Basic Information
Locus ID:
Ag3G00481
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
PHD zinc finger
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr3 | 12264862 | 12272427 | - | Ag3G00481 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 8.85 | 85,613.82 Da | 44.32 | 75.09 | -0.52 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd04370 | BAH | 655 | 783 | 2.79765E-9 | - |
| Pfam | PF00628 | PHD-finger | 386 | 433 | 5.2E-9 | IPR019787 |
| SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 377 | 440 | 9.52E-14 | IPR011011 |
| Gene3D | G3DSA:2.30.30.490 | - | 635 | 784 | 1.1E-23 | IPR043151 |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 320 | 441 | 9.2E-13 | IPR013083 |
| SMART | SM00249 | PHD_3 | 385 | 433 | 7.4E-9 | IPR001965 |
| ProSiteProfiles | PS51038 | BAH domain profile. | 656 | 783 | 12.525611 | IPR001025 |
| ProSiteProfiles | PS50016 | Zinc finger PHD-type profile. | 383 | 435 | 9.4633 | IPR019787 |
| ProSitePatterns | PS01359 | Zinc finger PHD-type signature. | 386 | 432 | - | IPR019786 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 148 | 172 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 23 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 143 | 172 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 558 | 601 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 558 | 592 | - | - |
Gene Ontology
Molecular Function:
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT1G50620.1 | RING/FYVE/PHD zinc finger superfamily protein. | 0 |
| RefSeq | XP_017247954.1 | PREDICTED: uncharacterized protein LOC108219167 [Daucus carota subsp. sativus] | 0 |
| Q5PNS0 | PHD finger protein At3g20280 OS=Arabidopsis thaliana OX=3702 GN=At3g20280 PE=2 SV=1 | 0 | |
| TrEMBL | A0A165YZQ2 | PHD-type domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_013201 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 14.094241 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 10.001152 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 13.683501 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 14.233275 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 13.555262 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 18.51549 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 14.603176 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 16.08449 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 22.426971 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 19.356159 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 21.880585 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 22.209242 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 20.470984 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 19.39506 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 4.112065 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 4.602905 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 6.222979 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 7.452635 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 6.144444 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 5.603619 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 4.440825 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 8.10301 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 7.913709 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 6.440636 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 8.12878 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 7.899121 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 6.592875 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 5.672338 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 6.842383 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 3.375027 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 3.732338 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 3.351203 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 6.249486 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 7.949524 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 6.444283 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 3.861146 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 4.250083 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 3.772573 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 14.470599 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 5.498349 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 3.416617 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 5.985743 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 9.184143 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 35.257183 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 27.230871 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 5.707809 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 15.066215 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 16.8423 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 18.593231 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 16.118387 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 3 | jg21564, jg24571, jg24572 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_12203 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah008912 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_4g089200 |
| Amaranthaceae | Salicornia bigelovii | 3 | Sbi_jg18347, Sbi_jg36730, Sbi_jg36732 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg4675 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00017424 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl23471, Sgl28598 |
| Amaranthaceae | Chenopodium album | 4 | gene:ENSEOMG00000009736, gene:ENSEOMG00000028115 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.4AG0023590, CQ.Regalona.r1.4BG0024900 |
| Anacardiaceae | Pistacia vera | 2 | pistato.v30156210, pistato.v30158710 |
| Apiaceae | Apium graveolens | 2 | Ag3G00481, Ag9G00996 |
| Arecaceae | Cocos nucifera | 1 | COCNU_01G012480 |
| Arecaceae | Phoenix dactylifera | 2 | gene-LOC103696217, gene-LOC103713628 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_05.2106.V1.1 |
| Asteraceae | Flaveria trinervia | 2 | Ftri16G29904, Ftri7G04246 |
| Brassicaceae | Arabidopsis thaliana | 2 | AT1G50620.1, AT3G20280.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10011311m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 2 | Sp1g37440.v2.2, Sp3g18310.v2.2 |
| Brassicaceae | Brassica nigra | 2 | BniB01g043610.2N, BniB06g030340.2N |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno03g09420 |
| Hydrocharitaceae | Thalassia testudinum | 2 | gene.Thate01g06300, gene.Thate05g06860 |
| Malvaceae | Hibiscus hamabo Siebold & Zucc. | 1 | nbisL1-mrna-2496 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG05.1943 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00008734 |
| Plumbaginaceae | Limonium bicolor | 2 | Lb1G03434, Lb2G10881 |
| Poaceae | Echinochloa crus-galli | 6 | AH06.1276, AH07.3244, BH06.1323, BH07.3072, CH06.1432 ... |
| Poaceae | Eleusine coracana subsp. coracana | 1 | gene-QOZ80_2BG0198990 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.6HG0609950.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_025306 |
| Poaceae | Oryza coarctata | 4 | Oco03G020010, Oco04G020780, Oco11G008010, Oco12G008060 |
| Poaceae | Oryza sativa | 3 | LOC_Os02g48800.1, LOC_Os02g48810.1, LOC_Os06g20410.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_04G256900 |
| Poaceae | Puccinellia tenuiflora | 2 | Pt_Chr0203552, Pt_Chr0303862 |
| Poaceae | Sporobolus alterniflorus | 4 | Chr06G003530, Chr09G021480, Chr15G004950, Chr21G005610 |
| Poaceae | Thinopyrum elongatum | 2 | Tel6E01G516600, Tel7E01G405400 |
| Poaceae | Triticum dicoccoides | 6 | gene_TRIDC5BG005160, gene_TRIDC5BG031310 ... |
| Poaceae | Triticum aestivum | 4 | TraesCS6A02G282700.1, TraesCS6B02G311000.1 ... |
| Poaceae | Zea mays | 2 | Zm00001eb189420_P001, Zm00001eb252930_P001 |
| Poaceae | Zoysia japonica | 2 | nbis-gene-22001, nbis-gene-8891 |
| Poaceae | Zoysia macrostachya | 2 | Zma_g14292, Zma_g17043 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG01.1461, evm.TU.LG14.738 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc02g22810 |
| Rhizophoraceae | Bruguiera sexangula | 2 | evm.TU.Scaffold_7_RagTag.124, evm.TU.Scaffold_8_RagTag.1598 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-8713 |
| Rhizophoraceae | Ceriops tagal | 2 | nbisL1-mrna-3980, nbisL1-mrna-416 |
| Rhizophoraceae | Ceriops zippeliana | 2 | nbisL1-mrna-15092, nbisL1-mrna-22294 |
| Rhizophoraceae | Kandelia candel | 2 | evm.TU.utg000018l.63, evm.TU.utg000028l.74 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00003690 |
| Rhizophoraceae | Rhizophora apiculata | 2 | nbisL1-mrna-8038, nbisL1-mrna-9406 |
| Rhizophoraceae | Rhizophora mangle | 2 | nbisL1-mrna-22639, nbisL1-mrna-22677 |
| Salicaceae | Populus euphratica | 1 | populus_peu00922 |
| Solanaceae | Lycium barbarum | 2 | gene-LOC132616870, gene-LOC132636315 |
| Solanaceae | Solanum chilense | 1 | SOLCI006720500 |
| Solanaceae | Solanum pennellii | 2 | gene-LOC107007659, gene-LOC107026536 |
| Tamaricaceae | Reaumuria soongarica | 2 | STRG.24698_chr08_+, gene_16914 |
| Tamaricaceae | Tamarix chinensis | 2 | TC05G2683, TC06G0399 |
| Zosteraceae | Zostera marina | 1 | Zosma01g03900.v3.1 |