARM repeat domain. | 0 |
| RefSeq | XP_017218760.1 | PREDICTED: U-box domain-containing protein 4 isoform X1 [Daucus carota subsp. sativus] | 0 |
| O22193 | U-box domain-containing protein 4 OS=Arabidopsis thaliana OX=3702 GN=PUB4 PE=1 SV=3 | 0 | |
| TrEMBL | A0A164UC46 | RING-type E3 ubiquitin transferase OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_025771 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 32.01413 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 28.82151 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 31.169634 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 31.761742 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 32.9715 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 33.70195 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 25.559902 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 24.717367 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 40.154484 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 38.849335 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 38.460331 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 33.047703 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 35.075645 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 33.280964 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 24.813955 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 25.366747 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 24.112776 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 26.466576 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 17.494205 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 29.500729 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 32.989128 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 23.843002 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 21.595741 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 21.619024 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 20.196857 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 27.346672 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 23.968145 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 20.637609 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 25.406946 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 7.263465 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 10.07741 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 8.667465 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 31.68111 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 22.2181 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 34.278435 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 21.661871 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 8.760981 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 12.855732 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 21.517429 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 18.490499 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 13.012701 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 48.001434 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 33.104935 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 24.387976 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 23.725082 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 45.083874 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 22.082575 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 24.214104 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 26.778076 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 22.876545 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 2 | jg4700, jg4701 |
| Aizoaceae | Mesembryanthemum crystallinum | 2 | gene_23981, gene_25145 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah031925 |
| Amaranthaceae | Beta vulgaris | 3 | BVRB_2g043480, BVRB_2g043510, BVRB_6g127640 |
| Amaranthaceae | Salicornia bigelovii | 5 | Sbi_jg13104, Sbi_jg30282, Sbi_jg43700, Sbi_jg51997 ... |
| Amaranthaceae | Salicornia europaea | 3 | Seu_jg18207, Seu_jg9099, Seu_jg9860 |
| Amaranthaceae | Suaeda aralocaspica | 2 | GOSA_00010153, GOSA_00023210 |
| Amaranthaceae | Suaeda glauca | 5 | Sgl33857, Sgl39230, Sgl65815, Sgl65847, Sgl70157 |
| Amaranthaceae | Chenopodium album | 6 | gene:ENSEOMG00000003241, gene:ENSEOMG00000013691 ... |
| Amaranthaceae | Chenopodium quinoa | 4 | CQ.Regalona.r1.2AG0001890, CQ.Regalona.r1.2BG0002930 ... |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30205470 |
| Apiaceae | Apium graveolens | 2 | Ag10G01048, Ag5G00312 |
| Arecaceae | Cocos nucifera | 4 | COCNU_09G009970, COCNU_10G009950, COCNU_10G009960 ... |
| Arecaceae | Phoenix dactylifera | 2 | gene-LOC103716639, gene-LOC103720451 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_04.3469.V1.1 |
| Asteraceae | Flaveria trinervia | 4 | Ftri17G13639, Ftri18G27750, Ftri1G22182, Ftri6G20170 |
| Brassicaceae | Arabidopsis thaliana | 2 | AT2G23140.1, AT5G67340.1 |
| Brassicaceae | Eutrema salsugineum | 2 | Thhalv10000047m.g.v1.0, Thhalv10003745m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 2 | Sp2g29320.v2.2, Sp4g02200.v2.2 |
| Brassicaceae | Brassica nigra | 4 | BniB01g020620.2N, BniB02g020030.2N, BniB06g014510.2N ... |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq05G1384 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl05G1385 |
| Cymodoceaceae | Cymodocea nodosa | 2 | gene.Cymno11g11290, gene.Cymno11g11310 |
| Hydrocharitaceae | Thalassia testudinum | 6 | gene.Thate05g03190, gene.Thate05g03210, gene.Thate05g03280 ... |
| Malvaceae | Hibiscus hamabo Siebold & Zucc. | 4 | nbisL1-mrna-10061, nbisL1-mrna-10549, nbisL1-mrna-10550 ... |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG02.945 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00003835 |
| Plumbaginaceae | Limonium bicolor | 2 | Lb1G05542, Lb2G08468 |
| Poaceae | Echinochloa crus-galli | 6 | AH02.4102, AH08.90, BH02.4117, BH08.39, CH02.4148, CH08.159 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_8AG0614970, gene-QOZ80_8BG0642450 |
| Poaceae | Hordeum vulgare | 2 | HORVU.MOREX.r3.3HG0297900.1, HORVU.MOREX.r3.3HG0327220.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_057192 |
| Poaceae | Oryza coarctata | 3 | Oco02G027740, Oco15G000510, Oco16G000650 |
| Poaceae | Oryza sativa | 2 | LOC_Os01g66130.1, LOC_Os08g01900.1 |
| Poaceae | Paspalum vaginatum | 2 | gene-BS78_03G359600, gene-BS78_07G013600 |
| Poaceae | Puccinellia tenuiflora | 3 | Pt_Chr0600380, Pt_Chr0700676, Pt_Chr0700704 |
| Poaceae | Sporobolus alterniflorus | 4 | Chr03G021530, Chr08G020670, Chr16G000010, Chr20G013580 |
| Poaceae | Thinopyrum elongatum | 4 | Tel3E01G618300, Tel3E01G651500, Tel3E01G878100 ... |
| Poaceae | Triticum dicoccoides | 5 | gene_TRIDC3AG055610, gene_TRIDC3AG058350 ... |
| Poaceae | Triticum aestivum | 7 | TraesCS3A02G390200.1, TraesCS3A02G521300.1 ... |
| Poaceae | Zea mays | 3 | Zm00001eb145570_P001, Zm00001eb174100_P001 ... |
| Poaceae | Zoysia japonica | 3 | nbis-gene-11168, nbis-gene-41408, nbis-gene-51935 |
| Poaceae | Zoysia macrostachya | 3 | Zma_g22360, Zma_g23507, Zma_g9143 |
| Portulacaceae | Portulaca oleracea | 4 | evm.TU.LG10.869, evm.TU.LG18.381, evm.TU.LG25.1223 ... |
| Posidoniaceae | Posidonia oceanica | 2 | gene.Posoc08g06870, gene.Posoc08g08720 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_6_RagTag.1819 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-17331 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-2336 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-11949 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000011l.1113 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00007880 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-15470 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-3267 |
| Salicaceae | Populus euphratica | 5 | populus_peu14468, populus_peu14478, populus_peu23323 ... |
| Solanaceae | Lycium barbarum | 3 | gene-LOC132601989, gene-LOC132604584, gene-LOC132626552 |
| Solanaceae | Solanum chilense | 3 | SOLCI005329600, SOLCI005442400, SOLCI006710000 |
| Solanaceae | Solanum pennellii | 2 | gene-LOC107007682, gene-LOC107008077 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.4815_chr03_- |
| Tamaricaceae | Tamarix chinensis | 1 | TC04G1828 |
| Zosteraceae | Zostera marina | 1 | Zosma01g09780.v3.1 |