Basic Information
Locus ID:
Ag6G02101
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Short Name:
DDB2
Description:
Protein DAMAGED DNA-BINDING
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr6 | 175914679 | 175920053 | - | Ag6G02101 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 8.70 | 60,783.36 Da | 50.68 | 77.84 | -0.54 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 152 | 488 | 2.65E-35 | IPR036322 |
| Gene3D | G3DSA:2.130.10.10 | - | 152 | 481 | 1.7E-92 | IPR015943 |
| SMART | SM00320 | WD40_4 | 333 | 372 | 1.2E-4 | IPR001680 |
| SMART | SM00320 | WD40_4 | 286 | 327 | 0.02 | IPR001680 |
| SMART | SM00320 | WD40_4 | 146 | 186 | 9.2E-4 | IPR001680 |
| SMART | SM00320 | WD40_4 | 445 | 477 | 110.0 | IPR001680 |
| SMART | SM00320 | WD40_4 | 188 | 230 | 30.0 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 339 | 372 | 11.277069 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 153 | 188 | 9.840087 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 339 | 372 | 9.441055 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 294 | 329 | 8.536777 | IPR001680 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 314 | 328 | - | IPR019775 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 500 | 523 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 500 | 529 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 50 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 22 | 38 | - | - |
| Coils | Coil | Coil | 29 | 49 | - | - |
Gene Ontology
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT5G58760.1 | damaged DNA binding 2. Encodes a DDB1a interacting protein DDB2 required for UV-B tolerance and genomic integrity. | 0 |
| RefSeq | XP_017235233.1 | PREDICTED: protein DAMAGED DNA-BINDING 2 [Daucus carota subsp. sativus] | 0 |
| Q84KJ3 | DNA damage-binding protein 2 OS=Oryza sativa subsp. japonica OX=39947 GN=DDB2 PE=1 SV=1 | 0 | |
| TrEMBL | A0A5B6ZCL1 | WD_REPEATS_REGION domain-containing protein (Fragment) OS=Davidia involucrata OX=16924 GN=Din_010989 PE=3 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 15.898704 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 19.74058 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 17.342554 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 19.598627 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 17.955677 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 24.107182 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 29.37491 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 30.33148 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 45.828857 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 44.782848 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 44.663036 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 40.376781 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 43.125103 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 38.776428 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 8.559864 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 7.204545 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 18.034668 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 31.636862 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 28.912416 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 24.105486 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 33.890797 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 29.49423 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 40.842983 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 36.463875 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 37.06279 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 32.102474 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 18.215849 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 25.242723 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 37.890892 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 14.513238 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 28.775291 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 21.481997 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 13.072857 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 14.64635 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 16.016918 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 10.040267 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 13.604347 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 9.073803 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 11.653406 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 25.247633 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 28.710018 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 82.565071 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 46.548714 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 26.004738 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 13.615975 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 81.407944 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 32.914417 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 29.930632 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 29.662401 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 31.755436 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg16657 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_5795 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah027850 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_1g015970 |
| Amaranthaceae | Salicornia bigelovii | 1 | Sbi_jg1581 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg3170 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00003356 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl72780, Sgl76319 |
| Amaranthaceae | Chenopodium album | 2 | gene:ENSEOMG00000036538, gene:ENSEOMG00000042418 |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.7AG0004240, CQ.Regalona.r1.9BG0001430 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30061520 |
| Apiaceae | Apium graveolens | 2 | Ag4G00308, Ag6G02101 |
| Arecaceae | Cocos nucifera | 1 | COCNU_04G000190 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103704021 |
| Asparagaceae | Asparagus officinalis | 3 | AsparagusV1_04.2205.V1.1, AsparagusV1_08.2566.V1.1 ... |
| Asteraceae | Flaveria trinervia | 1 | Ftri12G20624 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT5G58760.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10013126m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp6g20450.v2.2 |
| Brassicaceae | Brassica nigra | 2 | BniB05g038190.2N, BniB05g038200.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq08G1885 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl08G1939 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno04g18590 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0172s00013.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate06g00020 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG09.1100 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00025559 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb3G19189 |
| Poaceae | Echinochloa crus-galli | 3 | AH02.713, BH02.723, CH02.825 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_1AG0009130, gene-QOZ80_1BG0057820 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.3HG0227920.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_018075 |
| Poaceae | Oryza coarctata | 1 | Oco02G001650 |
| Poaceae | Oryza sativa | 1 | LOC_Os01g04870.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_03G070000 |
| Poaceae | Puccinellia tenuiflora | 2 | Pt_Chr0205738, Pt_Chr0205754 |
| Poaceae | Sporobolus alterniflorus | 2 | Chr03G004100, Chr08G001020 |
| Poaceae | Thinopyrum elongatum | 1 | Tel3E01G101600 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC3AG006370, gene_TRIDC3BG008520 |
| Poaceae | Triticum aestivum | 3 | TraesCS3A02G054700.1, TraesCS3B02G066200.1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb335650_P004 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-6982 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g9945 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG19.1041, evm.TU.LG24.1044 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc06g21680 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_13_RagTag.922 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-30094 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-15663 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-16289 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000015l.545 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00015404 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-4449 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-20861 |
| Salicaceae | Populus euphratica | 2 | populus_peu02006, populus_peu02010 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132631605 |
| Solanaceae | Solanum chilense | 1 | SOLCI002812400 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107029211 |
| Tamaricaceae | Reaumuria soongarica | 1 | gene_2993 |
| Tamaricaceae | Tamarix chinensis | 1 | TC11G1190 |
| Zosteraceae | Zostera marina | 1 | Zosma01g40750.v3.1 |