Basic Information
Locus ID:
Ag4G02647
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
Cleavage and polyadenylation specificity factor
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr4 | 306970642 | 306972482 | + | Ag4G02647 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 8.69 | 35,659.92 Da | 39.70 | 85.50 | -0.22 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| Pfam | PF07521 | Zn-dependent metallo-hydrolase RNA specificity domain | 119 | 169 | 4.7E-14 | IPR011108 |
| Pfam | PF00753 | Metallo-beta-lactamase superfamily | 15 | 86 | 4.6E-9 | IPR001279 |
| SUPERFAMILY | SSF56281 | Metallo-hydrolase/oxidoreductase | 108 | 188 | 2.43E-17 | IPR036866 |
| SUPERFAMILY | SSF56281 | Metallo-hydrolase/oxidoreductase | 3 | 108 | 7.99E-34 | IPR036866 |
| Gene3D | G3DSA:3.60.15.10 | - | 133 | 161 | 3.0E-10 | IPR036866 |
| Gene3D | G3DSA:3.40.50.10890 | - | 112 | 132 | 3.0E-10 | - |
| Gene3D | G3DSA:3.60.15.10 | - | 8 | 108 | 1.1E-35 | IPR036866 |
| SMART | SM00849 | Lactamase_B_5a | 15 | 201 | 0.0019 | IPR001279 |
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT2G01730.1 | cleavage and polyadenylation specificity factor 73 kDa subunit-II. a homolog of cleavage and polyadenylation specificity factor that plays an essential role in the development of female gametophyte and embryo | 0 |
| RefSeq | XP_017220213.1 | PREDICTED: cleavage and polyadenylation specificity factor subunit 3-II [Daucus carota subsp. sativus] | 0 |
| Q8GUU3 | Cleavage and polyadenylation specificity factor subunit 3-II OS=Arabidopsis thaliana OX=3702 GN=CPSF73-II PE=1 SV=2 | 0 | |
| TrEMBL | A0A175YQ71 | Cleavage and polyadenylation specificity factor subunit 3-II OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_026803 PE=3 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 1.758345 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 1.912479 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 1.053545 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 0.91383 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 0.453106 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 0.451386 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 1.711492 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 5.888067 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 0 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 0.145047 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 0.11811 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 0.187491 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 0.13875 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 0 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 0.283374 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 0.234573 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 0 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 0.111073 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 0.222814 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 0.406747 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 0.319573 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 0.483779 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 0.333707 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 0.383176 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 0.327065 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 0.258347 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 0.336444 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 0 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 0 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 0.078591 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 0 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 0 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 0.058756 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 0.11791 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 0 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 0.09458 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 0.09215 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 0.13512 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 0 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 0 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 0.135767 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 14.695245 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 2.244219 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 0 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 0 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 13.958874 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 0 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 0.673354 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 0.095632 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 1.696331 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg9731 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_5399 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah003441 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg39238, Sbi_jg54555 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg11091 |
| Amaranthaceae | Suaeda aralocaspica | 2 | GOSA_00019632, GOSA_00019634 |
| Amaranthaceae | Suaeda glauca | 5 | Sgl15128, Sgl20281, Sgl35697, Sgl35770, Sgl41081 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000006204, gene:ENSEOMG00000021036 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.5AG0009710, CQ.Regalona.r1.5BG0010130 |
| Anacardiaceae | Pistacia vera | 2 | pistato.v30218360, pistato.v30218370 |
| Apiaceae | Apium graveolens | 2 | Ag4G02647, Ag8G01881 |
| Arecaceae | Cocos nucifera | 1 | COCNU_08G002150 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103706807 |
| Asteraceae | Flaveria trinervia | 1 | Ftri13G23988 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT2G01730.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10005303m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp2g13180.v2.2 |
| Brassicaceae | Brassica nigra | 1 | BniB04g009470.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq05G0129 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl05G0135 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno15g04430 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0152s00021.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate09g05150 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG03.1237 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00002414 |
| Plumbaginaceae | Limonium bicolor | 2 | Lb2G14200, Lb2G14217 |
| Poaceae | Echinochloa crus-galli | 4 | AH03.1841, BH03.2077, CH03.2190, CH03.2191 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_6AG0534520, gene-QOZ80_6BG0487650 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.5HG0478980.1 |
| Poaceae | Lolium multiflorum | 3 | gene-QYE76_004961, gene-QYE76_004980, gene-QYE76_004986 |
| Poaceae | Oryza coarctata | 2 | Oco17G004350, Oco18G004270 |
| Poaceae | Oryza sativa | 1 | LOC_Os09g23380.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_02G176000 |
| Poaceae | Puccinellia tenuiflora | 2 | Pt_Chr0702284, Pt_Chr0702302 |
| Poaceae | Sporobolus alterniflorus | 2 | Chr10G010500, Chr11G011860 |
| Poaceae | Thinopyrum elongatum | 1 | Tel5E01G339500 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC5AG032900, gene_TRIDC5BG034730 |
| Poaceae | Triticum aestivum | 3 | TraesCS5A02G203800.1, TraesCS5B02G202500.1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb159740_P004 |
| Poaceae | Zoysia japonica | 2 | nbis-gene-30905, nbis-gene-57746 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g30275 |
| Portulacaceae | Portulaca oleracea | 3 | evm.TU.LG13.1186, evm.TU.LG21.856, evm.TU.LG21.857 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc07g06310 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_15_RagTag.248 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-26470 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-3468 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-17567 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000001l.153 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00004643 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-11570 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-2705 |
| Salicaceae | Populus euphratica | 1 | populus_peu21214 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132613683 |
| Solanaceae | Solanum chilense | 1 | SOLCI003966400 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107017849 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.17150_chr08_+ |
| Tamaricaceae | Tamarix chinensis | 1 | TC01G3639 |
| Zosteraceae | Zostera marina | 1 | Zosma01g23270.v3.1 |