Basic Information
Locus ID:
AgUnG00008
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
base-excision repair
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| ctg102 | 64477 | 68843 | - | AgUnG00008 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 8.16 | 23,721.96 Da | 49.27 | 81.42 | -0.55 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd00056 | ENDO3c | 86 | 202 | 8.41546E-25 | IPR003265 |
| Pfam | PF00730 | HhH-GPD superfamily base excision DNA repair protein | 87 | 202 | 8.2E-7 | IPR003265 |
| SUPERFAMILY | SSF48150 | DNA-glycosylase | 78 | 202 | 4.55E-30 | IPR011257 |
| Gene3D | G3DSA:1.10.340.30 | Hypothetical protein; domain 2 | 77 | 194 | 2.4E-38 | - |
| SMART | SM00478 | endo3end | 91 | 211 | 0.0066 | IPR003265 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 57 | 78 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 29 | 43 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 43 | - | - |
Gene Ontology
Biological Process:
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT3G47830.1 | DNA glycosylase superfamily protein. | 0 |
| RefSeq | XP_017250475.1 | PREDICTED: putative DNA glycosylase At3g47830 isoform X1 [Daucus carota subsp. sativus] | 0 |
| F4JCQ3 | Putative DNA glycosylase At3g47830 OS=Arabidopsis thaliana OX=3702 GN=At3g47830 PE=3 SV=1 | 0 | |
| TrEMBL | A0A6L5BC56 | ENDO3c domain-containing protein OS=Apium graveolens OX=4045 GN=AG4045_001319 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 6.343731 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 5.408278 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 5.965697 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 4.70624 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 5.152256 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 5.696659 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 7.242824 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 4.054626 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 18.036221 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 20.565712 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 20.600616 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 21.775719 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 16.92959 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 16.127304 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 2.712532 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 2.542097 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 4.056893 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 4.811185 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 1.766346 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 5.90977 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 4.067647 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 4.405198 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 5.49755 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 5.72365 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 4.312575 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 5.832414 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 4.753625 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 4.573546 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 5.613991 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 0.574779 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 2.912058 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 2.472851 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 3.342584 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 4.813169 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 3.810544 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 2.198506 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 1.764336 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 1.806723 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 6.699156 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 2.889867 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 1.50698 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 7.421631 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 0.360266 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 3.136065 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 3.485841 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 4.247984 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 3.749112 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 10.618094 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 11.098709 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 8.136912 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg27485 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_13717 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah001136 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_5g116310 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg30469, Sbi_jg58783 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg28652 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00015003 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl55291, Sgl60557 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000005221, gene:ENSEOMG00000023087 ... |
| Amaranthaceae | Chenopodium quinoa | 1 | CQ.Regalona.r1.5BG0023550 |
| Apiaceae | Apium graveolens | 1 | AgUnG00008 |
| Arecaceae | Cocos nucifera | 1 | COCNU_01G009580 |
| Asteraceae | Flaveria trinervia | 1 | Ftri18G17583 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT3G47830.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10010580m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp5g14130.v2.2 |
| Brassicaceae | Brassica nigra | 1 | BniB05g052000.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq04G1872 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl04G2057 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno06g10850 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate09g11190 |
| Malvaceae | Hibiscus hamabo Siebold & Zucc. | 1 | nbisL1-mrna-11934 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG10.812 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb5G26843 |
| Poaceae | Echinochloa crus-galli | 3 | AH06.977, BH06.999, CH06.1096 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_6AG0515230, gene-QOZ80_6BG0466940 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.7HG0667760.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_028996 |
| Poaceae | Oryza coarctata | 2 | Oco11G006320, Oco12G006350 |
| Poaceae | Oryza sativa | 1 | LOC_Os06g13070.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_10G102000 |
| Poaceae | Puccinellia tenuiflora | 2 | Pt_Chr0404644, Pt_Chr0404708 |
| Poaceae | Sporobolus alterniflorus | 3 | Chr11G018770, Chr11G019010, Chr14G004730 |
| Poaceae | Thinopyrum elongatum | 1 | Tel7E01G357000 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC7AG024300, gene_TRIDC7BG014960 |
| Poaceae | Triticum aestivum | 3 | TraesCS7A02G194800.1, TraesCS7B02G100500.1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb279940_P003 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-45440 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g31660 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG01.2537, evm.TU.LG14.1676 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc03g06740 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_4_RagTag.508 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-28858 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-8175 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-1826 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000008l.327 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00000029 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-14579 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-1491 |
| Salicaceae | Populus euphratica | 1 | populus_peu28586 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132632751 |
| Solanaceae | Solanum chilense | 1 | SOLCI000409700 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107012202 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.20091_chr07_- |
| Tamaricaceae | Tamarix chinensis | 1 | TC08G2386 |
| Zosteraceae | Zostera marina | 1 | Zosma03g04150.v3.1 |