Basic Information
Locus ID:
Ag6G00334
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
methyl-CpG-binding domain-containing protein
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr6 | 10392831 | 10408019 | - | Ag6G00334 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 6.50 | 222,675.94 Da | 47.58 | 77.40 | -0.45 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd15489 | PHD_SF | 25 | 70 | 2.18428E-7 | - |
| CDD | cd15519 | PHD1_Lid2p_like | 1237 | 1282 | 7.2444E-24 | - |
| Pfam | PF00628 | PHD-finger | 1237 | 1283 | 9.8E-12 | IPR019787 |
| Pfam | PF00439 | Bromodomain | 1118 | 1178 | 2.1E-6 | IPR001487 |
| Pfam | PF15612 | WSTF, HB1, Itc1p, MBD9 motif 1 | 1317 | 1357 | 2.1E-5 | IPR028942 |
| Pfam | PF02791 | DDT domain | 762 | 843 | 1.9E-6 | IPR018501 |
| Pfam | PF15613 | Williams-Beuren syndrome DDT (WSD), D-TOX E motif | 1439 | 1549 | 1.8E-6 | IPR028941 |
| SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 1230 | 1287 | 1.31E-16 | IPR011011 |
| SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 16 | 71 | 5.98E-11 | IPR011011 |
| SUPERFAMILY | SSF47370 | Bromodomain | 1073 | 1190 | 1.07E-11 | IPR036427 |
| Gene3D | G3DSA:3.30.160.360 | - | 407 | 517 | 1.8E-6 | - |
| Gene3D | G3DSA:1.20.920.10 | - | 1077 | 1200 | 1.3E-16 | IPR036427 |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 1227 | 1308 | 1.3E-19 | IPR013083 |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 14 | 77 | 1.3E-8 | IPR013083 |
| SMART | SM00249 | PHD_3 | 25 | 71 | 1.3E-7 | IPR001965 |
| SMART | SM00249 | PHD_3 | 1237 | 1283 | 4.7E-13 | IPR001965 |
| ProSiteProfiles | PS50016 | Zinc finger PHD-type profile. | 23 | 73 | 9.045 | IPR019787 |
| ProSiteProfiles | PS51543 | FYR domain FYRC motif profile. | 615 | 693 | 12.581243 | IPR003889 |
| ProSiteProfiles | PS51542 | FYR domain FYRN motif profile. | 406 | 459 | 16.579477 | IPR003888 |
| ProSiteProfiles | PS50014 | Bromodomain profile. | 1123 | 1174 | 9.0626 | IPR001487 |
| ProSiteProfiles | PS50016 | Zinc finger PHD-type profile. | 1235 | 1285 | 10.024 | IPR019787 |
| ProSitePatterns | PS01359 | Zinc finger PHD-type signature. | 26 | 70 | - | IPR019786 |
| ProSitePatterns | PS01359 | Zinc finger PHD-type signature. | 1238 | 1282 | - | IPR019786 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 81 | 125 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1794 | 1821 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1968 | 2003 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 81 | 121 | - | - |
Gene Ontology
Molecular Function:
Cellular Component:
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT3G01460.1 | methyl-CPG-binding domain 9. Encodes a protein with a methyl-CpG-binding domain. Has sequence similarity to human MBD proteins. Involved in the modification of the FLC chromatin acetylation state to affect FLC expression. Mutants show an early flowering, and enhanced shoot branching phenotypes. | 0 |
| RefSeq | XP_017235304.1 | PREDICTED: methyl-CpG-binding domain-containing protein 9-like [Daucus carota subsp. sativus] | 0 |
| Q9SGH2 | Methyl-CpG-binding domain-containing protein 9 OS=Arabidopsis thaliana OX=3702 GN=MBD9 PE=2 SV=1 | 0 | |
| TrEMBL | A0A166E927 | Methyl-CpG-binding domain-containing protein 9 OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_007093 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 9.283208 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 11.271746 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 10.355435 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 11.7196 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 11.414943 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 14.442073 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 13.797103 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 18.542801 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 9.309938 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 8.735889 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 9.85227 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 10.267768 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 9.523231 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 7.039114 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 2.348084 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 2.323898 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 2.611666 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 2.965713 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 1.892012 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 2.994347 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 2.425624 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 2.603539 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 2.939103 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 2.994445 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 2.552957 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 3.713737 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 2.933368 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 2.594612 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 3.481735 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 0.594286 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 1.167894 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 0.727646 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 1.664332 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 2.175435 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 1.870368 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 0.539695 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 0.344182 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 0.596379 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 5.300971 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 3.482886 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 1.646585 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 3.698097 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 2.410433 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 5.041048 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 3.810287 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 2.648111 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 4.265897 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 5.045264 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 3.952866 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 4.529031 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg9458 |
| Aizoaceae | Mesembryanthemum crystallinum | 3 | gene_1020, gene_22895, gene_7838 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah033754 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_6g144700 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg20195, Sbi_jg44291 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg17727 |
| Amaranthaceae | Suaeda aralocaspica | 3 | GOSA_00021410, GOSA_00021411, GOSA_00021412 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl63885, Sgl68373 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000014836, gene:ENSEOMG00000022800 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.2AG0009520, CQ.Regalona.r1.2BG0010050 |
| Anacardiaceae | Pistacia vera | 2 | pistato.v30022160, pistato.v30222520 |
| Apiaceae | Apium graveolens | 3 | Ag1G01335, Ag6G00334, Ag9G00488 |
| Arecaceae | Cocos nucifera | 2 | COCNU_01G005850, COCNU_11G011740 |
| Arecaceae | Phoenix dactylifera | 3 | gene-LOC103699157, gene-LOC103719046, gene-LOC120110853 |
| Asparagaceae | Asparagus officinalis | 3 | AsparagusV1_01.181.V1.1, AsparagusV1_05.3155.V1.1 ... |
| Asteraceae | Flaveria trinervia | 2 | Ftri5G02703, Ftri8G10451 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT3G01460.1 |
| Brassicaceae | Eutrema salsugineum | 2 | Thhalv10019872m.g.v1.0, Thhalv10022520m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp3g00610.v2.2 |
| Brassicaceae | Brassica nigra | 1 | BniB07g061780.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq02G1812 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl02G1888 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno01g03670 |
| Dunaliellaceae | Dunaliella salina | 2 | Dusal.0253s00014.v1.0, Dusal.0866s00006.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate09g16600 |
| Malvaceae | Hibiscus hamabo Siebold & Zucc. | 1 | nbisL1-mrna-2246 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG05.408 |
| Plantaginaceae | Plantago ovata | 6 | Pov_00023332, Pov_00023333, Pov_00034366, Pov_00041413 ... |
| Plumbaginaceae | Limonium bicolor | 1 | Lb7G33460 |
| Poaceae | Echinochloa crus-galli | 2 | AH07.671, BH07.799 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_2AG0104700, gene-QOZ80_2BG0158090 |
| Poaceae | Hordeum vulgare | 3 | HORVU.MOREX.r3.5HG0535640.1.CDS1 ... |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_021251 |
| Poaceae | Oryza coarctata | 2 | Oco03G005200, Oco04G004730 |
| Poaceae | Oryza sativa | 1 | LOC_Os02g09920.1 |
| Poaceae | Paspalum vaginatum | 2 | gene-BS78_04G069800, gene-BS78_04G070000 |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0202209 |
| Poaceae | Sporobolus alterniflorus | 1 | Chr06G033370 |
| Poaceae | Thinopyrum elongatum | 1 | Tel6E01G341600 |
| Poaceae | Triticum dicoccoides | 17 | gene_TRIDC3AG075090, gene_TRIDC3AG075100 ... |
| Poaceae | Triticum aestivum | 12 | TraesCS3A02G530300.1.cds1, TraesCS4A02G324900.1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb206240_P001 |
| Poaceae | Zoysia japonica | 2 | nbis-gene-33507, nbis-gene-44107 |
| Poaceae | Zoysia macrostachya | 2 | Zma_g12363, Zma_g15108 |
| Portulacaceae | Portulaca oleracea | 4 | evm.TU.LG04.1394, evm.TU.LG05.1917, evm.TU.LG16.1091 ... |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc03g07460 |
| Rhizophoraceae | Bruguiera sexangula | 8 | evm.TU.36567.1, evm.TU.45229.1, evm.TU.45229.2 ... |
| Rhizophoraceae | Carallia pectinifolia | 3 | nbisL1-mrna-23084, nbisL1-mrna-2318, nbisL1-mrna-2631 |
| Rhizophoraceae | Ceriops tagal | 2 | nbisL1-mrna-10399, nbisL1-mrna-11668 |
| Rhizophoraceae | Ceriops zippeliana | 2 | nbisL1-mrna-14785, nbisL1-mrna-3047 |
| Rhizophoraceae | Kandelia candel | 2 | evm.TU.utg000013l.179, evm.TU.utg000019l.96 |
| Rhizophoraceae | Kandelia obovata | 2 | Maker00001944, Maker00006668 |
| Rhizophoraceae | Rhizophora apiculata | 2 | nbisL1-mrna-12071, nbisL1-mrna-7085 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-15841 |
| Salicaceae | Populus euphratica | 1 | populus_peu24422 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132641362 |
| Solanaceae | Solanum chilense | 1 | SOLCI003618100 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107020445 |
| Tamaricaceae | Reaumuria soongarica | 2 | gene_4646, gene_4811 |
| Tamaricaceae | Tamarix chinensis | 2 | TC02G2325, TC02G3239 |
| Zosteraceae | Zostera marina | 1 | Zosma03g04350.v3.1 |