Basic Information
Locus ID:
Ag8G00720
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
E3 ubiquitin-protein ligase
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr8 | 44574418 | 44582662 | + | Ag8G00720 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 6.79 | 78,007.58 Da | 57.78 | 74.92 | -0.47 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd16504 | RING-HC_COP1 | 63 | 107 | 2.43167E-22 | - |
| Pfam | PF00400 | WD domain, G-beta repeat | 471 | 508 | 0.0029 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 557 | 593 | 6.2E-5 | IPR001680 |
| Pfam | PF13923 | Zinc finger, C3HC4 type (RING finger) | 66 | 103 | 2.1E-11 | - |
| SUPERFAMILY | SSF57850 | RING/U-box | 49 | 124 | 4.16E-17 | - |
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 389 | 686 | 3.53E-53 | IPR036322 |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 41 | 156 | 2.1E-19 | IPR013083 |
| Gene3D | G3DSA:2.130.10.10 | - | 359 | 691 | 2.0E-146 | IPR015943 |
| SMART | SM00320 | WD40_4 | 469 | 509 | 1.7E-7 | IPR001680 |
| SMART | SM00320 | WD40_4 | 596 | 635 | 11.0 | IPR001680 |
| SMART | SM00320 | WD40_4 | 427 | 466 | 0.83 | IPR001680 |
| SMART | SM00320 | WD40_4 | 555 | 593 | 1.4E-7 | IPR001680 |
| SMART | SM00320 | WD40_4 | 372 | 416 | 0.66 | IPR001680 |
| SMART | SM00320 | WD40_4 | 510 | 551 | 0.55 | IPR001680 |
| SMART | SM00184 | ring_2 | 66 | 103 | 1.3E-7 | IPR001841 |
| ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 66 | 104 | 12.25323 | IPR001841 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 476 | 508 | 10.207686 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 562 | 602 | 13.048234 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 476 | 508 | 8.597424 | - |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 562 | 595 | 10.23196 | - |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 580 | 594 | - | IPR019775 |
| ProSitePatterns | PS00518 | Zinc finger RING-type signature. | 81 | 90 | - | IPR017907 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 580 | 594 | 9.5E-5 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 453 | 467 | 9.5E-5 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 496 | 510 | 9.5E-5 | IPR020472 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 288 | 309 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 258 | 312 | - | - |
| Coils | Coil | Coil | 152 | 179 | - | - |
Gene Ontology
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT2G32950.1 | Transducin/WD40 repeat-like superfamily protein. Represses photomorphogenesis and induces skotomorphogenesis in the dark. Contains a ring finger zinc-binding motif, a coiled-coil domain, and several WD-40 repeats, similar to G-beta proteins. The C-terminus has homology to TAFII80, a subunit of the TFIID component of the RNA polymerase II of Drosophila. Nuclear localization in the dark and cytoplasmic in the light. | 0 |
| RefSeq | XP_017228304.1 | PREDICTED: E3 ubiquitin-protein ligase COP1-like [Daucus carota subsp. sativus] | 0 |
| P43254 | E3 ubiquitin-protein ligase COP1 OS=Arabidopsis thaliana OX=3702 GN=COP1 PE=1 SV=2 | 0 | |
| TrEMBL | A0A175Y8G0 | RING-type domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_000480 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 6.054528 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 5.116734 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 5.671878 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 8.447686 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 8.46598 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 6.526257 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 4.33 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 3.591728 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 26.63368 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 20.489813 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 25.37425 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 24.567999 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 24.406576 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 20.756363 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 14.187083 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 16.120754 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 9.646601 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 9.564123 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 12.09763 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 11.000728 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 10.314694 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 6.141775 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 6.929552 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 10.891978 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 8.83888 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 16.048807 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 11.540719 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 8.959734 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 15.581324 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 14.255363 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 30.160236 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 24.25386 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 7.523303 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 5.749935 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 6.531001 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 5.745337 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 12.930799 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 9.633489 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 13.588391 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 16.42905 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 16.614027 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 6.291176 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 8.992073 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 4.694753 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 3.557681 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 5.643463 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 2.923174 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 7.359303 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 5.102293 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 5.199228 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 3 | jg24134, jg24775, jg38579 |
| Aizoaceae | Mesembryanthemum crystallinum | 2 | gene_20601, gene_21986 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah038322 |
| Amaranthaceae | Beta vulgaris | 2 | BVRB_8g185250, BVRB_9g204280 |
| Amaranthaceae | Salicornia bigelovii | 4 | Sbi_jg14464, Sbi_jg40234, Sbi_jg50220, Sbi_jg53841 |
| Amaranthaceae | Salicornia europaea | 2 | Seu_jg10340, Seu_jg1818 |
| Amaranthaceae | Suaeda aralocaspica | 2 | GOSA_00011396, GOSA_00012661 |
| Amaranthaceae | Suaeda glauca | 6 | Sgl41576, Sgl41616, Sgl46385, Sgl46412, Sgl78203, Sgl80695 |
| Amaranthaceae | Chenopodium album | 8 | gene:ENSEOMG00000008754, gene:ENSEOMG00000011065 ... |
| Amaranthaceae | Chenopodium quinoa | 4 | CQ.Regalona.r1.8AG0001130, CQ.Regalona.r1.8BG0001040 ... |
| Anacardiaceae | Pistacia vera | 2 | pistato.v30017840, pistato.v30067900 |
| Apiaceae | Apium graveolens | 2 | Ag3G00015, Ag8G00720 |
| Arecaceae | Cocos nucifera | 1 | COCNU_01G010060 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103718513 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_08.1838.V1.1 |
| Asteraceae | Flaveria trinervia | 2 | Ftri4G03918, Ftri5G03367 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT2G32950.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10016348m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp4g15310.v2.2 |
| Brassicaceae | Brassica nigra | 2 | BniB01g011290.2N, BniB06g022040.2N |
| Casuarinaceae | Casuarina equisetifolia | 2 | Ceq02G2341, Ceq04G1673 |
| Casuarinaceae | Casuarina glauca | 2 | Cgl02G2426, Cgl04G1850 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno02g16220 |
| Dunaliellaceae | Dunaliella salina | 2 | Dusal.0161s00011.v1.0, Dusal.4798s00001.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate03g26290 |
| Malvaceae | Hibiscus hamabo Siebold & Zucc. | 1 | nbisL1-mrna-7213 |
| Nitrariaceae | Nitraria sibirica | 2 | evm.TU.LG04.2135, evm.TU.LG12.1193 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00039081 |
| Plumbaginaceae | Limonium bicolor | 2 | Lb4G22990, Lb6G31738 |
| Poaceae | Echinochloa crus-galli | 3 | AH07.3634, BH07.3444, CH07.3514 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_2AG0147420, gene-QOZ80_2BG0202840 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.6HG0618700.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_025729 |
| Poaceae | Oryza coarctata | 2 | Oco03G022920, Oco04G023530 |
| Poaceae | Oryza sativa | 1 | LOC_Os02g53140.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_04G290400 |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0203106 |
| Poaceae | Sporobolus alterniflorus | 5 | Chr06G001150, Chr09G007590, Chr09G018630, Chr13G003030 ... |
| Poaceae | Thinopyrum elongatum | 1 | Tel6E01G576200 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC6AG048850, gene_TRIDC6BG057160 |
| Poaceae | Triticum aestivum | 3 | TraesCS6A02G326100.1, TraesCS6B02G356400.1 ... |
| Poaceae | Zea mays | 2 | Zm00001eb193380_P001, Zm00001eb256270_P001 |
| Poaceae | Zoysia japonica | 2 | nbis-gene-40063, nbis-gene-8573 |
| Poaceae | Zoysia macrostachya | 2 | Zma_g14521, Zma_g17239 |
| Portulacaceae | Portulaca oleracea | 4 | evm.TU.LG01.1941, evm.TU.LG02.2235, evm.TU.LG14.1123 ... |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc03g17040 |
| Rhizophoraceae | Bruguiera sexangula | 2 | evm.TU.Scaffold_13_RagTag.16, evm.TU.Scaffold_9_RagTag.1386 |
| Rhizophoraceae | Carallia pectinifolia | 3 | nbisL1-mrna-20374, nbisL1-mrna-20527, nbisL1-mrna-29812 |
| Rhizophoraceae | Ceriops tagal | 2 | nbisL1-mrna-5463, nbisL1-mrna-6552 |
| Rhizophoraceae | Ceriops zippeliana | 2 | nbisL1-mrna-20744, nbisL1-mrna-21383 |
| Rhizophoraceae | Kandelia candel | 2 | evm.TU.utg000003l.867, evm.TU.utg000015l.11 |
| Rhizophoraceae | Kandelia obovata | 2 | Maker00009386, Maker00015866 |
| Rhizophoraceae | Rhizophora apiculata | 2 | nbisL1-mrna-1192, nbisL1-mrna-6080 |
| Rhizophoraceae | Rhizophora mangle | 2 | nbisL1-mrna-23396, nbisL1-mrna-4685 |
| Salicaceae | Populus euphratica | 3 | populus_peu10421, populus_peu18422, populus_peu26973 |
| Solanaceae | Lycium barbarum | 2 | gene-LOC132613854, gene-LOC132636661 |
| Solanaceae | Solanum chilense | 2 | SOLCI000134000, SOLCI003924200 |
| Solanaceae | Solanum pennellii | 2 | gene-LOC107003012, gene-LOC107007198 |
| Tamaricaceae | Reaumuria soongarica | 2 | STRG.29901_chr10_+, gene_442 |
| Tamaricaceae | Tamarix chinensis | 2 | TC03G0399, TC08G0159 |
| Zosteraceae | Zostera marina | 2 | Zosma03g17610.v3.1, Zosma05g29840.v3.1 |