Basic Information
Locus ID:
Ag3G00766
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
PHD-finger
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr3 | 22538387 | 22543237 | - | Ag3G00766 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 8.41 | 74,098.55 Da | 57.47 | 67.90 | -0.62 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd16574 | RING-HC_Topors | 51 | 92 | 5.43232E-15 | - |
| Pfam | PF00628 | PHD-finger | 141 | 185 | 9.0E-8 | IPR019787 |
| Pfam | PF13639 | Ring finger domain | 51 | 92 | 2.6E-6 | IPR001841 |
| SUPERFAMILY | SSF57850 | RING/U-box | 41 | 99 | 9.9E-12 | - |
| SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 134 | 186 | 5.32E-13 | IPR011011 |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 110 | 199 | 2.7E-12 | IPR013083 |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 23 | 101 | 1.5E-9 | IPR013083 |
| SMART | SM00184 | ring_2 | 51 | 91 | 1.7E-4 | IPR001841 |
| SMART | SM00249 | PHD_3 | 140 | 185 | 1.4E-6 | IPR001965 |
| ProSiteProfiles | PS50016 | Zinc finger PHD-type profile. | 138 | 187 | 9.2408 | IPR019787 |
| ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 51 | 92 | 11.913911 | IPR001841 |
| ProSitePatterns | PS00518 | Zinc finger RING-type signature. | 69 | 78 | - | IPR017907 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 342 | 364 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 35 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 40 | - | - |
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT3G05670.1 | RING/U-box protein. | 0 |
| RefSeq | XP_017243683.1 | PREDICTED: uncharacterized protein LOC108215659 [Daucus carota subsp. sativus] | 0 |
| Q63625 | PHD and RING finger domain-containing protein 1 OS=Rattus norvegicus OX=10116 GN=Phrf1 PE=1 SV=2 | 0 | |
| TrEMBL | A0A165XX30 | PHD and RING finger domain-containing protein 1 OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_014019 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 12.551115 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 14.070083 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 12.419689 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 13.969929 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 14.284862 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 16.01206 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 14.091267 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 14.525196 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 17.517431 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 20.512287 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 20.231087 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 18.67173 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 16.519236 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 14.436116 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 8.91388 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 7.63954 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 6.889341 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 4.831426 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 6.113121 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 5.8515 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 6.133073 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 8.701017 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 7.508396 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 6.86323 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 6.509984 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 7.758966 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 5.754233 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 5.092432 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 7.21987 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 3.914972 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 3.802189 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 2.545144 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 5.954902 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 6.586148 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 7.134779 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 7.256083 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 4.674731 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 5.202155 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 10.468855 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 6.554034 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 3.729609 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 8.064697 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 9.528404 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 18.043463 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 15.067318 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 8.133364 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 14.403801 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 10.428773 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 10.866722 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 9.449227 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg27375 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_13883 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah001318 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_5g113630 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg30945, Sbi_jg58329 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg25932 |
| Amaranthaceae | Suaeda aralocaspica | 2 | GOSA_00004797, GOSA_00004798 |
| Amaranthaceae | Suaeda glauca | 1 | Sgl12850 |
| Amaranthaceae | Chenopodium album | 4 | gene:ENSEOMG00000006821, gene:ENSEOMG00000021717 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.5AG0018930, CQ.Regalona.r1.5BG0020340 |
| Anacardiaceae | Pistacia vera | 2 | pistato.v30145520, pistato.v30146700 |
| Apiaceae | Apium graveolens | 1 | Ag3G00766 |
| Arecaceae | Cocos nucifera | 1 | COCNU_01G013980 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103706589 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_05.2240.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri18G17658 |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq03G2339 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl03G2476 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno01g04110 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate03g25360 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG10.490 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00036220 |
| Poaceae | Echinochloa crus-galli | 3 | AH06.1161, BH06.1209, CH06.1326 |
| Poaceae | Eleusine coracana subsp. coracana | 1 | gene-QOZ80_6AG0517320 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.7HG0671880.1 |
| Poaceae | Oryza coarctata | 2 | Oco11G007360, Oco12G007420 |
| Poaceae | Oryza sativa | 1 | LOC_Os06g17280.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_10G119000 |
| Poaceae | Puccinellia tenuiflora | 5 | Pt_Chr0102777, Pt_Chr0404252, Pt_Chr0404425, Pt_Chr0502350 ... |
| Poaceae | Sporobolus alterniflorus | 3 | Chr11G017870, Chr14G005570, Chr21G005120 |
| Poaceae | Thinopyrum elongatum | 1 | Tel7E01G386000 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC7AG026820, gene_TRIDC7BG017370 |
| Poaceae | Triticum aestivum | 3 | TraesCS7A02G212900.1, TraesCS7B02G119600.1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb380630_P001 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-45577 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g31749 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG02.98, evm.TU.LG09.1332 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc03g08200 |
| Rhizophoraceae | Bruguiera sexangula | 2 | evm.TU.Scaffold_11_RagTag.208, evm.TU.Scaffold_11_RagTag.209 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-14236 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-10055 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-14372 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000005l.255 |
| Rhizophoraceae | Kandelia obovata | 2 | Maker00009987, Maker00010107 |
| Rhizophoraceae | Rhizophora apiculata | 2 | nbisL1-mrna-338, nbisL1-mrna-339 |
| Rhizophoraceae | Rhizophora mangle | 2 | nbisL1-mrna-19024, nbisL1-mrna-19025 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132600198 |
| Solanaceae | Solanum chilense | 1 | SOLCI003178700 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107021212 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.15354_chr06_- |
| Tamaricaceae | Tamarix chinensis | 1 | TC09G1267 |
| Zosteraceae | Zostera marina | 1 | Zosma05g22100.v3.1 |