Basic Information
Locus ID:
Ag6G02063
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
PHD-finger
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr6 | 160876111 | 160881341 | - | Ag6G02063 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.33 | 104,467.09 Da | 64.49 | 58.27 | -1.00 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd16574 | RING-HC_Topors | 556 | 598 | 1.43409E-16 | - |
| Pfam | PF00628 | PHD-finger | 649 | 694 | 1.7E-8 | IPR019787 |
| Pfam | PF13639 | Ring finger domain | 555 | 598 | 9.4E-8 | IPR001841 |
| SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 632 | 694 | 1.23E-13 | IPR011011 |
| SUPERFAMILY | SSF57850 | RING/U-box | 555 | 604 | 5.2E-14 | - |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 531 | 625 | 5.5E-10 | IPR013083 |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 626 | 699 | 1.3E-11 | IPR013083 |
| SMART | SM00184 | ring_2 | 556 | 597 | 1.2E-4 | IPR001841 |
| SMART | SM00249 | PHD_3 | 649 | 694 | 9.3E-7 | IPR001965 |
| ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 556 | 598 | 11.95817 | IPR001841 |
| ProSiteProfiles | PS50016 | Zinc finger PHD-type profile. | 647 | 696 | 9.1518 | IPR019787 |
| ProSitePatterns | PS00518 | Zinc finger RING-type signature. | 575 | 584 | - | IPR017907 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 27 | 62 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 210 | 272 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 901 | 922 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 26 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 250 | 270 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 438 | 464 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 185 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 130 | 146 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 438 | 461 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 829 | 850 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 108 | 129 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 210 | 226 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 74 | 99 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 147 | 185 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 235 | 249 | - | - |
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT3G05670.1 | RING/U-box protein. | 0 |
| RefSeq | XP_017235459.1 | PREDICTED: uncharacterized protein LOC108209187 isoform X1 [Daucus carota subsp. sativus] | 0 |
| TrEMBL | A0A166D0J0 | PHD-type domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_005407 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 16.713074 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 14.731143 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 14.756164 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 16.354374 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 14.183599 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 19.831244 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 18.703318 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 22.752167 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 27.80047 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 27.774441 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 28.504276 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 28.471949 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 25.02883 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 20.83779 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 13.536657 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 15.394897 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 8.88816 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 12.754932 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 12.088424 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 19.52886 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 15.313082 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 13.480237 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 13.010976 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 12.524447 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 13.376413 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 12.013154 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 10.093973 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 10.506389 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 12.960241 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 3.937686 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 5.402204 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 3.46258 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 10.898714 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 9.813729 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 14.868052 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 6.636966 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 4.973334 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 4.196733 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 15.117976 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 10.209437 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 9.725075 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 25.696974 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 38.586887 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 23.15584 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 23.406157 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 23.439501 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 23.430607 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 17.102674 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 16.712929 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 12.981124 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 2 | jg26527, jg28262 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_10380 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah005682 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_4g076600 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg17219, Sbi_jg61829 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg476 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00015399 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl24416, Sgl29591 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000009935, gene:ENSEOMG00000030557 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.4AG0007440, CQ.Regalona.r1.4BG0007720 |
| Anacardiaceae | Pistacia vera | 3 | pistato.v30081940, pistato.v30082070, pistato.v30082100 |
| Apiaceae | Apium graveolens | 1 | Ag6G02063 |
| Arecaceae | Cocos nucifera | 1 | scaffold024213G000010 |
| Arecaceae | Phoenix dactylifera | 2 | gene-LOC103720028, gene-LOC120108412 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_07.1338.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri15G20990 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT3G05670.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10020032m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp3g04540.v2.2 |
| Brassicaceae | Brassica nigra | 3 | BniB01g057980.2N, BniB05g067800.2N, BniB07g032810.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq06G1137 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl06G1184 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate06g04620 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG03.2515 |
| Plantaginaceae | Plantago ovata | 2 | Pov_00007189, Pov_00039226 |
| Plumbaginaceae | Limonium bicolor | 2 | Lb1G06598, Lb2G14161 |
| Poaceae | Echinochloa crus-galli | 3 | AH01.3911, BH01.4248, CH01.4540 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_3AG0245130, gene-QOZ80_3BG0282930 |
| Poaceae | Hordeum vulgare | 2 | HORVU.MOREX.r3.2HG0109660.1, HORVU.MOREX.r3.4HG0383230.1 |
| Poaceae | Lolium multiflorum | 3 | gene-QYE76_038611, gene-QYE76_038612, gene-QYE76_068545 |
| Poaceae | Oryza coarctata | 4 | Oco05G011270, Oco06G011510, Oco13G016490, Oco14G017290 |
| Poaceae | Oryza sativa | 2 | LOC_Os03g19020.1, LOC_Os07g49030.2 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_01G382100 |
| Poaceae | Puccinellia tenuiflora | 2 | Pt_Chr0305325, Pt_Chr0500117 |
| Poaceae | Sporobolus alterniflorus | 4 | Chr01G032590, Chr04G009320, Chr07G002400, Chr12G006950 |
| Poaceae | Thinopyrum elongatum | 2 | Tel2E01G203000, Tel4E01G334900 |
| Poaceae | Triticum dicoccoides | 4 | gene_TRIDC2AG010810, gene_TRIDC2BG013170 ... |
| Poaceae | Triticum aestivum | 6 | TraesCS2A02G094000.1, TraesCS2B02G108800.1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb396440_P001 |
| Poaceae | Zoysia japonica | 3 | nbis-gene-1436, nbis-gene-1879, nbis-gene-3554 |
| Poaceae | Zoysia macrostachya | 3 | Zma_g1120, Zma_g1390, Zma_g3791 |
| Portulacaceae | Portulaca oleracea | 4 | evm.TU.LG08.726, evm.TU.LG18.1288, evm.TU.LG20.599 ... |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_2_RagTag.2086 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-2899 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-15205 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-13662 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000009l.38 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00005172 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-13000 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-16132 |
| Salicaceae | Populus euphratica | 2 | populus_peu13319, populus_peu15637 |
| Solanaceae | Lycium barbarum | 2 | gene-LOC132643430, gene-LOC132646008 |
| Solanaceae | Solanum chilense | 1 | SOLCI002719200 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107007013 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.32667_chr09_- |
| Tamaricaceae | Tamarix chinensis | 1 | TC02G0896 |