Basic Information
Locus ID:
Ag10G02438
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
E3 ubiquitin-protein ligase
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr10 | 227680036 | 227690235 | + | Ag10G02438 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 6.87 | 61,825.08 Da | 47.72 | 87.25 | -0.06 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd16479 | RING-H2_synoviolin | 289 | 330 | 1.12574E-27 | - |
| Pfam | PF13639 | Ring finger domain | 291 | 330 | 1.2E-10 | IPR001841 |
| SUPERFAMILY | SSF57850 | RING/U-box | 272 | 336 | 5.74E-21 | - |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 264 | 339 | 6.9E-23 | IPR013083 |
| SMART | SM00184 | ring_2 | 292 | 329 | 7.6E-4 | IPR001841 |
| ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 292 | 330 | 12.622055 | IPR001841 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 340 | 367 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 511 | 542 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 511 | 548 | - | - |
| Coils | Coil | Coil | 485 | 505 | - | - |
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT3G16090.1 | RING/U-box superfamily protein. | 0 |
| RefSeq | XP_017258984.1 | PREDICTED: ERAD-associated E3 ubiquitin-protein ligase HRD1B-like [Daucus carota subsp. sativus] | 0 |
| Q9LW77 | ERAD-associated E3 ubiquitin-protein ligase HRD1A OS=Arabidopsis thaliana OX=3702 GN=HRD1A PE=2 SV=1 | 0 | |
| TrEMBL | A0A161ZYC8 | RING-type domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_020405 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 65.786415 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 56.923943 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 51.541 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 54.605389 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 53.486656 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 52.142254 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 45.305622 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 41.378101 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 40.383976 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 42.130394 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 41.98164 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 55.532932 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 48.678837 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 38.570312 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 29.757956 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 35.274197 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 33.206436 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 37.429119 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 29.127111 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 54.01944 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 56.315929 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 33.896236 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 33.42651 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 35.752769 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 40.89056 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 42.963184 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 29.967733 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 36.837963 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 31.147207 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 15.459227 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 18.779287 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 16.079697 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 35.687965 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 36.555988 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 25.291824 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 25.174492 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 12.396241 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 16.803118 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 23.020679 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 20.947123 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 14.782143 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 77.878868 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 55.753448 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 35.854229 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 31.65678 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 70.674911 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 31.956028 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 30.774897 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 27.667118 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 29.283049 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 3 | jg5387, jg7134, jg9292 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_3435 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah018379 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_3g049980 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg14854, Sbi_jg55630 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg26186 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00017954 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl01101, Sgl06185 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000003064, gene:ENSEOMG00000029388 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.3AG0007250, CQ.Regalona.r1.3BG0007330 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30095450 |
| Apiaceae | Apium graveolens | 1 | Ag10G02438 |
| Arecaceae | Cocos nucifera | 1 | COCNU_08G005470 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103716829 |
| Asparagaceae | Asparagus officinalis | 2 | AsparagusV1_05.485.V1.1, AsparagusV1_08.107.V1.1 |
| Asteraceae | Flaveria trinervia | 2 | Ftri16G11248, Ftri2G31926 |
| Brassicaceae | Arabidopsis thaliana | 2 | AT1G65040.2, AT3G16090.1 |
| Brassicaceae | Eutrema salsugineum | 2 | Thhalv10020585m.g.v1.0, Thhalv10022466m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 2 | Sp3g14440.v2.2, Sp5g19570.v2.2 |
| Brassicaceae | Brassica nigra | 2 | BniB05g061080.2N, BniB07g053670.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq09G1996 |
| Casuarinaceae | Casuarina glauca | 2 | Cgl09G2183, Cgl09G2191 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno02g19700 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0127s00002.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate01g22770 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG03.1707 |
| Plantaginaceae | Plantago ovata | 2 | Pov_00002329, Pov_00027048 |
| Plumbaginaceae | Limonium bicolor | 2 | Lb4G24854, Lb6G30037 |
| Poaceae | Echinochloa crus-galli | 5 | AH06.1227, AH07.2349, BH06.1279, CH06.1411, CH07.2230 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_6AG0518320, gene-QOZ80_6BG0470380 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.7HG0674480.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_052303 |
| Poaceae | Oryza coarctata | 2 | Oco11G007840, Oco12G007850 |
| Poaceae | Oryza sativa | 1 | LOC_Os06g19680.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_10G126200 |
| Poaceae | Puccinellia tenuiflora | 4 | Pt_Chr0404404, Pt_Chr0404407, Pt_Chr0603907, Pt_Chr0603926 |
| Poaceae | Sporobolus alterniflorus | 5 | Chr10G001340, Chr11G017400, Chr14G007030, Chr15G011850 ... |
| Poaceae | Thinopyrum elongatum | 1 | Tel7E01G401200 |
| Poaceae | Triticum dicoccoides | 3 | gene_TRIDC3AG024980, gene_TRIDC7AG028070 ... |
| Poaceae | Triticum aestivum | 5 | TraesCS3A02G179300.1, TraesCS3D02G184200.2 ... |
| Poaceae | Zea mays | 2 | Zm00001eb092590_P005, Zm00001eb197180_P004 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-52613 |
| Poaceae | Zoysia macrostachya | 2 | Zma_g29541, Zma_g31780 |
| Portulacaceae | Portulaca oleracea | 3 | evm.TU.LG02.1497, evm.TU.LG09.1231, evm.TU.LG09.506 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc02g02230 |
| Rhizophoraceae | Bruguiera sexangula | 3 | evm.TU.Scaffold_1_RagTag.599, evm.TU.Scaffold_1_RagTag.838 ... |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-7563 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-2529 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-5611 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000012l.361 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00011092 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-8441 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-710 |
| Salicaceae | Populus euphratica | 1 | populus_peu09039 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132632234 |
| Solanaceae | Solanum chilense | 2 | SOLCI000095500, SOLCI001334600 |
| Solanaceae | Solanum pennellii | 2 | gene-LOC107015413, gene-LOC107023773 |
| Tamaricaceae | Reaumuria soongarica | 2 | STRG.5528_chr04_+, gene_10738 |
| Tamaricaceae | Tamarix chinensis | 1 | TC12G0214 |
| Zosteraceae | Zostera marina | 1 | Zosma05g01190.v3.1 |