Basic Information
Locus ID:
Ag5G01302
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
Tyrosyl-DNA phosphodiesterase
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr5 | 104050835 | 104055557 | + | Ag5G01302 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 8.49 | 47,253.03 Da | 44.90 | 76.15 | -0.30 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd09080 | TDP2 | 153 | 418 | 7.80318E-86 | - |
| Pfam | PF03372 | Endonuclease/Exonuclease/phosphatase family | 156 | 375 | 9.0E-12 | IPR005135 |
| SUPERFAMILY | SSF90209 | Ran binding protein zinc finger-like | 47 | 72 | 1.96E-5 | IPR036443 |
| SUPERFAMILY | SSF56219 | DNase I-like | 152 | 418 | 2.22E-32 | IPR036691 |
| Gene3D | G3DSA:2.30.30.380 | - | 6 | 46 | 4.6E-6 | - |
| Gene3D | G3DSA:2.30.30.380 | - | 47 | 84 | 5.2E-6 | - |
| Gene3D | G3DSA:3.60.10.10 | Endonuclease/exonuclease/phosphatase | 145 | 419 | 2.7E-81 | IPR036691 |
| SMART | SM00547 | zf_4 | 11 | 36 | 0.47 | IPR001876 |
| SMART | SM00547 | zf_4 | 49 | 73 | 4.4E-4 | IPR001876 |
| ProSitePatterns | PS01358 | Zinc finger RanBP2-type signature. | 51 | 70 | - | IPR001876 |
Gene Ontology
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT1G11800.1 | endonuclease/exonuclease/phosphatase family protein. | 0 |
| RefSeq | XP_017216363.1 | PREDICTED: tyrosyl-DNA phosphodiesterase 2-like [Daucus carota subsp. sativus] | 0 |
| TrEMBL | A0A161ZNE9 | RanBP2-type domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_024931 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 12.069095 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 9.261355 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 6.214339 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 7.896991 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 8.125576 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 6.399697 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 4.792208 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 3.025252 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 26.543375 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 24.843786 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 26.135107 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 22.981564 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 21.001431 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 17.617599 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 10.608509 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 9.331596 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 11.577286 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 13.227636 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 15.787215 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 12.611885 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 14.486429 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 11.781219 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 13.972168 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 13.018463 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 13.152635 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 17.445312 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 13.142667 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 15.822549 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 14.677913 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 8.032563 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 13.316422 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 12.409145 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 10.805129 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 11.115608 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 8.517044 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 6.691432 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 5.234308 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 6.788177 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 15.377253 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 9.232921 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 11.462399 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 2.364668 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 6.403216 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 11.436372 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 11.198502 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 5.264167 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 11.07619 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 21.589903 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 18.428659 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 20.002737 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg20433 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_86 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah017508 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_8g185970 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg40165, Sbi_jg50120 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg1744 |
| Amaranthaceae | Suaeda aralocaspica | 2 | GOSA_00011341, GOSA_00011342 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl46334, Sgl51050 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000011037, gene:ENSEOMG00000035131 ... |
| Amaranthaceae | Chenopodium quinoa | 3 | CQ.Regalona.r1.2AG0006990, CQ.Regalona.r1.8AG0001570 ... |
| Anacardiaceae | Pistacia vera | 4 | pistato.v30196780, pistato.v30196810, pistato.v30196820 ... |
| Apiaceae | Apium graveolens | 2 | Ag5G01302, Ag8G01080 |
| Arecaceae | Cocos nucifera | 3 | COCNU_06G011960, COCNU_14G009720, contig69461970G000010 |
| Arecaceae | Phoenix dactylifera | 2 | gene-LOC103707196, gene-LOC103707197 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_03.1168.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri18G22915 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT1G11800.1 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp1g10430.v2.2 |
| Brassicaceae | Brassica nigra | 2 | BniB02g006540.2N, BniB02g006560.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq04G1618 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl04G1796 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno02g15000 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0488s00013.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate04g15670 |
| Malvaceae | Hibiscus hamabo Siebold & Zucc. | 1 | nbisL1-mrna-1793 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG12.1143 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00005939 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb4G22922 |
| Poaceae | Echinochloa crus-galli | 21 | AH01.1539, AH01.2122, AH03.3128, AH03.3129, BH01.1740 ... |
| Poaceae | Eleusine coracana subsp. coracana | 11 | gene-QOZ80_2AG0122960, gene-QOZ80_2BG0179150 ... |
| Poaceae | Hordeum vulgare | 2 | HORVU.MOREX.r3.3HG0318330.1, HORVU.MOREX.r3.6HG0567060.1 |
| Poaceae | Lolium multiflorum | 2 | gene-QYE76_020756, gene-QYE76_052711 |
| Poaceae | Oryza coarctata | 5 | Oco14G008820, Oco19G003780, Oco20G003620, Oco23G005660 ... |
| Poaceae | Oryza sativa | 3 | LOC_Os07g32610.2, LOC_Os10g26164.1, LOC_Os12g22620.1 |
| Poaceae | Paspalum vaginatum | 4 | gene-BS78_01G172300, gene-BS78_01G245700 ... |
| Poaceae | Puccinellia tenuiflora | 6 | Pt_Chr0104213, Pt_Chr0105761, Pt_Chr0202450, Pt_Chr0202470 ... |
| Poaceae | Sporobolus alterniflorus | 14 | Chr01G010540, Chr09G008600, Chr09G008610, Chr09G008620 ... |
| Poaceae | Thinopyrum elongatum | 3 | Tel3E01G768500, Tel6E01G294900, Tel7E01G811800 |
| Poaceae | Triticum dicoccoides | 1 | gene_TRIDC6BG025190 |
| Poaceae | Triticum aestivum | 10 | TraesCS1A02G372500.1, TraesCS1A02G372600.1 ... |
| Poaceae | Zea mays | 2 | Zm00001eb043220_P002, Zm00001eb048580_P002 |
| Poaceae | Zoysia japonica | 4 | nbis-gene-27866, nbis-gene-38338, nbis-gene-38340 ... |
| Poaceae | Zoysia macrostachya | 1 | Zma_g13188 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG01.1895, evm.TU.LG14.1082 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc04g19860 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_13_RagTag.50 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-29773 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-5440 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-20777 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000015l.35 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00015359 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-6058 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-23430 |
| Salicaceae | Populus euphratica | 1 | populus_peu10361 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132606312 |
| Solanaceae | Solanum chilense | 1 | SOLCI002134900 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107009074 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.18470_chr09_- |
| Tamaricaceae | Tamarix chinensis | 1 | TC07G1633 |
| Zosteraceae | Zostera marina | 1 | Zosma01g08160.v3.1 |