Basic Information
Locus ID:
Ag8G00689
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Short Name:
SCD1
Description:
Domain always found downstream of DENN domain, found in a variety of signalling proteins
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr8 | 39272032 | 39295260 | + | Ag8G00689 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.86 | 126,296.17 Da | 41.00 | 90.93 | -0.17 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd00200 | WD40 | 782 | 1078 | 8.9208E-57 | - |
| Pfam | PF00400 | WD domain, G-beta repeat | 1000 | 1036 | 0.0032 | IPR001680 |
| Pfam | PF02141 | DENN (AEX-3) domain | 51 | 231 | 1.4E-45 | IPR001194 |
| Pfam | PF00400 | WD domain, G-beta repeat | 840 | 872 | 0.0011 | IPR001680 |
| Pfam | PF03455 | dDENN domain | 324 | 374 | 2.2E-6 | IPR005112 |
| Pfam | PF00400 | WD domain, G-beta repeat | 782 | 830 | 5.2E-4 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 960 | 995 | 0.022 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 877 | 913 | 3.9E-4 | IPR001680 |
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 783 | 1137 | 6.11E-63 | IPR036322 |
| Gene3D | G3DSA:3.40.50.11500 | - | 129 | 314 | 4.0E-43 | IPR043153 |
| Gene3D | G3DSA:2.130.10.10 | - | 962 | 1141 | 8.6E-25 | IPR015943 |
| Gene3D | G3DSA:2.130.10.10 | - | 747 | 961 | 6.3E-37 | IPR015943 |
| SMART | SM00320 | WD40_4 | 875 | 913 | 7.9E-7 | IPR001680 |
| SMART | SM00320 | WD40_4 | 835 | 872 | 7.8E-4 | IPR001680 |
| SMART | SM00320 | WD40_4 | 998 | 1037 | 2.6E-7 | IPR001680 |
| SMART | SM00801 | dDENN_cls | 293 | 361 | 3.4E-14 | IPR005112 |
| SMART | SM00799 | DENN_cls | 49 | 233 | 1.5E-64 | IPR001194 |
| SMART | SM00320 | WD40_4 | 916 | 955 | 0.056 | IPR001680 |
| SMART | SM00320 | WD40_4 | 1042 | 1079 | 160.0 | IPR001680 |
| SMART | SM00320 | WD40_4 | 1097 | 1136 | 0.62 | IPR001680 |
| SMART | SM00320 | WD40_4 | 958 | 995 | 8.1E-4 | IPR001680 |
| SMART | SM00320 | WD40_4 | 779 | 830 | 0.014 | IPR001680 |
| ProSiteProfiles | PS50211 | Tripartite DENN domain profile. | 1 | 369 | 55.37257 | IPR037516 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 1005 | 1037 | 11.410742 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 882 | 922 | 12.881143 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 965 | 1004 | 10.14085 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 842 | 872 | 8.676514 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 812 | 830 | 8.503359 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 882 | 916 | 9.783781 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 842 | 881 | 11.07656 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 1005 | 1037 | 9.54651 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 927 | 964 | 8.770704 | IPR001680 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 1123 | 1137 | - | IPR019775 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 900 | 914 | - | IPR019775 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 859 | 873 | 2.2E-5 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 982 | 996 | 2.2E-5 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 900 | 914 | 2.2E-5 | IPR020472 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 451 | 472 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 757 | 776 | - | - |
Gene Ontology
Molecular Function:
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT1G49040.1 | stomatal cytokinesis defective / SCD1 protein (SCD1). Encodes soluble protein containing N-terminal DENN domain and eight C-terminal WD-40 repeats. Involved in cytokinesis of guard mother cells and leaf epidermal cells. The overall growth and development of mutant plants is severely affected, they are smaller than wt, with defects in seedling development, leaf expansion and flower morphology which renders the mutant conditionally sterile. | 0 |
| RefSeq | XP_017222550.1 | PREDICTED: DENN domain and WD repeat-containing protein SCD1 isoform X1 [Daucus carota subsp. sativus] | 0 |
| Q8RXA7 | DENN domain and WD repeat-containing protein SCD1 OS=Arabidopsis thaliana OX=3702 GN=SCD1 PE=1 SV=1 | 0 | |
| TrEMBL | A0A175YNQ3 | UDENN domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_027817 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 16.936331 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 12.962459 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 13.423563 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 14.21102 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 13.919845 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 12.284954 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 11.952345 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 11.927221 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 33.35828 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 29.921366 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 35.062843 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 32.015728 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 28.247377 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 23.456854 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 16.073793 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 19.329184 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 17.994102 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 19.473551 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 17.173931 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 18.499443 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 16.180019 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 19.081448 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 20.918055 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 22.386257 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 18.413719 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 22.333675 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 20.324066 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 18.44681 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 21.085827 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 4.834144 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 5.073247 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 4.362128 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 7.648796 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 9.654346 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 9.676138 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 6.293969 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 3.998413 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 3.907215 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 19.316545 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 10.280528 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 6.043451 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 13.250339 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 14.584556 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 22.108568 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 19.41872 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 12.14802 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 20.540943 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 24.100918 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 23.968821 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 20.47835 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg26987 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_22578 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah002039 |
| Amaranthaceae | Beta vulgaris | 2 | BVRB_5g110800, BVRB_5g110810 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg28100, Sbi_jg32435 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg7325 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00015748 |
| Amaranthaceae | Suaeda glauca | 4 | Sgl53780, Sgl53785, Sgl59043, Sgl59048 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000006812, gene:ENSEOMG00000022168 ... |
| Amaranthaceae | Chenopodium quinoa | 5 | CQ.Regalona.r1.2AG0010700, CQ.Regalona.r1.3AG0015290 ... |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30146250 |
| Apiaceae | Apium graveolens | 1 | Ag8G00689 |
| Arecaceae | Cocos nucifera | 1 | COCNU_06G001720 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103712861 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_05.1767.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri5G21468 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT1G49040.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10011186m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp1g35950.v2.2 |
| Brassicaceae | Brassica nigra | 3 | BniB04g061410.2N, BniB04g061420.2N, BniB07g008560.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq03G2407 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl03G2546 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno16g01280 |
| Dunaliellaceae | Dunaliella salina | 2 | Dusal.0074s00025.v1.0, Dusal.1115s00001.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate03g18560 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG10.393 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00033367 |
| Plumbaginaceae | Limonium bicolor | 4 | Lb7G33581, Lb7G33582, Lb7G33899, Lb7G33920 |
| Poaceae | Echinochloa crus-galli | 3 | AH02.2105, BH02.2171, CH02.2332 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_1AG0021780, gene-QOZ80_1BG0071730 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.3HG0267340.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_053426 |
| Poaceae | Oryza coarctata | 1 | Oco01G013100 |
| Poaceae | Oryza sativa | 1 | LOC_Os01g39380.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_03G171900 |
| Poaceae | Puccinellia tenuiflora | 2 | Pt_Chr0603071, Pt_Chr0603098 |
| Poaceae | Sporobolus alterniflorus | 2 | Chr05G016920, Chr08G009050 |
| Poaceae | Thinopyrum elongatum | 1 | Tel3E01G361500 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC3AG030960, gene_TRIDC3BG035530 |
| Poaceae | Triticum aestivum | 3 | TraesCS3A02G204600.3, TraesCS3B02G236700.5 ... |
| Poaceae | Zea mays | 1 | Zm00001eb160220_P001 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-29429 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g8107 |
| Portulacaceae | Portulaca oleracea | 3 | evm.TU.LG02.258, evm.TU.LG02.259, evm.TU.LG09.1496 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc09g09950 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_4_RagTag.777 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-28585 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-21414 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-1599 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000008l.502 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00000915 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-14401 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-19268 |
| Salicaceae | Populus euphratica | 3 | populus_peu28383, populus_peu29836, populus_peu29949 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132633292 |
| Solanaceae | Solanum chilense | 1 | SOLCI006253400 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107014520 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.14190_chr08_+ |
| Tamaricaceae | Tamarix chinensis | 1 | TC05G0860 |
| Zosteraceae | Zostera marina | 2 | Zosma05g14010.v3.1, Zosma05g14020.v3.1 |