Basic Information
Locus ID:
Ag4G02167
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
E3 ubiquitin-protein ligase ORTHRUS
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr4 | 284886225 | 284893311 | - | Ag4G02167 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 8.61 | 72,121.78 Da | 49.45 | 63.29 | -0.71 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd16449 | RING-HC | 125 | 163 | 5.35533E-10 | - |
| Pfam | PF13445 | RING-type zinc-finger | 497 | 539 | 1.5E-7 | IPR027370 |
| Pfam | PF13920 | Zinc finger, C3HC4 type (RING finger) | 122 | 167 | 1.1E-7 | - |
| Pfam | PF02182 | SAD/SRA domain | 255 | 403 | 3.1E-53 | IPR003105 |
| SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 6 | 60 | 1.51E-8 | IPR011011 |
| SUPERFAMILY | SSF57850 | RING/U-box | 116 | 186 | 3.31E-16 | - |
| SUPERFAMILY | SSF88697 | PUA domain-like | 225 | 420 | 3.98E-68 | IPR015947 |
| SUPERFAMILY | SSF57850 | RING/U-box | 491 | 579 | 1.04E-12 | - |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 482 | 608 | 2.8E-17 | IPR013083 |
| Gene3D | G3DSA:2.30.280.10 | - | 223 | 420 | 6.5E-76 | IPR036987 |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 77 | 192 | 4.3E-20 | IPR013083 |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 2 | 76 | 1.3E-8 | IPR013083 |
| SMART | SM00249 | PHD_3 | 14 | 60 | 5.5E-6 | IPR001965 |
| SMART | SM00184 | ring_2 | 497 | 553 | 2.9E-7 | IPR001841 |
| SMART | SM00184 | ring_2 | 125 | 163 | 9.4E-6 | IPR001841 |
| SMART | SM00184 | ring_2 | 15 | 59 | 5.2 | IPR001841 |
| SMART | SM00466 | G9a_1 | 247 | 404 | 1.2E-78 | IPR003105 |
| ProSiteProfiles | PS51015 | YDG domain profile. | 252 | 400 | 51.091423 | IPR003105 |
| ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 125 | 164 | 11.677863 | IPR001841 |
| ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 497 | 553 | 10.350093 | IPR001841 |
| ProSiteProfiles | PS50016 | Zinc finger PHD-type profile. | 12 | 62 | 8.742399 | IPR019787 |
| ProSitePatterns | PS01359 | Zinc finger PHD-type signature. | 15 | 59 | - | IPR019786 |
| ProSitePatterns | PS00518 | Zinc finger RING-type signature. | 512 | 521 | - | IPR017907 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 579 | 648 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 593 | 641 | - | - |
| Coils | Coil | Coil | 563 | 583 | - | - |
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT1G57820.1 | Zinc finger (C3HC4-type RING finger) family protein. Encodes a 645-amino acid methylcytosine-binding protein with a PHD domain, two RING finger domains, and an SRA domain that is involved in centromere heterochromatinization. This protein functions as an E3 ubiquitin ligase in vitro. The protein has been shown to bind to methylated cytosines of CG, CNG and CNN motifs via its SRA domain but has a preference for the former. It plays a role in the establishment/maintenance of chromatin structure during cell division and is localized in the nucleus. Plants over-expressing VIM1/ORTH2 show an inhibition in root growth and a delay in flowering. Both over-expression of GFP:ORTH2 and loss of ORTH2/VIM1 lead to decreased levels of DNA methylation. GFP:ORTH2 over-expressers also have increased levels of FWA transcripts. | 0 |
| RefSeq | XP_017232391.1 | PREDICTED: E3 ubiquitin-protein ligase ORTHRUS 2-like [Daucus carota subsp. sativus] | 0 |
| Q8VYZ0 | E3 ubiquitin-protein ligase ORTHRUS 2 OS=Arabidopsis thaliana OX=3702 GN=ORTH2 PE=1 SV=1 | 0 | |
| TrEMBL | A0A7J7C9A5 | RING-type E3 ubiquitin transferase OS=Tripterygium wilfordii OX=458696 GN=HS088_TW20G00699 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 3.874572 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 1.449365 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 0.729415 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 0.629122 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 0.933101 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 0.584147 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 1.033643 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 0.866709 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 28.915947 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 25.222162 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 27.915361 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 25.686018 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 20.815582 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 17.632465 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 0.382646 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 0.552303 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 2.500476 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 2.188181 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 1.911815 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 0.693664 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 1.81911 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 6.989895 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 5.53537 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 7.486724 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 7.13897 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 4.441572 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 4.32809 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 2.693959 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 5.222867 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 0.065335 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 0.063842 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 0.06439 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 0.097368 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 3.361447 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 0 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 0 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 0.061831 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 0.059637 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 9.835264 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 0.738492 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 0.284014 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 0.239408 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 0.312222 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 0.294853 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 0.350009 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 0.336127 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 0.675463 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 11.08696 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 13.17561 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 9.326379 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 2 | jg18373, jg34442 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_19762 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah001521 |
| Amaranthaceae | Salicornia bigelovii | 5 | Sbi_jg30851, Sbi_jg30852, Sbi_jg30853, Sbi_jg30854 ... |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg28291 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00004867 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl54951, Sgl60210 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000004456, gene:ENSEOMG00000022957 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.5AG0018120, CQ.Regalona.r1.5BG0019260 |
| Anacardiaceae | Pistacia vera | 2 | pistato.v30012630, pistato.v30150320 |
| Apiaceae | Apium graveolens | 5 | Ag10G00146, Ag4G02166, Ag4G02167, Ag5G00218, Ag8G02293 |
| Arecaceae | Cocos nucifera | 4 | COCNU_15G005780, scaffold001173G000010 ... |
| Arecaceae | Phoenix dactylifera | 3 | gene-LOC103702448, gene-LOC103708115, gene-LOC103724070 |
| Asparagaceae | Asparagus officinalis | 3 | AsparagusV1_02.1381.V1.1, AsparagusV1_04.1580.V1.1 ... |
| Asteraceae | Flaveria trinervia | 3 | Ftri13G20519, Ftri13G21510, Ftri3G17037 |
| Brassicaceae | Arabidopsis thaliana | 6 | AT1G57800.1, AT1G57820.1, AT1G66040.1, AT1G66050.1 ... |
| Brassicaceae | Eutrema salsugineum | 2 | Thhalv10000084m.g.v1.0, Thhalv10000657m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 5 | Sp1g40830.v2.2, Sp4g01540.v2.2, Sp4g04310.v2.2 ... |
| Brassicaceae | Brassica nigra | 6 | BniB02g018820.2N, BniB02g023540.2N, BniB02g023570.2N ... |
| Casuarinaceae | Casuarina equisetifolia | 2 | Ceq01G1932, Ceq07G0931 |
| Casuarinaceae | Casuarina glauca | 2 | Cgl01G2097, Cgl07G0976 |
| Cymodoceaceae | Cymodocea nodosa | 2 | gene.Cymno05g02020, gene.Cymno07g03030 |
| Dunaliellaceae | Dunaliella salina | 2 | Dusal.0188s00016.v1.0, Dusal.0767s00006.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 3 | gene.Thate01g26300, gene.Thate08g08150, gene.Thate08g08160 |
| Nitrariaceae | Nitraria sibirica | 2 | evm.TU.LG05.551, evm.TU.LG10.269 |
| Plantaginaceae | Plantago ovata | 4 | Pov_00033006, Pov_00033473, Pov_00034139, Pov_00041321 |
| Plumbaginaceae | Limonium bicolor | 2 | Lb2G08931, Lb2G08937 |
| Poaceae | Echinochloa crus-galli | 10 | AH05.1221, AH05.506, BH05.1258, BH05.553, CH03.1082 ... |
| Poaceae | Eleusine coracana subsp. coracana | 6 | gene-QOZ80_5AG0378020, gene-QOZ80_5AG0408960 ... |
| Poaceae | Hordeum vulgare | 2 | HORVU.MOREX.r3.1HG0000630.1 ... |
| Poaceae | Lolium multiflorum | 2 | gene-QYE76_036803, gene-QYE76_058630 |
| Poaceae | Oryza coarctata | 2 | Oco09G000090, Oco10G000150 |
| Poaceae | Oryza sativa | 2 | LOC_Os04g22240.1, LOC_Os05g01230.1 |
| Poaceae | Paspalum vaginatum | 4 | gene-BS78_02G116300, gene-BS78_02G116400, gene-BS78_K283300 ... |
| Poaceae | Puccinellia tenuiflora | 3 | Pt_Chr0500024, Pt_Chr0501852, Pt_Chr0600910 |
| Poaceae | Sporobolus alterniflorus | 5 | Chr01G014260, Chr0G017890, Chr12G022610, Chr18G003230 ... |
| Poaceae | Thinopyrum elongatum | 1 | Tel1E01G016200 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC1AG000340, gene_TRIDC1BG001330 |
| Poaceae | Triticum aestivum | 3 | TraesCS1A02G005700.1, TraesCS1B02G007900.1 ... |
| Poaceae | Zea mays | 3 | Zm00001eb267610_P002, Zm00001eb304730_P001 ... |
| Poaceae | Zoysia japonica | 2 | nbis-gene-18432, nbis-gene-48834 |
| Poaceae | Zoysia macrostachya | 2 | Zma_g26233, Zma_g27516 |
| Portulacaceae | Portulaca oleracea | 3 | evm.TU.LG01.2730, evm.TU.LG02.154, evm.TU.LG09.1392 |
| Posidoniaceae | Posidonia oceanica | 5 | gene.Posoc01g04440, gene.Posoc02g05620, gene.Posoc05g05850 ... |
| Rhizophoraceae | Bruguiera sexangula | 3 | evm.TU.Scaffold_15_RagTag.931, evm.TU.Scaffold_15_RagTag.932 ... |
| Rhizophoraceae | Carallia pectinifolia | 6 | nbisL1-mrna-23301, nbisL1-mrna-26702, nbisL1-mrna-27117 ... |
| Rhizophoraceae | Ceriops tagal | 3 | nbisL1-mrna-10622, nbisL1-mrna-11411, nbisL1-mrna-11412 |
| Rhizophoraceae | Ceriops zippeliana | 3 | nbisL1-mrna-14569, nbisL1-mrna-15485, nbisL1-mrna-15486 |
| Rhizophoraceae | Kandelia candel | 2 | evm.TU.utg000001l.522, evm.TU.utg000013l.20 |
| Rhizophoraceae | Kandelia obovata | 2 | Maker00002594, Maker00006471 |
| Rhizophoraceae | Rhizophora apiculata | 4 | nbisL1-mrna-11129, nbisL1-mrna-17005, nbisL1-mrna-23165 ... |
| Rhizophoraceae | Rhizophora mangle | 4 | nbisL1-mrna-16056, nbisL1-mrna-17606, nbisL1-mrna-24760 ... |
| Salicaceae | Populus euphratica | 2 | populus_peu03909, populus_peu34735 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132640810 |
| Solanaceae | Solanum chilense | 1 | SOLCI006477600 |
| Solanaceae | Solanum pennellii | 2 | gene-LOC107020773, gene-LOC114077251 |
| Tamaricaceae | Reaumuria soongarica | 3 | gene_1175, gene_15409, gene_16694 |
| Tamaricaceae | Tamarix chinensis | 2 | TC04G2407, TC09G0753 |
| Zosteraceae | Zostera marina | 4 | Zosma01g25690.v3.1, Zosma04g17410.v3.1, Zosma04g17420.v3.1 ... |