Basic Information
Locus ID:
gene_12326
Species & Taxonomic ID:
Mesembryanthemum crystallinum & 3544
Genome Assembly:
Koichi Toyokura Assembly
Description:
U5 small nuclear ribonucleoprotein 40
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| Super-Scaffold_12_Chr_6 | 4219946 | 4228386 | + | gene_12326 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 7.44 | 101,188.19 Da | 40.01 | 91.82 | -0.14 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd00200 | WD40 | 53 | 344 | 1.78831E-71 | - |
| Pfam | PF00400 | WD domain, G-beta repeat | 91 | 128 | 4.6E-4 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 187 | 212 | 0.042 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 310 | 344 | 0.1 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 49 | 85 | 4.4E-5 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 134 | 171 | 0.0041 | IPR001680 |
| Pfam | PF08387 | FBD | 824 | 868 | 1.8E-9 | IPR006566 |
| Pfam | PF00400 | WD domain, G-beta repeat | 263 | 304 | 2.2E-6 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 219 | 254 | 2.4E-4 | IPR001680 |
| Pfam | PF00646 | F-box domain | 486 | 521 | 2.1E-4 | IPR001810 |
| SUPERFAMILY | SSF52047 | RNI-like | 584 | 888 | 7.85E-9 | - |
| SUPERFAMILY | SSF81383 | F-box domain | 482 | 565 | 7.98E-13 | IPR036047 |
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 50 | 344 | 3.4E-83 | IPR036322 |
| Gene3D | G3DSA:2.130.10.10 | - | 45 | 347 | 1.3E-119 | IPR015943 |
| Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 527 | 894 | 1.5E-7 | IPR032675 |
| Gene3D | G3DSA:1.20.1280.50 | - | 476 | 526 | 6.4E-6 | - |
| SMART | SM00579 | 9598neu4hmm | 829 | 900 | 3.1E-15 | IPR006566 |
| SMART | SM00320 | WD40_4 | 131 | 171 | 1.9E-7 | IPR001680 |
| SMART | SM00320 | WD40_4 | 174 | 212 | 3.9E-4 | IPR001680 |
| SMART | SM00320 | WD40_4 | 89 | 128 | 5.9E-8 | IPR001680 |
| SMART | SM00320 | WD40_4 | 215 | 254 | 1.9E-7 | IPR001680 |
| SMART | SM00320 | WD40_4 | 307 | 348 | 0.027 | IPR001680 |
| SMART | SM00320 | WD40_4 | 46 | 85 | 1.2E-7 | IPR001680 |
| SMART | SM00320 | WD40_4 | 261 | 304 | 1.1E-7 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 283 | 313 | 11.477578 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 222 | 256 | 12.780889 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 222 | 256 | 10.627413 | - |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 96 | 133 | 12.710129 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 187 | 221 | 12.045688 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 180 | 217 | 8.808332 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 53 | 86 | 14.919653 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 138 | 180 | 10.408196 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 272 | 307 | 8.544697 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 96 | 137 | 16.690819 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 53 | 86 | 12.314676 | - |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 158 | 172 | - | IPR019775 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 115 | 129 | - | IPR019775 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 291 | 305 | - | IPR019775 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 199 | 213 | - | IPR019775 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 72 | 86 | - | IPR019775 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 158 | 172 | 4.8E-7 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 72 | 86 | 4.8E-7 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 115 | 129 | 4.8E-7 | 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_010694211.1 | U5 small nuclear ribonucleoprotein 40 kDa protein [Beta vulgaris subsp. vulgaris] | 0 |
| Q96DI7 | U5 small nuclear ribonucleoprotein 40 kDa protein OS=Homo sapiens OX=9606 GN=SNRNP40 PE=1 SV=1 | 0 | |
| TrEMBL | A0A803ML12 | WD_REPEATS_REGION domain-containing protein OS=Chenopodium quinoa OX=63459 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| No sample metadata found. | |||||||
Network
No network data available for this species.
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 |