Basic Information
Locus ID:
Ag3G00114
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
DNA excision repair protein
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr3 | 2453169 | 2461639 | + | Ag3G00114 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 9.03 | 50,609.43 Da | 38.53 | 76.54 | -0.38 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| Pfam | PF00400 | WD domain, G-beta repeat | 391 | 429 | 0.064 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 311 | 342 | 0.046 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 183 | 219 | 8.4E-7 | IPR001680 |
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 38 | 435 | 2.26E-49 | IPR036322 |
| Gene3D | G3DSA:2.130.10.10 | - | 298 | 449 | 4.9E-17 | IPR015943 |
| Gene3D | G3DSA:2.130.10.10 | - | 1 | 291 | 1.1E-66 | IPR015943 |
| SMART | SM00320 | WD40_4 | 179 | 219 | 1.4E-7 | IPR001680 |
| SMART | SM00320 | WD40_4 | 390 | 429 | 0.0014 | IPR001680 |
| SMART | SM00320 | WD40_4 | 90 | 132 | 0.014 | IPR001680 |
| SMART | SM00320 | WD40_4 | 32 | 72 | 0.0013 | IPR001680 |
| SMART | SM00320 | WD40_4 | 300 | 342 | 0.0059 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 99 | 135 | 8.623787 | - |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 186 | 221 | 10.996502 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 186 | 228 | 13.315579 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 99 | 141 | 11.343905 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 397 | 429 | 8.781968 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 397 | 429 | 10.441614 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 310 | 345 | 12.981398 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 310 | 345 | 10.785595 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 39 | 81 | 9.338814 | IPR001680 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 206 | 220 | - | IPR019775 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 329 | 343 | - | IPR019775 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 119 | 133 | 2.8E-6 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 206 | 220 | 2.8E-6 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 329 | 343 | 2.8E-6 | IPR020472 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 250 | 290 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 250 | 296 | - | - |
Gene Ontology
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT1G27840.1 | Transducin/WD40 repeat-like superfamily protein. Encodes a DDB1a interacting protein ATCSA-1 required for UV-B tolerance and genomic integrity. | 0 |
| RefSeq | XP_017248254.1 | PREDICTED: DNA excision repair protein ERCC-8-like isoform X1 [Daucus carota subsp. sativus] | 0 |
| Q93ZG3 | WD repeat-containing protein ATCSA-1 OS=Arabidopsis thaliana OX=3702 GN=ATCSA-1 PE=1 SV=1 | 0 | |
| TrEMBL | A0A162AE52 | WD_REPEATS_REGION domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_012816 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 46.024601 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 27.739155 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 43.802059 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 37.703785 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 35.955948 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 49.134663 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 49.045734 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 87.363823 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 21.57218 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 19.991726 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 23.252937 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 19.713062 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 17.595701 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 16.378368 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 7.712567 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 8.901789 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 10.276052 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 9.724427 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 10.878669 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 9.910497 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 7.764153 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 11.425646 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 14.718727 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 12.019135 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 12.937891 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 14.426475 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 10.861437 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 12.362884 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 15.5939 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 9.453804 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 16.731207 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 10.373717 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 6.105141 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 5.275359 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 5.196484 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 5.587894 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 5.631548 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 5.044708 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 11.270339 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 9.672965 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 9.870564 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 8.083059 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 16.192047 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 20.105806 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 20.047071 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 8.585762 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 18.82431 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 16.706369 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 13.616104 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 12.620983 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 2 | jg10720, jg6202 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_6040 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah036803 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_1g015130 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg39669, Sbi_jg55044 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg14640 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00013177 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl12515, Sgl12516 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000016659, gene:ENSEOMG00000033617 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.1AG0017920, CQ.Regalona.r1.1BG0007190 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30043060 |
| Apiaceae | Apium graveolens | 1 | Ag3G00114 |
| Arecaceae | Cocos nucifera | 1 | scaffold000870G000010 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103706189 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_10.1725.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri18G27038 |
| Brassicaceae | Arabidopsis thaliana | 2 | AT1G19750.1, AT1G27840.3 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10007615m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp1g24040.v2.2 |
| Brassicaceae | Brassica nigra | 1 | BniB04g042110.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq03G1286 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl03G1390 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno02g18400 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0011s00042.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate01g17890 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG06.337 |
| Plantaginaceae | Plantago ovata | 2 | Pov_00021744, Pov_00037071 |
| Poaceae | Echinochloa crus-galli | 4 | AH02.3941, AH02.3942, BH02.3962, BH07.4272 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_1AG0040540, gene-QOZ80_1BG0090590 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.3HG0300880.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_056500 |
| Poaceae | Oryza coarctata | 2 | Oco01G025390, Oco02G026300 |
| Poaceae | Oryza sativa | 2 | LOC_Os01g63900.1, LOC_Os02g20430.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_03G343000 |
| Poaceae | Puccinellia tenuiflora | 4 | Pt_Chr0105920, Pt_Chr0105957, Pt_Chr0601407, Pt_Chr0601466 |
| Poaceae | Sporobolus alterniflorus | 2 | Chr02G004100, Chr08G021670 |
| Poaceae | Thinopyrum elongatum | 1 | Tel3E01G590800 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC3AG053330, gene_TRIDC3BG060000 |
| Poaceae | Triticum aestivum | 3 | TraesCS3A02G371000.2, TraesCS3B02G403200.2 ... |
| Poaceae | Zea mays | 1 | Zm00001eb147340_P002 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-11325 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g9044 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG01.282, evm.TU.LG04.470 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc02g09100 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_7_RagTag.822 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-19263 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-19250 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-6656 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000002l.636 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00010672 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-13131 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-10076 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132604063 |
| Solanaceae | Solanum chilense | 1 | SOLCI005838500 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107007238 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.31061_chr11_- |
| Tamaricaceae | Tamarix chinensis | 1 | TC04G2652 |
| Zosteraceae | Zostera marina | 2 | Zosma04g06990.v3.1, Zosma04g07040.v3.1 |