Basic Information
Locus ID:
Ag9G00278
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
Protein RMD5 homolog A-like
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr9 | 12077744 | 12080133 | + | Ag9G00278 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 7.08 | 43,206.33 Da | 45.95 | 91.40 | -0.24 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd16652 | dRing_Rmd5p_like | 326 | 372 | 4.34966E-27 | IPR037683 |
| Pfam | PF13445 | RING-type zinc-finger | 328 | 369 | 4.7E-9 | IPR027370 |
| Pfam | PF10607 | CTLH/CRA C-terminal to LisH motif domain | 149 | 290 | 1.0E-28 | IPR024964 |
| SUPERFAMILY | SSF57850 | RING/U-box | 322 | 382 | 1.77E-9 | - |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 318 | 384 | 1.0E-9 | IPR013083 |
| SMART | SM00667 | Lish | 110 | 142 | 4.1E-5 | IPR006594 |
| SMART | SM00757 | toby_final6 | 202 | 296 | 1.1E-17 | IPR013144 |
| SMART | SM00184 | ring_2 | 328 | 371 | 1.7E-4 | IPR001841 |
| SMART | SM00668 | ctlh | 149 | 206 | 4.7E-7 | IPR006595 |
| ProSiteProfiles | PS51867 | Gid-type RING finger profile. | 328 | 371 | 13.937696 | IPR044063 |
| ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 328 | 371 | 8.845287 | IPR001841 |
| ProSiteProfiles | PS50897 | C-terminal to LisH (CTLH) motif profile. | 149 | 206 | 10.770212 | IPR006595 |
| ProSiteProfiles | PS50896 | LIS1 homology (LisH) motif profile. | 110 | 142 | 10.146605 | IPR006594 |
Gene Ontology
Molecular Function:
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT4G37880.1 | LisH/CRA/RING-U-box domains-containing protein. | 0 |
| RefSeq | XP_017255348.1 | PREDICTED: protein RMD5 homolog A-like [Daucus carota subsp. sativus] | 0 |
| Q9T075 | Protein RMD5 homolog OS=Arabidopsis thaliana OX=3702 GN=RMD5 PE=1 SV=1 | 0 | |
| TrEMBL | A0A164VRD5 | Protein RMD5 homolog A-like OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_021897 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 17.303663 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 15.135168 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 14.667779 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 15.251216 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 15.163555 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 13.727969 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 16.37117 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 11.632901 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 20.804796 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 20.766699 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 21.681486 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 20.983381 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 22.177071 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 19.559765 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 7.017558 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 9.237113 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 7.731 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 6.642465 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 7.187599 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 7.17737 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 6.512853 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 11.70679 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 12.213926 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 11.878574 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 13.084502 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 8.484568 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 6.794812 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 6.863428 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 7.373098 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 4.1228 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 5.178464 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 3.577385 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 8.746697 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 12.905695 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 10.516504 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 5.55629 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 4.465567 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 4.550457 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 9.925183 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 6.005034 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 3.875094 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 8.732758 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 11.800949 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 8.899342 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 12.027967 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 9.26578 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 8.695374 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 20.729538 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 18.464657 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 17.103041 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 3 | jg17323, jg28549, jg39879 |
| Aizoaceae | Mesembryanthemum crystallinum | 2 | gene_21428, gene_9073 |
| Amaranthaceae | Atriplex hortensis | 2 | Ah009315, Ah014529 |
| Amaranthaceae | Beta vulgaris | 2 | BVRB_8g196350, BVRB_9g222230 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg24960, Sbi_jg8818 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg19789 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00007819 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl42195, Sgl46964 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000010385, gene:ENSEOMG00000032337 ... |
| Amaranthaceae | Chenopodium quinoa | 4 | CQ.Regalona.r1.2AG0010330, CQ.Regalona.r1.7BG0000950 ... |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30103320 |
| Apiaceae | Apium graveolens | 2 | Ag5G00386, Ag9G00278 |
| Arecaceae | Cocos nucifera | 2 | COCNU_07G004720, COCNU_10G003320 |
| Arecaceae | Phoenix dactylifera | 2 | gene-LOC103704607, gene-LOC103710793 |
| Asparagaceae | Asparagus officinalis | 2 | AsparagusV1_02.1416.V1.1, AsparagusV1_09.1599.V1.1 |
| Asteraceae | Flaveria trinervia | 2 | Ftri18G12146, Ftri1G11278 |
| Brassicaceae | Arabidopsis thaliana | 3 | AT2G22690.1, AT4G37880.1, AT5G09630.1 |
| Brassicaceae | Eutrema salsugineum | 2 | Thhalv10013917m.g.v1.0, Thhalv10025455m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp6g33750.v2.2 |
| Brassicaceae | Brassica nigra | 3 | BniB03g014520.2N, BniB05g001190.2N, BniB08g004210.2N |
| Casuarinaceae | Casuarina equisetifolia | 2 | Ceq06G0407, Ceq09G0515 |
| Casuarinaceae | Casuarina glauca | 2 | Cgl06G0423, Cgl09G0553 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno07g00080 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0027s00011.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate02g16400 |
| Malvaceae | Hibiscus hamabo Siebold & Zucc. | 2 | nbisL1-mrna-10098, nbisL1-mrna-6691 |
| Nitrariaceae | Nitraria sibirica | 2 | evm.TU.LG02.2643, evm.TU.LG08.707 |
| Plantaginaceae | Plantago ovata | 2 | Pov_00024147, Pov_00030066 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb1G05996 |
| Poaceae | Echinochloa crus-galli | 3 | AH06.2137, BH06.1947, CH06.2171 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_6AG0543730, gene-QOZ80_6BG0497090 |
| Poaceae | Hordeum vulgare | 3 | HORVU.MOREX.r3.3HG0303420.1.CDS1 ... |
| Poaceae | Lolium multiflorum | 6 | gene-QYE76_019145, gene-QYE76_020308, gene-QYE76_024259 ... |
| Poaceae | Oryza coarctata | 2 | Oco11G011820, Oco12G010310 |
| Poaceae | Oryza sativa | 1 | LOC_Os06g38940.2 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_10G176500 |
| Poaceae | Sporobolus alterniflorus | 4 | Chr02G029420, Chr05G007120, Chr10G017150, Chr11G005340 |
| Poaceae | Thinopyrum elongatum | 3 | Tel3E01G566400, Tel6E01G470800, Tel7E01G610300 |
| Poaceae | Triticum dicoccoides | 6 | gene_TRIDC3AG050920, gene_TRIDC3BG057400 ... |
| Poaceae | Triticum aestivum | 9 | TraesCS3A02G353800.1.cds1, TraesCS3B02G386500.1.cds1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb044600_P001 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-41127 |
| Poaceae | Zoysia macrostachya | 2 | Zma_g30749, Zma_g32991 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG02.2888, evm.TU.LG23.1085 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc05g22950 |
| Rhizophoraceae | Bruguiera sexangula | 3 | evm.TU.Scaffold_2_RagTag.461, evm.TU.Scaffold_3_RagTag.1158 ... |
| Rhizophoraceae | Carallia pectinifolia | 2 | nbisL1-mrna-4738, nbisL1-mrna-816 |
| Rhizophoraceae | Ceriops tagal | 4 | nbisL1-mrna-1311, nbisL1-mrna-19214, nbisL1-mrna-760 ... |
| Rhizophoraceae | Ceriops zippeliana | 4 | nbisL1-mrna-12031, nbisL1-mrna-2411, nbisL1-mrna-3560 ... |
| Rhizophoraceae | Kandelia candel | 2 | evm.TU.utg000009l.681, evm.TU.utg000019l.546 |
| Rhizophoraceae | Kandelia obovata | 3 | Maker00001598, Maker00005594, Maker00007392 |
| Rhizophoraceae | Rhizophora apiculata | 3 | nbisL1-mrna-18661, nbisL1-mrna-2585, nbisL1-mrna-6169 |
| Rhizophoraceae | Rhizophora mangle | 4 | nbisL1-mrna-13913, nbisL1-mrna-16543, nbisL1-mrna-1850 ... |
| Salicaceae | Populus euphratica | 4 | populus_peu01680, populus_peu29125, populus_peu29142 ... |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132621085 |
| Solanaceae | Solanum chilense | 1 | SOLCI004025500 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107011816 |
| Tamaricaceae | Reaumuria soongarica | 3 | STRG.12808_chr02_+, STRG.16344_chr06_+, STRG.8863_chr03_+ |
| Tamaricaceae | Tamarix chinensis | 2 | TC09G0285, TC11G0617 |
| Zosteraceae | Zostera marina | 1 | Zosma04g24490.v3.1 |