Basic Information
Locus ID:
Ag9G00023
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
Dual-specificity RNA methyltransferase
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr9 | 1704717 | 1713193 | + | Ag9G00023 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 9.41 | 45,578.43 Da | 48.70 | 96.08 | -0.16 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd01335 | Radical_SAM | 160 | 353 | 1.00802E-12 | - |
| Pfam | PF04055 | Radical SAM superfamily | 156 | 322 | 1.6E-14 | IPR007197 |
| SUPERFAMILY | SSF102114 | Radical SAM enzymes | 150 | 350 | 1.44E-17 | - |
| Gene3D | G3DSA:3.20.20.70 | Aldolase class I | 110 | 393 | 3.6E-109 | IPR013785 |
| Gene3D | G3DSA:1.10.150.530 | - | 47 | 103 | 3.3E-12 | - |
| SMART | SM00729 | MiaB | 151 | 368 | 0.0016 | IPR006638 |
| TIGRFAM | TIGR00048 | rRNA_mod_RlmN: 23S rRNA (adenine(2503)-C(2))-methyltransferase | 49 | 388 | 1.6E-119 | IPR027492 |
| PIRSF | PIRSF006004 | Cfr | 36 | 401 | 8.1E-129 | IPR004383 |
| ProSiteProfiles | PS51918 | Radical SAM core domain profile. | 147 | 377 | 35.78978 | IPR007197 |
| Hamap | MF_01849 | Dual-specificity RNA methyltransferase RlmN [rlmN]. | 46 | 391 | 62.558609 | IPR027492 |
| SFLD | SFLDF00275 | adenosine C2 methyltransferase (RlmN-like) | 47 | 391 | 0.0 | IPR004383 |
| SFLD | SFLDS00029 | Radical SAM | 47 | 391 | 0.0 | IPR007197 |
Gene Ontology
Biological Process:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT2G39670.1 | Radical SAM superfamily protein. | 0 |
| RefSeq | XP_017231263.1 | PREDICTED: probable dual-specificity RNA methyltransferase RlmN isoform X1 [Daucus carota subsp. sativus] | 0 |
| B0C9F4 | Probable dual-specificity RNA methyltransferase RlmN OS=Acaryochloris marina (strain MBIC 11017) OX=329726 GN=rlmN PE=3 SV=1 | 0 | |
| TrEMBL | A0A166CR53 | Radical SAM core domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_005051 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 19.710869 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 10.893612 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 11.786478 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 12.999245 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 12.458266 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 17.11717 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 9.601678 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 7.23912 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 30.792898 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 27.491791 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 27.075619 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 25.76833 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 26.101061 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 27.917992 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 11.113542 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 13.199838 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 14.465877 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 17.257259 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 28.97476 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 16.706419 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 15.89237 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 18.109142 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 20.552677 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 17.953922 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 18.339342 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 25.293344 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 24.820597 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 33.510429 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 25.541517 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 9.61884 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 20.902315 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 15.327478 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 20.622498 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 15.675541 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 16.137608 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 15.335896 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 8.605564 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 9.633086 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 50.896603 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 29.111055 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 50.072105 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 10.534887 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 20.929001 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 34.033909 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 23.74946 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 19.694016 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 22.28911 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 20.771961 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 16.213264 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 22.525955 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg14338 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_16563 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah035392 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_2g024800 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg21198, Sbi_jg22605 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg16497 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00016311 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl62581, Sgl67128 |
| Amaranthaceae | Chenopodium album | 2 | gene:ENSEOMG00000019492, gene:ENSEOMG00000048731 |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.1BG0018360, CQ.Regalona.r1.2AG0020180 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30175600 |
| Apiaceae | Apium graveolens | 1 | Ag9G00023 |
| Arecaceae | Cocos nucifera | 1 | COCNU_16G008010 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103721994 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_07.185.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri1G03425 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT2G39670.2 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10016689m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp4g21930.v2.2 |
| Brassicaceae | Brassica nigra | 1 | BniB06g005180.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq02G1121 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl02G1164 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno03g00780 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0489s00006.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate07g14040 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG02.1738 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00040119 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb7G33725 |
| Poaceae | Echinochloa crus-galli | 3 | AH02.4657, BH02.4725, CH02.4745 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_1AG0048280, gene-QOZ80_1BG0098170 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.3HG0329300.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_059015 |
| Poaceae | Oryza coarctata | 2 | Oco01G031110, Oco02G032270 |
| Poaceae | Oryza sativa | 1 | LOC_Os01g74190.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_03G419500 |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0201670 |
| Poaceae | Sporobolus alterniflorus | 2 | Chr03G024100, Chr08G017570 |
| Poaceae | Thinopyrum elongatum | 1 | Tel3E01G895700 |
| Poaceae | Triticum dicoccoides | 1 | gene_TRIDC3BG086420 |
| Poaceae | Triticum aestivum | 3 | TraesCS3A02G530100.1, TraesCS3B02G600200.1 ... |
| Poaceae | Zea mays | 2 | Zm00001eb179610_P001, Zm00001eb362190_P003 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-10745 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g9448 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG05.886, evm.TU.LG25.446 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc02g01260 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_4_RagTag.1733 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-26004 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-7647 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-4537 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000008l.966 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00001314 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-2087 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-9453 |
| Salicaceae | Populus euphratica | 1 | populus_peu06439 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132606149 |
| Solanaceae | Solanum chilense | 1 | SOLCI004452500 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107023407 |
| Tamaricaceae | Reaumuria soongarica | 1 | gene_10680 |
| Tamaricaceae | Tamarix chinensis | 1 | TC08G0770 |
| Zosteraceae | Zostera marina | 1 | Zosma01g16270.v3.1 |