Basic Information
Locus ID:
Ag6G01412
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Short Name:
UBP6
Description:
Ubiquitin carboxyl-terminal hydrolase
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr6 | 69050579 | 69058982 | - | Ag6G01412 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 6.01 | 54,219.20 Da | 48.38 | 81.10 | -0.51 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd16104 | Ubl_USP14_like | 1 | 75 | 2.56988E-43 | - |
| CDD | cd02657 | Peptidase_C19A | 105 | 477 | 3.56568E-145 | - |
| Pfam | PF00443 | Ubiquitin carboxyl-terminal hydrolase | 105 | 476 | 2.6E-49 | IPR001394 |
| Pfam | PF00240 | Ubiquitin family | 15 | 73 | 2.4E-7 | IPR000626 |
| SUPERFAMILY | SSF54236 | Ubiquitin-like | 3 | 90 | 4.14E-23 | IPR029071 |
| SUPERFAMILY | SSF54001 | Cysteine proteinases | 103 | 477 | 4.91E-86 | IPR038765 |
| Gene3D | G3DSA:3.10.20.90 | - | 2 | 73 | 5.1E-29 | - |
| Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 100 | 481 | 4.0E-96 | - |
| SMART | SM00213 | ubq_7 | 2 | 73 | 1.6E-10 | IPR000626 |
| ProSiteProfiles | PS50235 | Ubiquitin specific protease (USP) domain profile. | 104 | 479 | 37.013302 | IPR028889 |
| ProSiteProfiles | PS50053 | Ubiquitin domain profile. | 2 | 71 | 11.855915 | IPR000626 |
| ProSitePatterns | PS00972 | Ubiquitin specific protease (USP) domain signature 1. | 105 | 120 | - | IPR018200 |
| ProSitePatterns | PS00299 | Ubiquitin domain signature. | 28 | 53 | - | IPR019954 |
| ProSitePatterns | PS00973 | Ubiquitin specific protease (USP) domain signature 2. | 414 | 432 | - | IPR018200 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 373 | 404 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 381 | 402 | - | - |
Gene Ontology
Biological Process:
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT1G51710.1 | ubiquitin-specific protease 6. Ubiquitin-specific protease 6 (UBP6). Deubiquinating enzyme. Interacts with calmodulin. | 0 |
| RefSeq | XP_017235358.1 | PREDICTED: ubiquitin carboxyl-terminal hydrolase 6-like [Daucus carota subsp. sativus] | 0 |
| Q949Y0 | Ubiquitin carboxyl-terminal hydrolase 6 OS=Arabidopsis thaliana OX=3702 GN=UBP6 PE=1 SV=1 | 0 | |
| TrEMBL | A0A166EMX6 | Ubiquitin carboxyl-terminal hydrolase OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_007611 PE=3 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 16.620842 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 15.059493 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 17.494383 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 19.049088 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 20.423981 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 23.079453 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 18.94549 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 23.369076 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 30.429096 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 29.538435 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 30.338392 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 27.747362 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 28.413029 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 26.19595 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 11.691968 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 13.197694 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 14.006751 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 18.052814 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 13.770498 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 21.216877 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 26.457506 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 28.737558 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 35.625355 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 33.730446 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 29.47382 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 23.233007 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 17.872147 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 18.083303 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 17.038002 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 13.048564 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 11.03213 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 8.351193 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 16.172844 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 18.391813 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 17.846867 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 11.201321 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 8.055326 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 9.416549 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 19.553152 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 11.648227 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 11.634453 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 89.593918 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 55.909199 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 36.702198 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 32.29718 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 84.943329 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 24.178005 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 33.337475 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 43.975422 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 33.805672 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg18076 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_26059 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah033814 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg20125, Sbi_jg44395 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg17582 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00021384 |
| Amaranthaceae | Suaeda glauca | 3 | Sgl63936, Sgl68425, Sgl68459 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000019283, gene:ENSEOMG00000020096 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.2AG0009100, CQ.Regalona.r1.2BG0010340 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30116210 |
| Apiaceae | Apium graveolens | 2 | Ag5G00890, Ag6G01412 |
| Arecaceae | Cocos nucifera | 1 | COCNU_06G002340 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103712935 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_05.2904.V1.1 |
| Asteraceae | Flaveria trinervia | 2 | Ftri18G20259, Ftri1G33440 |
| Brassicaceae | Arabidopsis thaliana | 2 | AT1G51710.1, AT3G21280.1 |
| Brassicaceae | Eutrema salsugineum | 2 | Thhalv10011383m.g.v1.0, Thhalv10020636m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 2 | Sp1g38350.v2.2, Sp3g19320.v2.2 |
| Brassicaceae | Brassica nigra | 2 | BniB04g058230.2N, BniB07g004080.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq02G0893 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl02G0907 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno06g03570 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0701s00003.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate09g07440 |
| Malvaceae | Hibiscus hamabo Siebold & Zucc. | 2 | nbisL1-mrna-4581, nbisL1-mrna-5502 |
| Nitrariaceae | Nitraria sibirica | 2 | evm.TU.LG01.22, evm.TU.LG10.250 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00025793 |
| Plumbaginaceae | Limonium bicolor | 3 | Lb0G36736, Lb3G18083, Lb3G18086 |
| Poaceae | Echinochloa crus-galli | 4 | AH02.2011, BH02.2058, BH02.2397, CH02.2232 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_1AG0020710, gene-QOZ80_1BG0070560 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.3HG0266440.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_053316 |
| Poaceae | Oryza coarctata | 2 | Oco01G012380, Oco02G012520 |
| Poaceae | Oryza sativa | 1 | LOC_Os01g36930.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_03G162200 |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0603032 |
| Poaceae | Sporobolus alterniflorus | 4 | Chr02G017840, Chr03G008810, Chr05G016180, Chr08G009740 |
| Poaceae | Thinopyrum elongatum | 1 | Tel3E01G349000 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC3AG029400, gene_TRIDC3BG032970 |
| Poaceae | Triticum aestivum | 4 | TraesCS3A02G201000.1, TraesCS3B02G226300.4 ... |
| Poaceae | Zea mays | 2 | Zm00001eb162410_P002, Zm00001eb356540_P002 |
| Poaceae | Zoysia japonica | 2 | nbis-gene-21442, nbis-gene-47353 |
| Poaceae | Zoysia macrostachya | 2 | Zma_g10462, Zma_g8047 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG07.1610, evm.TU.LG15.1646 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc03g21630 |
| Rhizophoraceae | Bruguiera sexangula | 2 | evm.TU.Scaffold_10_RagTag.1345 ... |
| Rhizophoraceae | Carallia pectinifolia | 2 | nbisL1-mrna-27764, nbisL1-mrna-7070 |
| Rhizophoraceae | Ceriops tagal | 2 | nbisL1-mrna-15519, nbisL1-mrna-8074 |
| Rhizophoraceae | Ceriops zippeliana | 2 | nbisL1-mrna-8026, nbisL1-mrna-8775 |
| Rhizophoraceae | Kandelia candel | 2 | evm.TU.utg000004l.65, evm.TU.utg000023l.74 |
| Rhizophoraceae | Kandelia obovata | 2 | Maker00003999, Maker00018915 |
| Rhizophoraceae | Rhizophora apiculata | 2 | nbisL1-mrna-16444, nbisL1-mrna-7403 |
| Rhizophoraceae | Rhizophora mangle | 2 | nbisL1-mrna-17925, nbisL1-mrna-24319 |
| Salicaceae | Populus euphratica | 2 | populus_peu02605, populus_peu12128 |
| Solanaceae | Lycium barbarum | 2 | gene-LOC132603709, gene-LOC132632788 |
| Solanaceae | Solanum chilense | 1 | SOLCI004044400 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107007362 |
| Tamaricaceae | Reaumuria soongarica | 1 | gene_10033 |
| Tamaricaceae | Tamarix chinensis | 2 | TC08G1782, TC10G2096 |
| Zosteraceae | Zostera marina | 1 | Zosma06g11350.v3.1 |