Basic Information
Locus ID:
Ag2G00042
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
Protein ROOT INITIATION DEFECTIVE 3-like
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr2 | 590193 | 591440 | + | Ag2G00042 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.96 | 44,854.46 Da | 46.03 | 91.52 | -0.11 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| Pfam | PF00400 | WD domain, G-beta repeat | 114 | 147 | 1.5E-4 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 170 | 206 | 0.06 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 269 | 298 | 0.18 | IPR001680 |
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 7 | 318 | 8.06E-38 | IPR036322 |
| Gene3D | G3DSA:2.130.10.10 | - | 29 | 244 | 3.8E-26 | IPR015943 |
| Gene3D | G3DSA:2.130.10.10 | - | 255 | 336 | 1.7E-9 | IPR015943 |
| SMART | SM00320 | WD40_4 | 258 | 298 | 0.0046 | IPR001680 |
| SMART | SM00320 | WD40_4 | 164 | 206 | 0.082 | IPR001680 |
| SMART | SM00320 | WD40_4 | 112 | 151 | 5.6E-6 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 119 | 149 | 9.739832 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 266 | 307 | 12.513543 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 266 | 303 | 9.520146 | - |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 285 | 299 | - | IPR019775 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 394 | 415 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 401 | 415 | - | - |
Gene Ontology
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT3G49180.1 | Transducin/WD40 repeat-like superfamily protein. | 0 |
| RefSeq | XP_017251199.1 | PREDICTED: protein ROOT INITIATION DEFECTIVE 3-like [Daucus carota subsp. sativus] | 0 |
| Q9M3B4 | Protein ROOT INITIATION DEFECTIVE 3 OS=Arabidopsis thaliana OX=3702 GN=RID3 PE=1 SV=1 | 0 | |
| TrEMBL | A0A162A575 | WD_REPEATS_REGION domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_019614 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 11.83723 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 5.772907 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 6.690204 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 7.969308 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 9.919703 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 5.309151 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 6.757772 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 2.89797 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 7.206141 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 4.055903 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 6.603244 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 5.469318 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 6.534967 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 5.939958 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 15.146382 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 13.281094 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 18.426239 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 14.047812 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 11.25869 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 10.730679 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 15.367603 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 17.318546 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 19.496527 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 21.00246 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 18.340145 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 14.591847 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 14.214189 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 11.318854 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 16.490944 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 1.282457 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 5.042227 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 3.122359 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 6.004531 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 5.860816 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 5.760247 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 6.521375 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 4.122266 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 2.719022 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 4.138509 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 7.175939 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 3.659014 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 11.272 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 7.681234 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 15.987684 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 20.150785 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 7.724347 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 18.136091 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 18.088287 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 23.147541 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 19.525127 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Apiaceae | Apium graveolens | 1 | Ag2G00042 |
| Arecaceae | Cocos nucifera | 1 | COCNU_01G013610 |
| Arecaceae | Phoenix dactylifera | 4 | gene-LOC103720694, gene-LOC103720696, gene-LOC120111278 ... |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_05.2221.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri15G13586 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_6AG0538730, gene-QOZ80_6BG0491960 |
| Poaceae | Oryza coarctata | 2 | Oco17G007400, Oco18G007630 |
| Poaceae | Oryza sativa | 1 | LOC_Os09g30090.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_02G215900 |
| Poaceae | Sporobolus alterniflorus | 1 | Chr10G007920 |
| Poaceae | Zoysia japonica | 2 | nbis-gene-10343, nbis-gene-30513 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_5_RagTag.133 |
| Rhizophoraceae | Carallia pectinifolia | 2 | nbisL1-mrna-11100, nbisL1-mrna-11103 |
| Rhizophoraceae | Ceriops tagal | 3 | nbisL1-mrna-12411, nbisL1-mrna-12412, nbisL1-mrna-9616 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-10654 |
| Rhizophoraceae | Kandelia candel | 1 | add.evm.TU.utg000006l.34 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00013812 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-20369 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-15323 |
| Salicaceae | Populus euphratica | 1 | populus_peu00751 |