Basic Information
Locus ID:
Ag3G00874
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
U5 small nuclear ribonucleoprotein 40
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr3 | 33742534 | 33746572 | + | Ag3G00874 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 6.89 | 38,267.72 Da | 36.17 | 72.72 | -0.48 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd00200 | WD40 | 52 | 341 | 7.48109E-74 | - |
| Pfam | PF00400 | WD domain, G-beta repeat | 90 | 127 | 2.0E-5 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 48 | 84 | 4.1E-7 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 309 | 342 | 0.18 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 133 | 170 | 0.0011 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 262 | 303 | 1.6E-5 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 218 | 253 | 3.2E-7 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 186 | 211 | 0.05 | IPR001680 |
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 49 | 342 | 2.88E-85 | IPR036322 |
| Gene3D | G3DSA:2.130.10.10 | - | 44 | 346 | 4.8E-122 | IPR015943 |
| SMART | SM00320 | WD40_4 | 306 | 345 | 0.0017 | IPR001680 |
| SMART | SM00320 | WD40_4 | 130 | 170 | 2.1E-6 | IPR001680 |
| SMART | SM00320 | WD40_4 | 45 | 84 | 8.2E-9 | IPR001680 |
| SMART | SM00320 | WD40_4 | 214 | 253 | 1.6E-9 | IPR001680 |
| SMART | SM00320 | WD40_4 | 88 | 127 | 4.6E-8 | IPR001680 |
| SMART | SM00320 | WD40_4 | 173 | 211 | 0.001 | IPR001680 |
| SMART | SM00320 | WD40_4 | 260 | 303 | 8.3E-6 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 283 | 312 | 10.942887 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 95 | 136 | 16.991583 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 95 | 132 | 12.947401 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 313 | 346 | 8.870959 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 221 | 255 | 13.527399 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 186 | 220 | 11.744925 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 179 | 216 | 8.57106 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 52 | 85 | 15.855363 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 52 | 85 | 13.052855 | - |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 313 | 346 | 8.861059 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 221 | 255 | 16.45689 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 158 | 179 | 9.672996 | IPR001680 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 114 | 128 | - | IPR019775 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 71 | 85 | - | IPR019775 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 290 | 304 | - | IPR019775 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 198 | 212 | - | IPR019775 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 157 | 171 | - | IPR019775 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 114 | 128 | 4.5E-8 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 198 | 212 | 4.5E-8 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 157 | 171 | 4.5E-8 | IPR020472 |
Gene Ontology
Molecular Function:
KEGG Pathway
KO Term:
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT2G43770.1 | Transducin/WD40 repeat-like superfamily protein. | 0 |
| RefSeq | XP_017231351.1 | PREDICTED: U5 small nuclear ribonucleoprotein 40 kDa protein [Daucus carota subsp. sativus] | 0 |
| Q96DI7 | U5 small nuclear ribonucleoprotein 40 kDa protein OS=Homo sapiens OX=9606 GN=SNRNP40 PE=1 SV=1 | 0 | |
| TrEMBL | A0A166D1I2 | WD_REPEATS_REGION domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_005453 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 8.310472 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 5.017778 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 5.23562 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 3.978488 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 4.733174 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 4.761096 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 4.381417 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 3.458272 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 12.53461 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 14.848411 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 13.569205 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 14.115635 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 13.781917 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 13.544134 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 6.304432 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 5.046341 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 6.966402 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 5.677263 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 6.798075 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 6.179468 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 7.188782 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 5.411036 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 6.218302 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 8.613526 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 8.271452 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 5.605247 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 5.470349 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 4.196089 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 7.084657 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 5.556934 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 6.676241 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 6.507726 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 7.728532 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 7.577219 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 6.738938 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 9.097733 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 6.441382 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 6.88383 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 7.954825 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 4.863187 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 3.842754 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 5.621654 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 6.693771 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 4.535047 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 4.372467 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 6.358708 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 6.003436 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 9.20225 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 8.231722 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 8.937013 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg5975 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_12326 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah008608 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg18879, Sbi_jg37326 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg5143 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00026241 |
| Amaranthaceae | Suaeda glauca | 7 | Sgl22751, Sgl22753, Sgl27883, Sgl27889, Sgl27901, Sgl27903 ... |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000011580, gene:ENSEOMG00000030236 ... |
| Amaranthaceae | Chenopodium quinoa | 3 | CQ.Regalona.r1.2AG0005710, CQ.Regalona.r1.4AG0021830 ... |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30247390 |
| Apiaceae | Apium graveolens | 3 | Ag11G03683, Ag1G01006, Ag3G00874 |
| Arecaceae | Cocos nucifera | 2 | COCNU_06G008700, COCNU_14G005760 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103708149 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_06.420.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri9G10053 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT2G43770.1 |
| Brassicaceae | Eutrema salsugineum | 2 | Thhalv10001531m.g.v1.0, Thhalv10006086m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 2 | Sp4g25840.v2.2, Sp5g03440.v2.2 |
| Brassicaceae | Brassica nigra | 3 | BniB01g002390.2N, BniB06g002410.2N, BniB06g053920.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq09G1378 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl09G1469 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno01g01840 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0361s00016.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate04g07070 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00025134 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_6AG0546890, gene-QOZ80_6BG0500360 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.7HG0741190.1.CDS1 |
| Poaceae | Lolium multiflorum | 2 | gene-QYE76_036531, gene-QYE76_036533 |
| Poaceae | Oryza coarctata | 2 | Oco11G014210, Oco12G014390 |
| Poaceae | Oryza sativa | 1 | LOC_Os06g44370.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_10G212200 |
| Poaceae | Sporobolus alterniflorus | 3 | Chr02G031190, Chr05G008900, Chr0G000390 |
| Poaceae | Thinopyrum elongatum | 1 | Tel7E01G856000 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC7AG069910, gene_TRIDC7BG064370 |
| Poaceae | Triticum aestivum | 3 | TraesCS7A02G499900.1.cds1, TraesCS7B02G406900.1.cds1 ... |
| Poaceae | Zea mays | 2 | Zm00001eb274960_P001, Zm00001eb389600_P002 |
| Poaceae | Zoysia japonica | 2 | nbis-gene-40866, nbis-gene-9867 |
| Poaceae | Zoysia macrostachya | 2 | Zma_g30921, Zma_g33177 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG02.1468, evm.TU.LG09.427 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc03g03660 |
| Rhizophoraceae | Bruguiera sexangula | 2 | evm.TU.Scaffold_3_RagTag.1543, evm.TU.Scaffold_6_RagTag.1152 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-1856 |
| Rhizophoraceae | Ceriops tagal | 2 | nbisL1-mrna-17907, nbisL1-mrna-18239 |
| Rhizophoraceae | Ceriops zippeliana | 2 | nbisL1-mrna-2760, nbisL1-mrna-992 |
| Rhizophoraceae | Kandelia candel | 1 | add.evm.TU.utg000019l.132 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00001877 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-5407 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-12915 |
| Salicaceae | Populus euphratica | 1 | populus_peu18766 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132636093 |
| Solanaceae | Solanum chilense | 1 | SOLCI005994700 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107015323 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.4561_chr02_- |
| Tamaricaceae | Tamarix chinensis | 1 | TC12G1440 |
| Zosteraceae | Zostera marina | 1 | Zosma04g01990.v3.1 |