Basic Information
Locus ID:
Ag4G00955
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
Required for maturation of ribosomal RNAs and formation of the large ribosomal subunit
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr4 | 97961348 | 97966136 | - | Ag4G00955 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.72 | 48,807.66 Da | 42.40 | 84.78 | -0.22 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd00200 | WD40 | 117 | 437 | 1.15714E-48 | - |
| Pfam | PF00400 | WD domain, G-beta repeat | 361 | 398 | 0.061 | IPR001680 |
| Pfam | PF08154 | NLE (NUC135) domain | 15 | 87 | 2.1E-18 | IPR012972 |
| Pfam | PF00400 | WD domain, G-beta repeat | 148 | 193 | 2.1E-6 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 274 | 310 | 0.0029 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 209 | 243 | 9.6E-7 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 326 | 352 | 0.17 | IPR001680 |
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 117 | 437 | 1.99E-51 | IPR036322 |
| Gene3D | G3DSA:2.130.10.10 | - | 112 | 443 | 5.0E-65 | IPR015943 |
| SMART | SM00320 | WD40_4 | 147 | 193 | 1.3E-5 | IPR001680 |
| SMART | SM00320 | WD40_4 | 272 | 310 | 2.8E-5 | IPR001680 |
| SMART | SM00320 | WD40_4 | 107 | 145 | 2.6 | IPR001680 |
| SMART | SM00320 | WD40_4 | 358 | 398 | 5.5E-6 | IPR001680 |
| SMART | SM00320 | WD40_4 | 401 | 439 | 0.039 | IPR001680 |
| SMART | SM00320 | WD40_4 | 205 | 244 | 3.7E-5 | IPR001680 |
| SMART | SM00320 | WD40_4 | 314 | 352 | 7.4 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 279 | 319 | 10.174269 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 365 | 401 | 8.676514 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 212 | 249 | 11.744925 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 212 | 249 | 9.810144 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 365 | 407 | 10.34136 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 154 | 202 | 9.906923 | IPR001680 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 385 | 399 | - | IPR019775 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 385 | 399 | 5.4E-6 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 297 | 311 | 5.4E-6 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 180 | 194 | 5.4E-6 | IPR020472 |
| Hamap | MF_03029 | Ribosome biogenesis protein @gn(WDR12) [WDR12]. | 9 | 442 | 30.347979 | IPR028599 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 253 | 272 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 253 | 275 | - | - |
Gene Ontology
Biological Process:
Molecular Function:
KEGG Pathway
KO Term:
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT5G15550.1 | Transducin/WD40 repeat-like superfamily protein. | 0 |
| RefSeq | XP_017237341.1 | PREDICTED: ribosome biogenesis protein WDR12 homolog [Daucus carota subsp. sativus] | 0 |
| Q9LF27 | Ribosome biogenesis protein WDR12 homolog OS=Arabidopsis thaliana OX=3702 GN=WDR12 PE=1 SV=1 | 0 | |
| TrEMBL | A0A166B2Z2 | Ribosome biogenesis protein WDR12 homolog OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_011042 PE=3 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 23.218422 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 15.485476 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 14.902758 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 15.37899 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 14.255101 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 16.892277 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 14.031716 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 12.156752 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 30.282921 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 30.981655 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 32.973965 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 37.290012 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 38.06004 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 30.589787 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 7.596332 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 10.941652 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 17.52035 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 17.697901 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 19.971899 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 26.593422 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 19.211716 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 24.363014 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 26.150202 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 25.814697 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 27.001616 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 22.603722 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 23.797323 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 21.72109 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 22.882671 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 10.986077 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 17.692085 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 18.174698 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 25.10796 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 21.465845 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 24.748039 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 13.283578 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 13.58696 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 11.789914 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 14.338887 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 8.253926 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 2.813664 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 29.6814 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 18.517342 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 88.05648 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 57.43742 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 43.797676 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 29.645821 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 42.156513 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 33.409824 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 37.082897 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg30563 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_14585 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah033568 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg51064, Sbi_jg60138 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg24317 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00015835 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl78419, Sgl80928 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000018781, gene:ENSEOMG00000039770 ... |
| Amaranthaceae | Chenopodium quinoa | 3 | CQ.Regalona.r1.9AG0004050, CQ.Regalona.r1.9AG0004060 ... |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30192970 |
| Apiaceae | Apium graveolens | 2 | Ag4G00955, Ag5G00955 |
| Arecaceae | Cocos nucifera | 3 | COCNU_05G001960, COCNU_13G005680, scaffold018987G000010 |
| Arecaceae | Phoenix dactylifera | 2 | gene-LOC103708248, gene-LOC103710242 |
| Asparagaceae | Asparagus officinalis | 3 | AsparagusV1_03.2073.V1.1, AsparagusV1_03.2074.V1.1 ... |
| Asteraceae | Flaveria trinervia | 1 | Ftri18G32960 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT5G15550.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10013619m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp6g28530.v2.2 |
| Brassicaceae | Brassica nigra | 3 | BniB02g047340.2N, BniB05g023180.2N, BniB08g007450.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq08G0430 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl08G0383 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno01g09480 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0179s00021.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate05g01080 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG02.285 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00028053 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb3G18482 |
| Poaceae | Echinochloa crus-galli | 5 | AH03.3616, AH06.2319, AH07.2940, BH03.3950, CH03.4060 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_5AG0396340, gene-QOZ80_5BG0444630 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.2HG0127540.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_039888 |
| Poaceae | Oryza coarctata | 2 | Oco13G011880, Oco14G012680 |
| Poaceae | Oryza sativa | 1 | LOC_Os07g40930.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_02G340900 |
| Poaceae | Puccinellia tenuiflora | 2 | Pt_Chr0205994, Pt_Chr0307527 |
| Poaceae | Sporobolus alterniflorus | 4 | Chr01G035580, Chr04G012410, Chr07G011830, Chr12G003990 |
| Poaceae | Thinopyrum elongatum | 3 | Tel2E01G346000, Tel2E01G616200, Tel7E01G537300 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC2AG022730, gene_TRIDC2BG026650 |
| Poaceae | Triticum aestivum | 3 | TraesCS2A02G177700.1, TraesCS2B02G204800.1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb326820_P001 |
| Poaceae | Zoysia japonica | 3 | nbis-gene-27820, nbis-gene-32873, nbis-gene-57074 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g5506 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG05.1376, evm.TU.LG07.1498 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc03g19950 |
| Rhizophoraceae | Bruguiera sexangula | 2 | evm.TU.Scaffold_3_RagTag.1712, evm.TU.Scaffold_6_RagTag.356 |
| Rhizophoraceae | Carallia pectinifolia | 2 | nbisL1-mrna-2025, nbisL1-mrna-2166 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-10591 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-2905 |
| Rhizophoraceae | Kandelia candel | 2 | add.evm.TU.utg000023l.135, evm.TU.utg000019l.198 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00002165 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-12174 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-18222 |
| Salicaceae | Populus euphratica | 3 | populus_peu09341, populus_peu25183, populus_peu37959 |
| Solanaceae | Lycium barbarum | 2 | gene-LOC132599276, gene-LOC132623186 |
| Solanaceae | Solanum chilense | 2 | SOLCI005080000, SOLCI007044900 |
| Solanaceae | Solanum pennellii | 2 | gene-LOC107009695, gene-LOC107012676 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.11856_chr02_- |
| Tamaricaceae | Tamarix chinensis | 1 | TC02G1578 |
| Zosteraceae | Zostera marina | 1 | Zosma04g06050.v3.1 |