Basic Information
Locus ID:
Ag4G01782
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
zinc-RING finger domain
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr4 | 248268047 | 248270562 | - | Ag4G01782 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 9.84 | 25,508.84 Da | 70.73 | 63.61 | -0.53 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| Pfam | PF13923 | Zinc finger, C3HC4 type (RING finger) | 175 | 212 | 1.6E-10 | - |
| SUPERFAMILY | SSF57850 | RING/U-box | 169 | 219 | 2.91E-17 | - |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 116 | 228 | 8.7E-18 | IPR013083 |
| SMART | SM00184 | ring_2 | 175 | 212 | 9.9E-6 | IPR001841 |
| ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 175 | 213 | 12.563043 | IPR001841 |
| ProSitePatterns | PS00518 | Zinc finger RING-type signature. | 190 | 199 | - | IPR017907 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 72 | 92 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 120 | 156 | - | - |
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT5G48655.1 | RING/U-box superfamily protein. | 0 |
| RefSeq | XP_017240670.1 | PREDICTED: E3 ubiquitin-protein ligase RNF4-like [Daucus carota subsp. sativus] | 0 |
| P78317 | E3 ubiquitin-protein ligase RNF4 OS=Homo sapiens OX=9606 GN=RNF4 PE=1 SV=1 | 0 | |
| TrEMBL | A0A166A2Y0 | RING-type domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_009433 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 1.276015 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 0.120874 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 0.540886 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 0 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 0 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 0.528897 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 0.612713 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 0 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 0.32037 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 0.941736 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 0.670819 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 0.718714 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 0.490071 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 1.178645 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 3.699334 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 0 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 2.482998 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 0.863154 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 1.338609 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 0.395452 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 0 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 0.231913 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 0 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 0.936734 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 0.879903 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 0 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 0.253425 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 0.33798 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 0.794023 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 0 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 0 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 0 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 0 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 1.196722 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 0 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 0 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 0 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 0 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 0 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 0 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 0 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 0 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 0 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 0 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 0 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 0 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 0 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 0.767547 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 0.913064 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 0.476913 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 2 | jg36108, jg8055 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_6490 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah028321 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg26580, Sbi_jg33980 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg15100 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00011885 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000005011, gene:ENSEOMG00000035979 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.7AG0009940, CQ.Regalona.r1.7BG0012110 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30014250 |
| Apiaceae | Apium graveolens | 3 | Ag10G00798, Ag4G01782, Ag7G00073 |
| Arecaceae | Cocos nucifera | 3 | COCNU_02G008590, COCNU_02G015890, scaffold138810G000020 |
| Arecaceae | Phoenix dactylifera | 6 | gene-LOC103697201, gene-LOC103706523, gene-LOC103710584 ... |
| Asparagaceae | Asparagus officinalis | 4 | AsparagusV1_02.443.V1.1, AsparagusV1_09.1052.V1.1 ... |
| Asteraceae | Flaveria trinervia | 4 | Ftri10G27683, Ftri10G33108, Ftri15G22394, Ftri9G33219 |
| Brassicaceae | Arabidopsis thaliana | 2 | AT3G07200.1, AT5G48655.2 |
| Brassicaceae | Eutrema salsugineum | 3 | Thhalv10004921m.g.v1.0, Thhalv10021611m.g.v1.0 ... |
| Brassicaceae | Schrenkiella parvula | 2 | Sp2g19060.v2.2, Sp3g06150.v2.2 |
| Brassicaceae | Brassica nigra | 5 | BniB01g056690.2N, BniB02g069710.2N, BniB04g005810.2N ... |
| Casuarinaceae | Casuarina equisetifolia | 2 | Ceq05G0038, Ceq07G0707 |
| Cymodoceaceae | Cymodocea nodosa | 4 | gene.Cymno04g02630, gene.Cymno05g02670, gene.Cymno07g09610 ... |
| Dunaliellaceae | Dunaliella salina | 2 | Dusal.0009s00030.v1.0, Dusal.0462s00002.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate09g08930 |
| Malvaceae | Hibiscus hamabo Siebold & Zucc. | 1 | nbisL1-mrna-9763 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG04.1597 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00036463 |
| Plumbaginaceae | Limonium bicolor | 3 | Lb4G23954, Lb5G28645, Lb5G28647 |
| Poaceae | Echinochloa crus-galli | 5 | AH02.4325, BH02.4353, BH03.2641, CH02.4400, CH03.2848 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_1AG0044520, gene-QOZ80_1BG0094530 |
| Poaceae | Hordeum vulgare | 10 | HORVU.MOREX.r3.3HG0309940.1, HORVU.MOREX.r3.3HG0309960.1 ... |
| Poaceae | Lolium multiflorum | 12 | gene-QYE76_006451, gene-QYE76_018607, gene-QYE76_026282 ... |
| Poaceae | Oryza coarctata | 4 | Oco01G028450, Oco02G029550, Oco15G010370, Oco17G008730 |
| Poaceae | Oryza sativa | 2 | LOC_Os01g69040.1, LOC_Os09g32690.2 |
| Poaceae | Paspalum vaginatum | 2 | gene-BS78_02G232300, gene-BS78_03G382000 |
| Poaceae | Puccinellia tenuiflora | 9 | Pt_Chr0202939, Pt_Chr0202953, Pt_Chr0600509, Pt_Chr0600511 ... |
| Poaceae | Sporobolus alterniflorus | 6 | Chr02G002560, Chr03G022810, Chr05G031870, Chr08G019220 ... |
| Poaceae | Thinopyrum elongatum | 8 | Tel3E01G675100, Tel3E01G676600, Tel3E01G677000 ... |
| Poaceae | Triticum dicoccoides | 18 | gene_TRIDC3AG060280, gene_TRIDC3AG060320 ... |
| Poaceae | Triticum aestivum | 30 | TraesCS3A02G425600.1, TraesCS3A02G425700.1 ... |
| Poaceae | Zea mays | 3 | Zm00001eb102300_P004, Zm00001eb143350_P001 ... |
| Poaceae | Zoysia macrostachya | 2 | Zma_g30591, Zma_g9264 |
| Portulacaceae | Portulaca oleracea | 3 | evm.TU.LG03.1052, evm.TU.LG12.678, evm.TU.LG16.1664 |
| Posidoniaceae | Posidonia oceanica | 4 | gene.Posoc01g05870, gene.Posoc05g04470, gene.Posoc05g08420 ... |
| Rhizophoraceae | Bruguiera sexangula | 2 | evm.TU.Scaffold_5_RagTag.1762, evm.TU.Scaffold_9_RagTag.1546 |
| Rhizophoraceae | Carallia pectinifolia | 3 | nbisL1-mrna-12258, nbisL1-mrna-20718, nbisL1-mrna-20776 |
| Rhizophoraceae | Ceriops tagal | 2 | nbisL1-mrna-12181, nbisL1-mrna-1935 |
| Rhizophoraceae | Ceriops zippeliana | 2 | nbisL1-mrna-10768, nbisL1-mrna-21529 |
| Rhizophoraceae | Kandelia candel | 2 | evm.TU.utg000003l.976, evm.TU.utg000006l.1028 |
| Rhizophoraceae | Kandelia obovata | 2 | Maker00009860, Maker00014112 |
| Rhizophoraceae | Rhizophora apiculata | 2 | nbisL1-mrna-10562, nbisL1-mrna-22389 |
| Rhizophoraceae | Rhizophora mangle | 2 | nbisL1-mrna-15696, nbisL1-mrna-4543 |
| Salicaceae | Populus euphratica | 5 | populus_peu03778, populus_peu17920, populus_peu30888 ... |
| Solanaceae | Lycium barbarum | 2 | gene-LOC132605685, gene-LOC132610062 |
| Solanaceae | Solanum chilense | 2 | SOLCI002926300, SOLCI004588000 |
| Solanaceae | Solanum pennellii | 2 | gene-LOC107021377, gene-LOC107029274 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.63_chr01_+ |
| Tamaricaceae | Tamarix chinensis | 2 | TC01G0698, TC08G0924 |
| Zosteraceae | Zostera marina | 3 | Zosma03g15740.v3.1, Zosma05g14590.v3.1, Zosma05g15210.v3.1 |