Basic Information
Locus ID:
Ag10G01297
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
Protein ROOT INITIATION DEFECTIVE
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr10 | 173851325 | 173857477 | + | Ag10G01297 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 6.70 | 49,728.97 Da | 47.61 | 89.47 | -0.19 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| Pfam | PF00400 | WD domain, G-beta repeat | 169 | 204 | 0.13 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 113 | 149 | 0.0073 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 261 | 296 | 1.3E-8 | IPR001680 |
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 3 | 319 | 2.93E-47 | IPR036322 |
| Gene3D | G3DSA:2.130.10.10 | - | 217 | 323 | 8.0E-19 | IPR015943 |
| Gene3D | G3DSA:2.130.10.10 | - | 1 | 216 | 1.2E-27 | IPR015943 |
| SMART | SM00320 | WD40_4 | 71 | 108 | 0.73 | IPR001680 |
| SMART | SM00320 | WD40_4 | 257 | 296 | 3.1E-10 | IPR001680 |
| SMART | SM00320 | WD40_4 | 207 | 245 | 20.0 | IPR001680 |
| SMART | SM00320 | WD40_4 | 163 | 204 | 0.026 | IPR001680 |
| SMART | SM00320 | WD40_4 | 111 | 149 | 1.8E-5 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 264 | 305 | 17.192091 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 264 | 299 | 13.448307 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 170 | 213 | 9.906923 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 118 | 150 | 9.539323 | IPR001680 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 283 | 297 | - | IPR019775 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 283 | 297 | 9.2E-8 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 136 | 150 | 9.2E-8 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 191 | 205 | 9.2E-8 | IPR020472 |
| Coils | Coil | Coil | 406 | 426 | - | - |
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_017237841.1 | PREDICTED: protein ROOT INITIATION DEFECTIVE 3 isoform X1 [Daucus carota subsp. sativus] | 0 |
| Q9M3B4 | Protein ROOT INITIATION DEFECTIVE 3 OS=Arabidopsis thaliana OX=3702 GN=RID3 PE=1 SV=1 | 0 | |
| TrEMBL | A0A166BZ57 | WD_REPEATS_REGION domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_011828 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 21.514515 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 16.525946 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 21.956156 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 23.310339 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 22.753975 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 31.600508 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 24.43671 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 26.315201 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 17.320625 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 18.534931 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 17.888773 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 19.969408 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 22.147953 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 17.733652 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 7.112356 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 8.859356 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 9.364206 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 10.400929 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 6.845348 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 11.000099 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 11.960178 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 11.237244 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 12.827734 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 10.981596 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 11.706941 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 11.30892 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 8.084742 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 9.907098 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 11.491126 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 18.619722 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 19.038263 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 18.323284 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 17.861094 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 20.822874 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 15.42084 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 13.601387 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 15.484529 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 16.80048 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 11.819153 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 7.239367 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 5.121666 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 11.216987 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 7.98524 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 21.276911 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 15.951311 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 15.290786 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 9.533146 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 21.718241 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 17.346264 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 17.269045 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg22751 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_14367 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah021063 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg39241, Sbi_jg54566 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg11100 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00020711 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl52544, Sgl57821 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000014312, gene:ENSEOMG00000030453 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.3AG0017840, CQ.Regalona.r1.3BG0018400 |
| Anacardiaceae | Pistacia vera | 2 | pistato.v30028180, pistato.v30045110 |
| Apiaceae | Apium graveolens | 6 | Ag10G01297, Ag3G02015, Ag3G02016, Ag4G00225, AgUnG00518 ... |
| Arecaceae | Cocos nucifera | 1 | COCNU_01G015070 |
| Arecaceae | Phoenix dactylifera | 2 | gene-LOC103716222, gene-LOC120108816 |
| Asparagaceae | Asparagus officinalis | 2 | AsparagusV1_02.1013.V1.1, AsparagusV1_05.3476.V1.1 |
| Asteraceae | Flaveria trinervia | 2 | Ftri16G05538, Ftri18G26433 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT3G49180.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10010392m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp5g12890.v2.2 |
| Brassicaceae | Brassica nigra | 2 | BniB05g048490.2N, BniB08g062530.2N |
| Casuarinaceae | Casuarina equisetifolia | 2 | Ceq03G1826, Ceq09G1371 |
| Casuarinaceae | Casuarina glauca | 3 | Cgl03G1967, Cgl04G1865, Cgl09G1461 |
| Cymodoceaceae | Cymodocea nodosa | 2 | gene.Cymno06g06900, gene.Cymno15g03570 |
| Dunaliellaceae | Dunaliella salina | 3 | Dusal.0064s00024.v1.0, Dusal.0420s00008.v1.0 ... |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate04g14700 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG06.786 |
| Plantaginaceae | Plantago ovata | 2 | Pov_00004430, Pov_00035461 |
| Plumbaginaceae | Limonium bicolor | 4 | Lb1G06474, Lb1G06482, Lb3G19796, Lb5G27650 |
| Poaceae | Echinochloa crus-galli | 3 | AH08.992, BH08.1028, CH08.1139 |
| Poaceae | Eleusine coracana subsp. coracana | 3 | gene-QOZ80_1AG0018550, gene-QOZ80_4BG0347390 ... |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.7HG0715150.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_032214 |
| Poaceae | Oryza coarctata | 2 | Oco13G006050, Oco14G006630 |
| Poaceae | Oryza sativa | 2 | LOC_Os05g23580.1, LOC_Os07g22534.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_01G114500 |
| Poaceae | Puccinellia tenuiflora | 2 | Pt_Chr0402994, Pt_Chr0403072 |
| Poaceae | Sporobolus alterniflorus | 2 | Chr23G016420, Chr26G003650 |
| Poaceae | Thinopyrum elongatum | 1 | Tel7E01G608500 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC7AG051470, gene_TRIDC7BG042420 |
| Poaceae | Triticum aestivum | 3 | TraesCS7A02G368600.2, TraesCS7B02G259800.2 ... |
| Poaceae | Zea mays | 1 | Zm00001eb296150_P003 |
| Poaceae | Zoysia japonica | 2 | nbis-gene-52490, nbis-gene-53041 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g19427 |
| Portulacaceae | Portulaca oleracea | 1 | evm.TU.LG11.1354 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc03g14220 |
| Rhizophoraceae | Bruguiera sexangula | 3 | evm.TU.Scaffold_11_RagTag.1120, evm.TU.Scaffold_8_RagTag.967 ... |
| Rhizophoraceae | Carallia pectinifolia | 4 | nbisL1-mrna-12314, nbisL1-mrna-8347, nbisL1-mrna-8426 ... |
| Rhizophoraceae | Ceriops tagal | 2 | nbisL1-mrna-17851, nbisL1-mrna-20991 |
| Rhizophoraceae | Ceriops zippeliana | 3 | nbisL1-mrna-12698, nbisL1-mrna-12699, nbisL1-mrna-20675 |
| Rhizophoraceae | Kandelia candel | 2 | evm.TU.utg000010l.196, evm.TU.utg000018l.309 |
| Rhizophoraceae | Kandelia obovata | 2 | Maker00003490, Maker00009036 |
| Rhizophoraceae | Rhizophora apiculata | 2 | nbisL1-mrna-11416, nbisL1-mrna-667 |
| Rhizophoraceae | Rhizophora mangle | 2 | nbisL1-mrna-23838, nbisL1-mrna-8772 |
| Salicaceae | Populus euphratica | 2 | populus_peu31990, populus_peu31991 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132627844 |
| Solanaceae | Solanum chilense | 1 | SOLCI007408300 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107015803 |
| Tamaricaceae | Reaumuria soongarica | 2 | MSTRG.7916_chr04_-, gene_1730 |
| Tamaricaceae | Tamarix chinensis | 1 | TC04G2535 |
| Zosteraceae | Zostera marina | 2 | Zosma02g15030.v3.1, Zosma05g19900.v3.1 |