Basic Information
Locus ID:
AgUnG00396
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
zinc finger
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| ctg2904 | 125528 | 128127 | + | AgUnG00396 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 4.82 | 46,860.67 Da | 60.20 | 76.29 | -0.26 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| Pfam | PF13456 | Reverse transcriptase-like | 92 | 193 | 8.4E-9 | IPR002156 |
| Pfam | PF00097 | Zinc finger, C3HC4 type (RING finger) | 224 | 268 | 1.7E-5 | IPR018957 |
| SUPERFAMILY | SSF57850 | RING/U-box | 379 | 414 | 1.35E-6 | - |
| SUPERFAMILY | SSF57850 | RING/U-box | 219 | 298 | 1.18E-13 | - |
| Gene3D | G3DSA:3.30.420.10 | - | 74 | 210 | 1.5E-8 | IPR036397 |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 218 | 305 | 1.4E-15 | IPR013083 |
| SMART | SM00647 | ibrneu5 | 295 | 366 | 2.4E-6 | IPR002867 |
| SMART | SM00184 | ring_2 | 224 | 270 | 4.0E-4 | IPR001841 |
| ProSiteProfiles | PS51873 | TRIAD supradomain profile. | 220 | 415 | 23.306276 | IPR044066 |
| ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 224 | 268 | 10.910707 | IPR001841 |
| ProSitePatterns | PS00518 | Zinc finger RING-type signature. | 241 | 250 | - | IPR017907 |
Gene Ontology
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT4G19670.1 | RING/U-box superfamily protein. | 0 |
| RefSeq | XP_017230689.1 | PREDICTED: probable E3 ubiquitin-protein ligase ARI10 [Daucus carota subsp. sativus] | 0 |
| TrEMBL | A0A6L5BAS4 | RING-type domain-containing protein OS=Apium graveolens OX=4045 GN=AG4045_015602 PE=3 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 7.631848 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 7.469339 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 7.685276 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 8.860737 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 9.275386 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 7.244523 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 5.676013 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 3.666058 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 10.592757 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 9.748448 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 13.070244 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 11.989636 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 13.594666 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 10.714841 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 18.589264 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 18.795559 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 17.461157 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 20.860266 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 17.149982 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 18.441563 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 21.976574 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 19.046202 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 22.058384 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 17.26392 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 20.532734 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 19.870842 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 21.147642 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 16.025576 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 23.190012 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 5.34005 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 9.195472 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 6.724713 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 11.191571 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 8.65217 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 9.831897 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 4.541176 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 2.835011 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 3.370803 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 14.391597 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 9.287102 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 6.552436 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 15.976994 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 19.148464 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 19.706465 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 18.594704 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 10.985891 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 24.997236 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 13.405161 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 9.092568 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 9.621121 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 3 | jg20879, jg20880, jg22388 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_5018 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah029577 |
| Amaranthaceae | Beta vulgaris | 2 | BVRB_5g105360, BVRB_7g163120 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg16124, Sbi_jg56771 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg24628 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000007042, gene:ENSEOMG00000034169 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.7AG0015650, CQ.Regalona.r1.7BG0019060 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30078190 |
| Apiaceae | Apium graveolens | 2 | Ag6G01200, AgUnG00396 |
| Arecaceae | Cocos nucifera | 1 | COCNU_06G019060 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103719299 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_06.101.V1.1 |
| Asteraceae | Flaveria trinervia | 2 | Ftri17G06246, Ftri18G29723 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT4G19670.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10024888m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp7g18240.v2.2 |
| Brassicaceae | Brassica nigra | 3 | BniB02g071270.2N, BniB05g016750.2N, BniB07g009220.2N |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno17g03630 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate04g15740 |
| Malvaceae | Hibiscus hamabo Siebold & Zucc. | 1 | nbisL1-mrna-852 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG12.188 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00012939 |
| Plumbaginaceae | Limonium bicolor | 3 | Lb6G29893, Lb6G31154, Lb6G31779 |
| Poaceae | Echinochloa crus-galli | 3 | AH05.4183, BH05.4260, CH05.4492 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_5AG0399190, gene-QOZ80_5BG0447880 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.5HG0422080.1 |
| Poaceae | Oryza coarctata | 2 | Oco23G011040, Oco24G010840 |
| Poaceae | Oryza sativa | 1 | LOC_Os12g43560.1 |
| Poaceae | Paspalum vaginatum | 2 | gene-BS78_08G165200, gene-BS78_K301400 |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0704696 |
| Poaceae | Sporobolus alterniflorus | 4 | Chr04G019720, Chr06G020660, Chr19G007170, Chr27G009720 |
| Poaceae | Thinopyrum elongatum | 1 | Tel5E01G035800 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC5AG002400, gene_TRIDC5BG002230 |
| Poaceae | Triticum aestivum | 3 | TraesCS5A02G015900.1, TraesCS5B02G014200.1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb032750_P001 |
| Poaceae | Zoysia japonica | 2 | nbis-gene-44433, nbis-gene-47436 |
| Poaceae | Zoysia macrostachya | 2 | Zma_g25396, Zma_g26186 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc10g09280 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_14_RagTag.1069 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-16921 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-15946 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-17351 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000025l.185 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-8576 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-23052 |
| Salicaceae | Populus euphratica | 2 | populus_peu29054, populus_peu30447 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132624884 |
| Solanaceae | Solanum chilense | 1 | SOLCI001298800 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107011703 |
| Zosteraceae | Zostera marina | 1 | Zosma03g24190.v3.1 |