Basic Information
Locus ID:
Ag4G00625
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
Cleavage stimulation factor subunit
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr4 | 39838570 | 39848679 | + | Ag4G00625 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 7.30 | 48,481.94 Da | 36.59 | 77.44 | -0.28 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd00200 | WD40 | 125 | 439 | 5.80792E-50 | - |
| Pfam | PF00400 | WD domain, G-beta repeat | 313 | 350 | 0.0054 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 126 | 160 | 3.9E-6 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 233 | 254 | 0.064 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 280 | 307 | 0.037 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 182 | 217 | 4.7E-6 | IPR001680 |
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 120 | 439 | 1.53E-58 | IPR036322 |
| Gene3D | G3DSA:2.130.10.10 | - | 113 | 441 | 1.5E-57 | IPR015943 |
| SMART | SM00320 | WD40_4 | 354 | 396 | 72.0 | IPR001680 |
| SMART | SM00320 | WD40_4 | 310 | 351 | 0.0032 | IPR001680 |
| SMART | SM00320 | WD40_4 | 399 | 439 | 0.44 | IPR001680 |
| SMART | SM00320 | WD40_4 | 122 | 161 | 2.1E-6 | IPR001680 |
| SMART | SM00320 | WD40_4 | 178 | 217 | 4.4E-8 | IPR001680 |
| SMART | SM00320 | WD40_4 | 270 | 307 | 0.0035 | IPR001680 |
| SMART | SM00320 | WD40_4 | 223 | 261 | 22.0 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 129 | 170 | 11.07656 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 129 | 162 | 9.151057 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 275 | 316 | 11.778342 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 185 | 226 | 11.143396 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 275 | 307 | 9.54651 | - |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 185 | 219 | 9.256512 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 327 | 360 | 10.107432 | IPR001680 |
| ProSiteProfiles | PS50896 | LIS1 homology (LisH) motif profile. | 20 | 52 | 7.625276 | IPR006594 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 338 | 352 | - | IPR019775 |
Gene Ontology
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT5G60940.1 | Transducin/WD40 repeat-like superfamily protein. | 0 |
| RefSeq | XP_017237955.1 | PREDICTED: cleavage stimulation factor subunit 50 [Daucus carota subsp. sativus] | 0 |
| Q8L4J2 | Cleavage stimulation factor subunit 50 OS=Arabidopsis thaliana OX=3702 GN=CSTF50 PE=1 SV=1 | 0 | |
| TrEMBL | A0A166AKL6 | Cleavage stimulation factor 50 kDa subunit OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_010163 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 13.744701 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 10.850268 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 11.041906 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 11.322444 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 12.087864 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 10.078506 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 10.042811 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 9.741864 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 17.009085 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 15.490344 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 17.8808 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 13.819464 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 18.187805 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 15.465271 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 12.608254 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 12.020141 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 13.810787 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 18.391298 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 18.001968 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 13.489803 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 15.935874 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 13.394324 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 16.191158 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 14.692331 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 17.164949 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 17.747517 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 17.488995 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 17.626957 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 15.329349 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 22.699533 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 21.319283 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 18.223186 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 20.880207 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 14.924907 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 19.505627 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 16.730696 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 15.7848 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 17.519266 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 17.609182 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 18.387201 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 17.822035 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 19.95714 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 20.616854 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 18.443596 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 18.829994 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 21.168674 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 15.683329 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 24.096006 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 23.232286 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 22.040113 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg25683 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_13874 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah001252 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg30972, Sbi_jg58304 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg25910 |
| Amaranthaceae | Suaeda aralocaspica | 4 | GOSA_00004775, GOSA_00013999, GOSA_00019137, GOSA_00019941 |
| Amaranthaceae | Suaeda glauca | 1 | Sgl54854 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000005534, gene:ENSEOMG00000022554 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.5AG0019140, CQ.Regalona.r1.5BG0020410 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30145240 |
| Apiaceae | Apium graveolens | 1 | Ag4G00625 |
| Arecaceae | Cocos nucifera | 1 | COCNU_14G011330 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103704490 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_06.1972.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri16G05043 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT5G60940.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10004278m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp2g24250.v2.2 |
| Brassicaceae | Brassica nigra | 1 | BniB02g076160.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq01G1758 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl01G1912 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno09g05900 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate09g06050 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG10.523 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00033117 |
| Plumbaginaceae | Limonium bicolor | 2 | Lb4G25951, Lb4G25953 |
| Poaceae | Echinochloa crus-galli | 3 | BH01.693, CH01.675, Contig309.51 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_3AG0215620, gene-QOZ80_3BG0260720 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.5HG0511430.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_061780 |
| Poaceae | Oryza coarctata | 2 | Oco05G023920, Oco06G024800 |
| Poaceae | Oryza sativa | 1 | LOC_Os03g54770.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_01G077000 |
| Poaceae | Sporobolus alterniflorus | 2 | Chr04G028830, Chr07G027830 |
| Poaceae | Thinopyrum elongatum | 1 | Tel5E01G623600 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC5AG057120, gene_TRIDC5BG061260 |
| Poaceae | Triticum aestivum | 3 | TraesCS5A02G392400.1, TraesCS5B02G397200.1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb057630_P001 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-16202 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g2768 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG02.80, evm.TU.LG09.1310 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc04g10630 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_4_RagTag.830 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-28516 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-20911 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-1551 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000008l.535 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00000539 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-14371 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-19317 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132603520 |
| Solanaceae | Solanum chilense | 2 | SOLCI004692800, SOLCI004693100 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107007424 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.14691_chr08_- |
| Tamaricaceae | Tamarix chinensis | 1 | TC05G0828 |
| Zosteraceae | Zostera marina | 1 | Zosma03g05190.v3.1 |