Basic Information
Locus ID:
Ag5G00387
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
Catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr5 | 12115229 | 12123619 | - | Ag5G00387 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 8.53 | 36,059.26 Da | 34.06 | 95.39 | -0.15 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd02801 | DUS_like_FMN | 6 | 249 | 3.22888E-99 | IPR035587 |
| Pfam | PF01207 | Dihydrouridine synthase (Dus) | 8 | 256 | 1.6E-58 | IPR035587 |
| SUPERFAMILY | SSF51395 | FMN-linked oxidoreductases | 5 | 281 | 1.61E-67 | - |
| Gene3D | G3DSA:3.20.20.70 | Aldolase class I | 2 | 252 | 1.6E-79 | IPR013785 |
| ProSitePatterns | PS01136 | Uncharacterized protein family UPF0034 signature. | 104 | 122 | - | IPR018517 |
Gene Ontology
Biological Process:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT3G49640.1 | Aldolase-type TIM barrel family protein. | 0 |
| RefSeq | XP_017218535.1 | PREDICTED: tRNA-dihydrouridine(20) synthase [NAD(P)+]-like [Daucus carota subsp. sativus] | 0 |
| Q9NX74 | tRNA-dihydrouridine(20) synthase [NAD(P)+]-like OS=Homo sapiens OX=9606 GN=DUS2 PE=1 SV=1 | 0 | |
| TrEMBL | A0A164UE59 | Dus domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_025846 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 5.387891 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 6.702067 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 7.013393 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 5.540661 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 6.180142 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 5.67634 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 5.576073 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 3.860949 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 9.20383 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 7.534282 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 8.50404 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 9.38451 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 10.195745 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 9.017684 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 9.35307 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 6.493781 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 9.284301 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 10.096777 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 9.851974 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 6.261649 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 9.398958 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 10.503073 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 11.362244 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 9.694416 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 10.293482 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 9.735281 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 8.848969 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 10.068441 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 10.260851 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 5.441815 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 8.164444 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 7.908797 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 8.037519 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 5.594574 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 6.44702 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 3.77428 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 3.187762 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 3.351831 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 6.032349 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 6.210926 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 7.697099 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 11.403993 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 11.656726 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 6.644119 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 8.614525 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 13.420056 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 13.749041 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 11.477233 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 11.356734 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 8.745838 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg19605 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_16443 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah012991 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_6g152950 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg43019, Sbi_jg45622 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg11467 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00002062 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl35765, Sgl41033 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000003029, gene:ENSEOMG00000012491 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.6AG0000260, CQ.Regalona.r1.6BG0000160 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30204270 |
| Apiaceae | Apium graveolens | 1 | Ag5G00387 |
| Arecaceae | Cocos nucifera | 1 | COCNU_07G000250 |
| Arecaceae | Phoenix dactylifera | 2 | gene-LOC103708392, gene-LOC120106513 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_04.1030.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri6G12878 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT3G49640.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10010537m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp5g12460.v2.2 |
| Brassicaceae | Brassica nigra | 1 | BniB08g063300.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq06G0408 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl06G0424 |
| Cymodoceaceae | Cymodocea nodosa | 2 | gene.Cymno07g08020, gene.Cymno13g01320 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate05g22270 |
| Malvaceae | Hibiscus hamabo Siebold & Zucc. | 2 | nbisL1-mrna-10097, nbisL1-mrna-10594 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG02.2642 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb8G36347 |
| Poaceae | Echinochloa crus-galli | 3 | AH09.1685, BH09.1869, CH09.2011 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_4AG0309500, gene-QOZ80_4BG0340560 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.2HG0183920.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_045230 |
| Poaceae | Oryza coarctata | 2 | Oco07G011380, Oco08G011140 |
| Poaceae | Oryza sativa | 1 | LOC_Os04g44890.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_06G169100 |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0301929 |
| Poaceae | Sporobolus alterniflorus | 3 | Chr25G006610, Chr26G011690, Chr30G006510 |
| Poaceae | Thinopyrum elongatum | 1 | Tel2E01G641900 |
| Poaceae | Triticum dicoccoides | 1 | gene_TRIDC2AG053780 |
| Poaceae | Triticum aestivum | 3 | TraesCS2A02G371800.1, TraesCS2B02G388900.2 ... |
| Poaceae | Zea mays | 1 | Zm00001eb427250_P001 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-37168 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g20113 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG05.1000, evm.TU.LG25.340 |
| Posidoniaceae | Posidonia oceanica | 2 | gene.Posoc10g03130, gene.Posoc10g03150 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_6_RagTag.1737 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-17422 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-1312 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-12030 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000011l.1057 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00008097 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-15413 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-3348 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132603147 |
| Solanaceae | Solanum chilense | 1 | SOLCI000119000 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107020981 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.8862_chr03_+ |
| Tamaricaceae | Tamarix chinensis | 1 | TC11G0616 |
| Zosteraceae | Zostera marina | 1 | Zosma03g22890.v3.1 |