Basic Information
Locus ID:
Ag9G01848
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
Belongs to the class I-like SAM-binding methyltransferase superfamily. RsmB NOP family
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr9 | 232616515 | 232626001 | + | Ag9G01848 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 8.46 | 57,921.24 Da | 42.25 | 98.44 | -0.13 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd02440 | AdoMet_MTases | 332 | 457 | 8.12919E-8 | - |
| Pfam | PF01189 | 16S rRNA methyltransferase RsmB/F | 322 | 518 | 8.8E-52 | IPR001678 |
| Pfam | PF01029 | NusB family | 90 | 193 | 7.2E-21 | IPR006027 |
| SUPERFAMILY | SSF53335 | S-adenosyl-L-methionine-dependent methyltransferases | 216 | 520 | 1.52E-62 | IPR029063 |
| SUPERFAMILY | SSF48013 | NusB-like | 91 | 228 | 1.07E-25 | IPR035926 |
| Gene3D | G3DSA:3.40.50.150 | Vaccinia Virus protein VP39 | 318 | 520 | 3.0E-61 | - |
| Gene3D | G3DSA:1.10.940.10 | - | 58 | 203 | 1.3E-22 | IPR035926 |
| Gene3D | G3DSA:3.30.70.1170 | Sun protein; domain 3 | 211 | 317 | 1.6E-9 | - |
| TIGRFAM | TIGR00563 | rsmB: 16S rRNA (cytosine(967)-C(5))-methyltransferase | 98 | 519 | 1.3E-83 | IPR004573 |
| ProSiteProfiles | PS51686 | SAM-dependent MTase RsmB/NOP-type domain profile. | 244 | 520 | 53.371693 | IPR001678 |
| ProSitePatterns | PS01153 | NOL1/NOP2/sun family signature. | 400 | 411 | - | IPR018314 |
| PRINTS | PR02009 | Viridiplantae FMU-related RCMT signature | 61 | 84 | 3.8E-32 | IPR023268 |
| PRINTS | PR02009 | Viridiplantae FMU-related RCMT signature | 201 | 214 | 3.8E-32 | IPR023268 |
| PRINTS | PR02009 | Viridiplantae FMU-related RCMT signature | 85 | 101 | 3.8E-32 | IPR023268 |
| PRINTS | PR02008 | RNA (C5-cytosine) methyltransferase signature | 502 | 519 | 1.7E-25 | IPR023267 |
| PRINTS | PR02008 | RNA (C5-cytosine) methyltransferase signature | 401 | 413 | 1.7E-25 | IPR023267 |
| PRINTS | PR02008 | RNA (C5-cytosine) methyltransferase signature | 333 | 343 | 1.7E-25 | IPR023267 |
| PRINTS | PR02008 | RNA (C5-cytosine) methyltransferase signature | 304 | 318 | 1.7E-25 | IPR023267 |
| PRINTS | PR02008 | RNA (C5-cytosine) methyltransferase signature | 451 | 467 | 1.7E-25 | IPR023267 |
| PRINTS | PR02009 | Viridiplantae FMU-related RCMT signature | 478 | 490 | 3.8E-32 | IPR023268 |
Gene Ontology
Biological Process:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT3G13180.1 | NOL1/NOP2/sun family protein / antitermination NusB domain-containing protein. | 0 |
| RefSeq | XP_017215048.1 | PREDICTED: ribosomal RNA small subunit methyltransferase B isoform X1 [Daucus carota subsp. sativus] | 0 |
| P94464 | Probable ribosomal RNA small subunit methyltransferase B OS=Bacillus subtilis (strain 168) OX=224308 GN=rsmB PE=3 SV=2 | 0 | |
| TrEMBL | A0A5B7C3N1 | Putative 28S rRNA (Cytosine-C(5))-methyltransferase (Fragment) OS=Davidia involucrata OX=16924 GN=Din_044327 PE=3 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 11.707713 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 6.920038 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 9.875839 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 8.779377 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 7.485437 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 9.200058 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 5.373806 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 5.448967 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 21.483669 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 23.476698 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 24.056467 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 21.126558 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 19.88467 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 21.745396 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 10.642109 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 12.984257 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 11.385894 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 18.323093 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 19.81329 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 12.108905 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 15.940559 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 12.094673 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 14.926488 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 14.139864 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 14.169341 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 20.689468 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 20.388205 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 25.273754 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 22.828663 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 7.751895 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 12.473437 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 10.139338 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 27.589493 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 18.679365 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 28.762791 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 16.943924 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 7.22176 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 9.37486 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 53.313217 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 36.75029 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 55.20713 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 2.271294 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 4.827502 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 6.980462 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 10.644795 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 2.101596 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 7.263366 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 27.58036 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 26.507381 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 26.334467 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg20187 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_12131 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah009070 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_4g090540 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg18530, Sbi_jg36928 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg4805 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00017319 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl23572, Sgl28773 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000009095, gene:ENSEOMG00000028930 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.2BG0001030, CQ.Regalona.r1.4BG0026080 |
| Anacardiaceae | Pistacia vera | 2 | pistato.v30153020, pistato.v30154760 |
| Apiaceae | Apium graveolens | 1 | Ag9G01848 |
| Arecaceae | Cocos nucifera | 1 | COCNU_01G013560 |
| Arecaceae | Phoenix dactylifera | 2 | gene-LOC103720692, gene-LOC120111926 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_05.2219.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri3G12432 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT3G13180.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10020504m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp3g11360.v2.2 |
| Brassicaceae | Brassica nigra | 1 | BniB07g055780.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq01G1491 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl01G1655 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno01g04230 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0470s00012.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate09g17210 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG05.2044 |
| Plumbaginaceae | Limonium bicolor | 4 | Lb2G11870, Lb3G20046, Lb3G20047, Lb4G23470 |
| Poaceae | Echinochloa crus-galli | 3 | AH03.2299, BH03.2094, CH03.2627 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_6AG0538740, gene-QOZ80_6BG0491980 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.5HG0488940.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_006001 |
| Poaceae | Oryza coarctata | 2 | Oco17G007410, Oco18G007640 |
| Poaceae | Oryza sativa | 1 | LOC_Os09g30100.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_02G216000 |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0701708 |
| Poaceae | Sporobolus alterniflorus | 1 | Chr15G016450 |
| Poaceae | Thinopyrum elongatum | 1 | Tel5E01G405200 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC5AG039480, gene_TRIDC5BG041910 |
| Poaceae | Triticum aestivum | 3 | TraesCS5A02G253000.1, TraesCS5B02G251800.1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb101440_P002 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-19562 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g32738 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG16.1660, evm.TU.LG26.5 |
| Posidoniaceae | Posidonia oceanica | 3 | gene.Posoc01g28450, gene.Posoc03g08440, gene.Posoc06g19540 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_8_RagTag.1648 |
| Rhizophoraceae | Carallia pectinifolia | 2 | nbisL1-mrna-8796, nbisL1-mrna-8797 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-377 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-15052 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000018l.36 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00002786 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-9378 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-23755 |
| Salicaceae | Populus euphratica | 1 | populus_peu00894 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132636292 |
| Solanaceae | Solanum chilense | 1 | SOLCI007328500 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107007700 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.31791_chr09_- |
| Tamaricaceae | Tamarix chinensis | 1 | TC06G0520 |
| Zosteraceae | Zostera marina | 1 | Zosma03g00130.v3.1 |