Basic Information
Locus ID:
Ag11G03683
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 |
|---|---|---|---|---|
| chr11 | 71753934 | 71757576 | + | Ag11G03683 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 8.51 | 43,337.61 Da | 38.46 | 73.09 | -0.49 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd00200 | WD40 | 97 | 386 | 1.74007E-74 | - |
| Pfam | PF00400 | WD domain, G-beta repeat | 263 | 298 | 3.7E-7 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 135 | 172 | 2.4E-5 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 307 | 348 | 2.0E-5 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 354 | 387 | 0.21 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 94 | 129 | 3.3E-6 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 231 | 256 | 0.058 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 178 | 215 | 0.0012 | IPR001680 |
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 94 | 387 | 8.11E-85 | IPR036322 |
| Gene3D | G3DSA:2.130.10.10 | - | 89 | 391 | 1.9E-121 | IPR015943 |
| SMART | SM00320 | WD40_4 | 351 | 390 | 0.0017 | IPR001680 |
| SMART | SM00320 | WD40_4 | 175 | 215 | 2.1E-6 | IPR001680 |
| SMART | SM00320 | WD40_4 | 90 | 129 | 8.3E-9 | IPR001680 |
| SMART | SM00320 | WD40_4 | 133 | 172 | 4.6E-8 | IPR001680 |
| SMART | SM00320 | WD40_4 | 259 | 298 | 1.6E-9 | IPR001680 |
| SMART | SM00320 | WD40_4 | 305 | 348 | 1.4E-5 | IPR001680 |
| SMART | SM00320 | WD40_4 | 218 | 256 | 0.001 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 266 | 300 | 13.527399 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 140 | 181 | 16.991583 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 358 | 391 | 8.870959 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 97 | 130 | 12.868311 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 231 | 265 | 11.744925 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 224 | 261 | 8.57106 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 203 | 224 | 9.672996 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 97 | 130 | 15.621435 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 328 | 357 | 10.809215 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 358 | 391 | 8.861059 | - |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 140 | 177 | 12.947401 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 266 | 300 | 16.45689 | IPR001680 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 243 | 257 | - | IPR019775 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 159 | 173 | - | IPR019775 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 116 | 130 | - | IPR019775 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 335 | 349 | - | IPR019775 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 202 | 216 | - | IPR019775 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 159 | 173 | 6.1E-8 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 243 | 257 | 6.1E-8 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 202 | 216 | 6.1E-8 | IPR020472 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 69 | 92 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 72 | 92 | - | - |
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 | 34.686535 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 30.825268 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 24.817434 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 27.929052 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 27.003267 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 34.64188 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 26.529654 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 28.048758 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 43.801144 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 46.512505 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 43.524551 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 49.335499 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 41.345234 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 44.058502 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 14.088632 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 16.284637 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 15.40349 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 16.742054 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 18.42433 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 17.558811 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 24.1007 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 21.874306 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 26.759493 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 21.732368 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 24.682091 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 18.446743 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 17.326567 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 19.955156 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 18.969006 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 27.188738 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 23.586811 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 23.435202 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 46.915768 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 30.669971 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 38.841133 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 47.367054 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 38.737392 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 42.049728 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 28.169773 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 15.011641 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 11.079376 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 18.977917 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 17.707685 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 52.352848 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 49.41827 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 24.75773 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 34.962929 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 37.335419 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 38.147995 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 35.936623 | 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 |