Basic Information
Locus ID:
Ag2G02308
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
Enhancer of mRNA-decapping protein 4-like
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr2 | 269768672 | 269779531 | + | Ag2G02308 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.61 | 149,714.73 Da | 47.88 | 87.92 | -0.31 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| Pfam | PF16529 | WD40 region of Ge1, enhancer of mRNA-decapping protein | 175 | 488 | 9.4E-21 | IPR032401 |
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 177 | 453 | 4.51E-21 | IPR036322 |
| Gene3D | G3DSA:2.130.10.10 | - | 188 | 535 | 1.3E-21 | IPR015943 |
| Gene3D | G3DSA:1.10.220.100 | - | 1283 | 1369 | 1.6E-23 | IPR044938 |
| SMART | SM00320 | WD40_4 | 216 | 256 | 0.0031 | IPR001680 |
| SMART | SM00320 | WD40_4 | 378 | 424 | 140.0 | IPR001680 |
| SMART | SM00320 | WD40_4 | 336 | 375 | 0.0069 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 223 | 257 | 8.837541 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 342 | 384 | 9.539323 | IPR001680 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 637 | 658 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 27 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 853 | 881 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 559 | 663 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 559 | 630 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 908 | 934 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 53 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 28 | 53 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 850 | 934 | - | - |
| Coils | Coil | Coil | 947 | 967 | - | - |
Gene Ontology
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT3G13300.1 | Transducin/WD40 repeat-like superfamily protein. Encodes VCS (VARICOSE). Involved in mRNA decapping. VCS forms a mRNA decapping complex with DCP1 (At1g08370) and DCP2 (At5g13570). Unlike DCP2, VCS itself does not have mRNA decapping activity in vitro. DCP1, DCP2 and VCS colocalize in cytoplasmic loci, which are putative Arabidopsis mRNA processing bodies. Null mutants of DCP1, DCP2, and VCS accumulate capped mRNAs with a reduced degradation rate. These mutants also share a similar lethal phenotype at the seedling cotyledon stage, with disorganized veins, swollen root hairs, and altered epidermal cell morphology. VCS is also required for leaf development. | 0 |
| RefSeq | XP_017252556.1 | PREDICTED: enhancer of mRNA-decapping protein 4-like [Daucus carota subsp. sativus] | 0 |
| Q9LTT8 | Enhancer of mRNA-decapping protein 4 OS=Arabidopsis thaliana OX=3702 GN=VCS PE=1 SV=1 | 0 | |
| TrEMBL | A0A164YDI1 | Ge1_WD40 domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_017598 PE=3 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 31.500191 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 24.295732 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 22.860205 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 24.766478 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 28.063969 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 21.758188 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 21.961216 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 17.716002 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 33.653324 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 31.623453 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 34.080448 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 33.495079 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 33.213661 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 25.961874 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 7.441947 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 11.530414 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 8.268881 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 14.165808 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 10.688809 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 13.033877 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 15.141221 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 11.293046 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 12.190987 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 12.196889 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 12.304749 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 18.483259 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 14.253886 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 14.428662 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 15.430724 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 3.328232 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 4.491892 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 3.318042 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 12.080523 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 8.205625 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 12.515345 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 5.876431 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 2.658966 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 4.337004 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 17.23772 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 11.990367 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 6.443765 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 7.944095 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 8.234377 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 13.369044 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 13.164617 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 8.891143 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 13.585744 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 14.868433 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 13.719682 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 13.801517 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 2 | jg20217, jg24642 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_7098 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah009135 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_4g091120 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg18599, Sbi_jg37024 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg4871 |
| Amaranthaceae | Suaeda aralocaspica | 2 | GOSA_00017262, GOSA_00017263 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl23632, Sgl28833 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000011001, gene:ENSEOMG00000030169 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.2BG0000180, CQ.Regalona.r1.4BG0026690 |
| Anacardiaceae | Pistacia vera | 3 | pistato.v30066310, pistato.v30151180, pistato.v30151450 |
| Apiaceae | Apium graveolens | 2 | Ag2G02308, Ag3G02426 |
| Arecaceae | Cocos nucifera | 2 | COCNU_01G013150, COCNU_11G006200 |
| Arecaceae | Phoenix dactylifera | 3 | gene-LOC103695987, gene-LOC103696209, gene-LOC120111829 |
| Asparagaceae | Asparagus officinalis | 2 | AsparagusV1_01.484.V1.1, AsparagusV1_05.2169.V1.1 |
| Asteraceae | Flaveria trinervia | 3 | Ftri14G07956, Ftri15G07998, Ftri7G09129 |
| Brassicaceae | Arabidopsis thaliana | 2 | AT3G13290.1, AT3G13300.1 |
| Brassicaceae | Eutrema salsugineum | 2 | Thhalv10019901m.g.v1.0, Thhalv10019903m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 2 | Sp3g11490.v2.2, Sp3g11500.v2.2 |
| Brassicaceae | Brassica nigra | 2 | BniB01g051920.2N, BniB01g059160.2N |
| Casuarinaceae | Casuarina equisetifolia | 2 | Ceq01G1552, Ceq02G1433 |
| Casuarinaceae | Casuarina glauca | 2 | Cgl01G1714, Cgl02G1477 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno04g07070 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0061s00002.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 3 | gene.Thate03g20720, gene.Thate04g27310, gene.Thate08g11560 |
| Malvaceae | Hibiscus hamabo Siebold & Zucc. | 1 | nbisL1-mrna-5478 |
| Nitrariaceae | Nitraria sibirica | 3 | evm.TU.LG05.2099, evm.TU.LG12.1301, evm.TU.LG12.1303 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00037982 |
| Plumbaginaceae | Limonium bicolor | 2 | Lb0G37320, Lb2G11789 |
| Poaceae | Echinochloa crus-galli | 7 | AH06.1226, AH07.3276, BH06.1277, BH07.3095, CH06.1410 ... |
| Poaceae | Eleusine coracana subsp. coracana | 4 | gene-QOZ80_2AG0143850, gene-QOZ80_2BG0199260 ... |
| Poaceae | Hordeum vulgare | 2 | HORVU.MOREX.r3.6HG0610930.1, HORVU.MOREX.r3.7HG0674380.1 |
| Poaceae | Oryza coarctata | 4 | Oco03G020230, Oco04G020930, Oco11G007830, Oco12G007840 |
| Poaceae | Oryza sativa | 2 | LOC_Os02g49090.1, LOC_Os06g19660.1 |
| Poaceae | Paspalum vaginatum | 3 | gene-BS78_04G258900, gene-BS78_10G126000, gene-BS78_K043000 |
| Poaceae | Puccinellia tenuiflora | 2 | Pt_Chr0203578, Pt_Chr0404397 |
| Poaceae | Sporobolus alterniflorus | 7 | Chr06G003400, Chr09G021350, Chr10G001330, Chr11G017420 ... |
| Poaceae | Thinopyrum elongatum | 2 | Tel6E01G522200, Tel7E01G400300 |
| Poaceae | Triticum dicoccoides | 4 | gene_TRIDC6AG043700, gene_TRIDC6BG051300 ... |
| Poaceae | Triticum aestivum | 6 | TraesCS6A02G286100.3, TraesCS6B02G314800.3 ... |
| Poaceae | Zea mays | 3 | Zm00001eb189120_P001, Zm00001eb253140_P001 ... |
| Poaceae | Zoysia japonica | 3 | nbis-gene-21986, nbis-gene-45616, nbis-gene-8875 |
| Poaceae | Zoysia macrostachya | 3 | Zma_g14306, Zma_g17051, Zma_g31778 |
| Portulacaceae | Portulaca oleracea | 4 | evm.TU.LG01.272, evm.TU.LG02.661, evm.TU.LG04.481 ... |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc01g16370 |
| Rhizophoraceae | Bruguiera sexangula | 2 | evm.TU.Scaffold_7_RagTag.1417, evm.TU.Scaffold_8_RagTag.360 |
| Rhizophoraceae | Carallia pectinifolia | 2 | nbisL1-mrna-20075, nbisL1-mrna-20216 |
| Rhizophoraceae | Ceriops tagal | 2 | nbisL1-mrna-13554, nbisL1-mrna-2818 |
| Rhizophoraceae | Ceriops zippeliana | 3 | nbisL1-mrna-13364, nbisL1-mrna-13365, nbisL1-mrna-17964 |
| Rhizophoraceae | Kandelia candel | 4 | evm.TU.utg000002l.239, evm.TU.utg000018l.762 ... |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00011642 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-9063 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-12103 |
| Salicaceae | Populus euphratica | 8 | populus_peu00036, populus_peu10494, populus_peu17074 ... |
| Solanaceae | Lycium barbarum | 2 | gene-LOC132617622, gene-LOC132627692 |
| Solanaceae | Solanum chilense | 2 | SOLCI005594100, SOLCI006743000 |
| Solanaceae | Solanum pennellii | 2 | gene-LOC107002190, gene-LOC107025807 |
| Tamaricaceae | Reaumuria soongarica | 2 | STRG.24580_chr08_-, gene_17897 |
| Tamaricaceae | Tamarix chinensis | 2 | TC05G2540, TC06G0575 |
| Zosteraceae | Zostera marina | 1 | Zosma01g39580.v3.1 |