Basic Information
Locus ID:
Ag8G00741
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Short Name:
DDB1A
Description:
DNA damage-binding protein
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr8 | 46134370 | 46147660 | - | Ag8G00741 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.17 | 121,202.52 Da | 37.07 | 98.80 | -0.11 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| Pfam | PF03178 | CPSF A subunit region | 747 | 1058 | 1.3E-81 | IPR004871 |
| Pfam | PF10433 | Mono-functional DNA-alkylating methyl methanesulfonate N-term | 76 | 537 | 6.2E-111 | IPR018846 |
| SUPERFAMILY | SSF50998 | Quinoprotein alcohol dehydrogenase-like | 416 | 888 | 2.98E-10 | IPR011047 |
| Gene3D | G3DSA:1.10.150.910 | - | 1003 | 1089 | 7.9E-30 | - |
| Gene3D | G3DSA:2.130.10.10 | - | 15 | 347 | 0.0 | IPR015943 |
| Gene3D | G3DSA:2.130.10.10 | - | 5 | 998 | 0.0 | IPR015943 |
| Gene3D | G3DSA:2.130.10.10 | - | 386 | 703 | 0.0 | IPR015943 |
| Coils | Coil | Coil | 422 | 442 | - | - |
Gene Ontology
Molecular Function:
Cellular Component:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT4G05420.1 | damaged DNA binding protein 1A. Structurally similar to damaged DNA binding proteins.DDB1a is part of a 350 KDa nuclear localized DET1 protein complex. This complex may physically interact with histone tails and while bound to chromatin- repress transcription of genes involved in photomorphogenesis. | 0 |
| RefSeq | XP_017222704.1 | PREDICTED: DNA damage-binding protein 1 [Daucus carota subsp. sativus] | 0 |
| Q6QNU4 | DNA damage-binding protein 1 OS=Solanum lycopersicum OX=4081 GN=DDB1 PE=1 SV=1 | 0 | |
| TrEMBL | A0A175YLW4 | DNA damage-binding protein 1 OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_027872 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 66.0485 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 46.409615 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 46.218918 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 50.5215 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 54.18615 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 55.471943 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 55.679657 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 52.655823 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 82.958961 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 80.755875 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 85.079056 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 92.973801 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 90.975456 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 79.408134 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 21.587503 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 26.006819 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 25.772865 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 34.086552 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 29.114653 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 34.263039 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 38.575439 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 33.283978 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 36.311432 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 34.262371 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 35.960129 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 43.382126 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 33.372459 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 36.091228 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 38.610054 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 23.961517 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 28.043268 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 22.18894 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 43.900639 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 31.270685 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 35.971207 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 22.279673 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 21.448484 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 22.679377 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 50.632824 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 30.1075 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 24.270626 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 34.67086 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 37.2244 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 63.223419 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 50.629169 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 38.876484 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 43.413555 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 37.077133 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 36.700348 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 34.446888 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg38772 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_640 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah016141 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_8g187500 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg25694, Sbi_jg9530 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg19100 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00027443 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl44090, Sgl48857 |
| Amaranthaceae | Chenopodium album | 4 | gene:ENSEOMG00000009240, gene:ENSEOMG00000010763 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.8AG0011040, CQ.Regalona.r1.8BG0012280 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30075990 |
| Apiaceae | Apium graveolens | 1 | Ag8G00741 |
| Arecaceae | Cocos nucifera | 3 | COCNU_12G000350, scaffold000669G000040 ... |
| Arecaceae | Phoenix dactylifera | 3 | gene-LOC120108331, gene-LOC120109131, gene-LOC120109791 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_10.1594.V1.1 |
| Asteraceae | Flaveria trinervia | 2 | Ftri15G13765, Ftri18G24988 |
| Brassicaceae | Arabidopsis thaliana | 2 | AT4G05420.1, AT4G21100.1 |
| Brassicaceae | Eutrema salsugineum | 2 | Thhalv10024273m.g.v1.0, Thhalv10028374m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 2 | Sp6g03670.v2.2, Sp7g19180.v2.2 |
| Brassicaceae | Brassica nigra | 3 | BniB03g022260.2N, BniB08g038640.2N, BniB08g046620.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq04G0537 |
| Casuarinaceae | Casuarina glauca | 2 | Cgl04G0633, Cgl04G0635 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno06g12740 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0512s00003.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate02g41100 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG12.165 |
| Plantaginaceae | Plantago ovata | 2 | Pov_00027850, Pov_00038547 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb4G24936 |
| Poaceae | Echinochloa crus-galli | 3 | BH05.1203, CH01.2695, CH05.1505 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_5AG0361010, gene-QOZ80_5BG0409460 |
| Poaceae | Hordeum vulgare | 2 | HORVU.MOREX.r3.1HG0094520.1, HORVU.MOREX.r3.3HG0268390.1 |
| Poaceae | Lolium multiflorum | 5 | gene-QYE76_014993, gene-QYE76_014995, gene-QYE76_015567 ... |
| Poaceae | Oryza coarctata | 4 | Oco01G013420, Oco02G013570, Oco09G018360, Oco10G018290 |
| Poaceae | Oryza sativa | 2 | LOC_Os01g40320.1, LOC_Os05g51480.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_09G257900 |
| Poaceae | Puccinellia tenuiflora | 6 | Pt_Chr0206315, Pt_Chr0505878, Pt_Chr0505880, Pt_Chr0505882 ... |
| Poaceae | Sporobolus alterniflorus | 5 | Chr01G016330, Chr0G020280, Chr0G030030, Chr12G020430 ... |
| Poaceae | Thinopyrum elongatum | 4 | Tel1E01G739100, Tel1E01G739300, Tel1E01G739500 ... |
| Poaceae | Triticum dicoccoides | 4 | gene_TRIDC1AG064150, gene_TRIDC1BG073390 ... |
| Poaceae | Triticum aestivum | 5 | TraesCS1B02G473400.1, TraesCS1D02G445700.1 ... |
| Poaceae | Zea mays | 2 | Zm00001eb297320_P004, Zm00001eb345240_P002 |
| Poaceae | Zoysia japonica | 4 | nbis-gene-13528, nbis-gene-13529, nbis-gene-13531 ... |
| Poaceae | Zoysia macrostachya | 1 | Zma_g28923 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG04.1142, evm.TU.LG05.1683 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc03g02890 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_14_RagTag.947 |
| Rhizophoraceae | Carallia pectinifolia | 2 | nbisL1-mrna-16722, nbisL1-mrna-16797 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-5827 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-17253 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000025l.118 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00012206 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-8647 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-9169 |
| Salicaceae | Populus euphratica | 1 | populus_peu00933 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132631575 |
| Solanaceae | Solanum chilense | 1 | SOLCI000078300 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107011170 |
| Tamaricaceae | Reaumuria soongarica | 1 | gene_9698 |
| Tamaricaceae | Tamarix chinensis | 2 | TC01G2861, TC06G1119 |
| Zosteraceae | Zostera marina | 1 | Zosma05g22680.v3.1 |