Basic Information
Locus ID:
Ag6G00188
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
U4 U6.U5 tri-snRNP-associated protein
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr6 | 5356384 | 5362870 | - | Ag6G00188 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.93 | 64,724.58 Da | 47.32 | 76.45 | -0.72 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd02669 | Peptidase_C19M | 103 | 553 | 0.0 | IPR033809 |
| Pfam | PF00443 | Ubiquitin carboxyl-terminal hydrolase | 222 | 552 | 1.1E-38 | IPR001394 |
| Pfam | PF02148 | Zn-finger in ubiquitin-hydrolases and other protein | 121 | 182 | 4.5E-14 | IPR001607 |
| SUPERFAMILY | SSF57850 | RING/U-box | 100 | 193 | 8.48E-24 | - |
| SUPERFAMILY | SSF54001 | Cysteine proteinases | 219 | 554 | 6.38E-59 | IPR038765 |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 102 | 190 | 1.0E-40 | IPR013083 |
| Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 191 | 556 | 1.3E-91 | - |
| SMART | SM00290 | Zf_UBP_1 | 120 | 169 | 3.4E-17 | IPR001607 |
| ProSiteProfiles | PS50235 | Ubiquitin specific protease (USP) domain profile. | 222 | 555 | 34.953323 | IPR028889 |
| ProSiteProfiles | PS50271 | Zinc finger UBP-type profile. | 119 | 180 | 17.801905 | IPR001607 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 18 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 85 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 70 | 84 | - | - |
Gene Ontology
Biological Process:
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT4G22350.2 | Ubiquitin C-terminal hydrolases superfamily protein. | 0 |
| RefSeq | XP_017236665.1 | PREDICTED: U4/U6.U5 tri-snRNP-associated protein 2-like [Daucus carota subsp. sativus] | 0 |
| Q3TIX9 | Ubiquitin carboxyl-terminal hydrolase 39 OS=Mus musculus OX=10090 GN=Usp39 PE=1 SV=2 | 0 | |
| TrEMBL | A0A162AYS9 | U4/U6.U5 tri-snRNP-associated protein 2 OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_008620 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 25.468866 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 16.592308 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 16.533293 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 17.608747 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 17.299591 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 17.337273 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 15.172202 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 20.162378 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 31.802307 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 31.659582 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 33.68037 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 33.707726 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 27.99482 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 26.315838 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 14.554994 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 17.342882 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 14.498139 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 13.210706 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 13.326199 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 18.506884 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 17.588949 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 14.914804 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 16.146141 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 16.626511 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 17.263384 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 16.384565 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 18.0123 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 15.686914 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 15.652875 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 8.596438 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 11.459963 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 8.106727 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 18.301739 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 16.678225 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 16.796478 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 13.76203 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 7.168313 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 9.137548 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 16.562351 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 10.808648 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 10.533256 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 15.215438 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 18.290022 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 22.078802 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 21.220339 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 19.164818 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 21.260937 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 30.273228 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 27.692751 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 24.973173 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg20469 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_4356 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_8g185090 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg2687, Sbi_jg28338 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg7137 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00011579 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl41702, Sgl46502 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000010785, gene:ENSEOMG00000021103 ... |
| Amaranthaceae | Chenopodium quinoa | 4 | CQ.Regalona.r1.6AG0012830, CQ.Regalona.r1.6AG0022840 ... |
| Anacardiaceae | Pistacia vera | 2 | pistato.v30166290, pistato.v30168420 |
| Apiaceae | Apium graveolens | 2 | Ag6G00188, Ag9G00070 |
| Arecaceae | Cocos nucifera | 2 | COCNU_01G012350, scaffold005311G000010 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103719061 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_05.2092.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri15G03405 |
| Brassicaceae | Arabidopsis thaliana | 3 | AT4G22285.1, AT4G22350.2, AT4G22410.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10024723m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp7g20480.v2.2 |
| Brassicaceae | Brassica nigra | 2 | BniB02g079820.2N, BniB05g014740.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq01G2088 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl01G2288 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno03g08090 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0249s00003.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate03g20960 |
| Malvaceae | Hibiscus hamabo Siebold & Zucc. | 1 | nbisL1-mrna-7734 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG11.1143 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00039099 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb1G00527 |
| Poaceae | Echinochloa crus-galli | 3 | AH06.2756, BH06.2552, CH06.2854 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_6AG0548730, gene-QOZ80_6BG0502330 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.2HG0168890.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_028033 |
| Poaceae | Oryza coarctata | 2 | Oco17G004510, Oco18G004550 |
| Poaceae | Oryza sativa | 1 | LOC_Os09g24250.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_10G236000 |
| Poaceae | Puccinellia tenuiflora | 2 | Pt_Chr0402311, Pt_Chr0404151 |
| Poaceae | Sporobolus alterniflorus | 3 | Chr05G010080, Chr10G020710, Chr11G001930 |
| Poaceae | Thinopyrum elongatum | 1 | Tel7E01G056100 |
| Poaceae | Triticum dicoccoides | 3 | gene_TRIDC2AG079010, gene_TRIDC4AG068100 ... |
| Poaceae | Triticum aestivum | 3 | TraesCS4A02G462100.1, TraesCS7A02G027300.1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb225610_P001 |
| Poaceae | Zoysia japonica | 2 | nbis-gene-40610, nbis-gene-9708 |
| Poaceae | Zoysia macrostachya | 2 | Zma_g31026, Zma_g33283 |
| Portulacaceae | Portulaca oleracea | 4 | evm.TU.LG01.1960, evm.TU.LG14.1139, evm.TU.LG19.531 ... |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc02g19980 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_7_RagTag.1494 |
| Rhizophoraceae | Carallia pectinifolia | 2 | nbisL1-mrna-19989, nbisL1-mrna-20307 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-20613 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-13434 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000002l.185 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00011706 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-14926 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-12179 |
| Salicaceae | Populus euphratica | 2 | populus_peu10562, populus_peu26470 |
| Solanaceae | Lycium barbarum | 2 | gene-LOC132621473, gene-LOC132642138 |
| Solanaceae | Solanum chilense | 1 | SOLCI006287900 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107011965 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.30448_chr10_- |
| Tamaricaceae | Tamarix chinensis | 1 | TC08G0180 |
| Zosteraceae | Zostera marina | 1 | Zosma04g08240.v3.1 |