Basic Information
Locus ID:
Ag7G01355
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
CHD3-type chromatin-remodeling factor
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr7 | 149984498 | 150013939 | + | Ag7G01355 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.94 | 148,900.55 Da | 42.34 | 80.99 | -0.59 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd18659 | CD2_tandem | 188 | 239 | 3.20202E-19 | - |
| CDD | cd18660 | CD1_tandem | 97 | 171 | 1.02702E-15 | - |
| CDD | cd18793 | SF2_C_SNF | 602 | 728 | 3.3179E-55 | - |
| Pfam | PF00176 | SNF2 family N-terminal domain | 304 | 582 | 5.6E-65 | IPR000330 |
| Pfam | PF06465 | Domain of Unknown Function (DUF1087) | 840 | 900 | 1.5E-20 | IPR009463 |
| Pfam | PF06461 | Domain of Unknown Function (DUF1086) | 938 | 1068 | 2.2E-51 | IPR009462 |
| Pfam | PF00628 | PHD-finger | 53 | 95 | 6.3E-8 | IPR019787 |
| Pfam | PF00271 | Helicase conserved C-terminal domain | 605 | 717 | 1.1E-16 | IPR001650 |
| Pfam | PF00385 | Chromo (CHRromatin Organisation MOdifier) domain | 102 | 156 | 3.2E-9 | IPR023780 |
| Pfam | PF00385 | Chromo (CHRromatin Organisation MOdifier) domain | 191 | 239 | 8.9E-15 | IPR023780 |
| SUPERFAMILY | SSF54160 | Chromo domain-like | 181 | 242 | 6.41E-15 | IPR016197 |
| SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 518 | 775 | 9.1E-63 | IPR027417 |
| SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 261 | 516 | 6.52E-54 | IPR027417 |
| SUPERFAMILY | SSF54160 | Chromo domain-like | 65 | 162 | 2.11E-17 | IPR016197 |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 29 | 100 | 6.7E-13 | IPR013083 |
| Gene3D | G3DSA:3.40.50.300 | - | 526 | 748 | 6.0E-191 | IPR027417 |
| Gene3D | G3DSA:1.10.10.60 | - | 1038 | 1172 | 1.7E-8 | - |
| Gene3D | G3DSA:2.40.50.40 | - | 179 | 239 | 4.4E-16 | - |
| Gene3D | G3DSA:2.40.50.40 | - | 101 | 174 | 3.9E-14 | - |
| Gene3D | G3DSA:3.40.50.10810 | - | 275 | 525 | 6.0E-191 | IPR038718 |
| SMART | SM00490 | helicmild6 | 633 | 717 | 2.6E-22 | IPR001650 |
| SMART | SM01147 | DUF1087_2 | 838 | 903 | 1.1E-24 | IPR009463 |
| SMART | SM00249 | PHD_3 | 52 | 95 | 1.3E-10 | IPR001965 |
| SMART | SM01146 | DUF1086_2 | 918 | 1071 | 1.1E-68 | IPR009462 |
| SMART | SM00487 | ultradead3 | 279 | 492 | 1.3E-31 | IPR014001 |
| SMART | SM00298 | chromo_7 | 99 | 161 | 1.7E-5 | IPR000953 |
| SMART | SM00298 | chromo_7 | 188 | 242 | 1.3E-13 | IPR000953 |
| ProSiteProfiles | PS50013 | Chromo and chromo shadow domain profile. | 99 | 181 | 9.969201 | IPR000953 |
| ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 295 | 481 | 22.870111 | IPR014001 |
| ProSiteProfiles | PS50016 | Zinc finger PHD-type profile. | 50 | 97 | 9.7659 | IPR019787 |
| ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 607 | 768 | 19.048599 | IPR001650 |
| ProSiteProfiles | PS50013 | Chromo and chromo shadow domain profile. | 190 | 239 | 11.942101 | IPR000953 |
| ProSitePatterns | PS01359 | Zinc finger PHD-type signature. | 53 | 94 | - | IPR019786 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 899 | 917 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 887 | 917 | - | - |
Gene Ontology
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT2G25170.1 | chromatin remodeling factor CHD3 (PICKLE). Encodes a SWI/SWF nuclear-localized chromatin remodeling factor of the CHD3 group. Involved in post-germination repression of embryonic development. Acts with GA to establish repression of embryonic genes upon germination. Protein preferentially accumulates in differentiating tissues. Loss of function alleles are associated with expression of embryonic traits in adult plants and derepression of embryonic genes such as PHEROS1. Is an extragenic suppressor of slr2 (SSL2). Mutations in PKL (SSL2) restores lateral root formation in the slr2 mutant slr-1. It was proposed that PKL/SSL2-mediated chromatin remodeling negatively regulates auxin-mediated LR formation in Arabidopsis. | 0 |
| RefSeq | XP_017228544.1 | PREDICTED: CHD3-type chromatin-remodeling factor PICKLE [Daucus carota subsp. sativus] | 0 |
| Q9S775 | CHD3-type chromatin-remodeling factor PICKLE OS=Arabidopsis thaliana OX=3702 GN=PKL PE=1 SV=1 | 0 | |
| TrEMBL | A0A162AKM5 | DNA helicase OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_003002 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 49.179752 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 31.34606 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 32.218533 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 34.006516 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 32.918224 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 34.575336 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 32.190533 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 33.316685 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 76.533264 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 74.999123 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 79.643227 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 72.567451 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 68.861374 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 57.10405 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 13.274826 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 20.256098 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 17.780298 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 24.49386 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 17.638737 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 20.294155 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 23.984283 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 25.299965 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 27.988966 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 27.772299 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 24.727953 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 30.635206 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 21.892797 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 22.36594 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 25.590006 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 11.677429 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 17.224028 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 14.33511 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 13.251502 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 13.344829 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 10.746259 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 13.691763 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 9.69788 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 10.251077 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 36.870621 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 15.78905 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 9.946144 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 14.631214 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 29.171492 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 55.115398 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 60.740181 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 14.216235 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 49.886555 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 29.962551 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 39.397991 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 35.446053 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 2 | jg24036, jg36561 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_13270 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah034823 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_2g031220 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg21073, Sbi_jg22724 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg16603 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00018284 |
| Amaranthaceae | Suaeda glauca | 3 | Sgl62396, Sgl66943, Sgl66945 |
| Amaranthaceae | Chenopodium album | 6 | gene:ENSEOMG00000016795, gene:ENSEOMG00000018331 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.1BG0021900, CQ.Regalona.r1.2AG0023680 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30250780 |
| Apiaceae | Apium graveolens | 2 | Ag6G01340, Ag7G01355 |
| Arecaceae | Cocos nucifera | 1 | COCNU_01G005290 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103714226 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_08.1846.V1.1 |
| Asteraceae | Flaveria trinervia | 2 | Ftri11G19512, Ftri12G11603 |
| Brassicaceae | Arabidopsis thaliana | 2 | AT2G25170.1, AT4G31900.1 |
| Brassicaceae | Eutrema salsugineum | 2 | Thhalv10000014m.g.v1.0, Thhalv10027006m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 2 | Sp4g04150.v2.2, Sp7g29720.v2.2 |
| Brassicaceae | Brassica nigra | 2 | BniB02g023330.2N, BniB02g085630.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq04G2427 |
| Casuarinaceae | Casuarina glauca | 2 | Cgl04G2631, Cgl04G2660 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno01g06310 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0001s00013.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate04g29410 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG07.1510 |
| Plantaginaceae | Plantago ovata | 2 | Pov_00006955, Pov_00013937 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb3G17059 |
| Poaceae | Echinochloa crus-galli | 2 | BH06.610, CH06.624 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_6AG0511350, gene-QOZ80_6BG0463330 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.7HG0658830.1 |
| Poaceae | Lolium multiflorum | 2 | gene-QYE76_028191, gene-QYE76_028236 |
| Poaceae | Oryza coarctata | 2 | Oco11G003860, Oco12G003850 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_10G065800 |
| Poaceae | Puccinellia tenuiflora | 3 | Pt_Chr0405231, Pt_Chr0405252, Pt_Chr0405255 |
| Poaceae | Sporobolus alterniflorus | 3 | Chr11G021470, Chr14G002860, Chr21G002040 |
| Poaceae | Thinopyrum elongatum | 1 | Tel7E01G299600 |
| Poaceae | Triticum aestivum | 3 | TraesCS7A02G147100.2, TraesCS7B02G050100.3 ... |
| Poaceae | Zoysia japonica | 2 | nbis-gene-34880, nbis-gene-4997 |
| Poaceae | Zoysia macrostachya | 2 | Zma_g29235, Zma_g31473 |
| Portulacaceae | Portulaca oleracea | 4 | evm.TU.LG05.1548, evm.TU.LG07.1217, evm.TU.LG07.596 ... |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc03g12610 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_10_RagTag.892 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-13581 |
| Rhizophoraceae | Ceriops tagal | 2 | nbisL1-mrna-20561, nbisL1-mrna-838 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-9145 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000004l.200 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00003979 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-3742 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-7816 |
| Salicaceae | Populus euphratica | 2 | populus_peu04702, populus_peu12984 |
| Solanaceae | Lycium barbarum | 2 | gene-LOC132636060, gene-LOC132643757 |
| Solanaceae | Solanum chilense | 2 | SOLCI006571200, SOLCI006784900 |
| Solanaceae | Solanum pennellii | 2 | gene-LOC107023146, gene-LOC107028501 |
| Tamaricaceae | Reaumuria soongarica | 2 | gene_17290, gene_6399 |
| Tamaricaceae | Tamarix chinensis | 2 | TC01G0997, TC06G0063 |
| Zosteraceae | Zostera marina | 1 | Zosma03g06310.v3.1 |