Basic Information
Locus ID:
Ag6G00331
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
pre-mRNA-processing factor
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr6 | 10365604 | 10368647 | + | Ag6G00331 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 6.77 | 65,393.51 Da | 39.41 | 65.12 | -0.73 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd00200 | WD40 | 279 | 578 | 2.00902E-67 | - |
| Pfam | PF00400 | WD domain, G-beta repeat | 541 | 578 | 0.14 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 278 | 316 | 3.6E-6 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 321 | 359 | 1.2E-6 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 500 | 535 | 0.037 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 407 | 444 | 0.0013 | IPR001680 |
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 274 | 578 | 4.95E-72 | IPR036322 |
| Gene3D | G3DSA:2.130.10.10 | - | 262 | 578 | 1.1E-96 | IPR015943 |
| SMART | SM00320 | WD40_4 | 362 | 403 | 3.6 | IPR001680 |
| SMART | SM00320 | WD40_4 | 449 | 488 | 14.0 | IPR001680 |
| SMART | SM00320 | WD40_4 | 494 | 535 | 0.42 | IPR001680 |
| SMART | SM00320 | WD40_4 | 538 | 578 | 5.4E-5 | IPR001680 |
| SMART | SM00320 | WD40_4 | 406 | 445 | 4.1E-6 | IPR001680 |
| SMART | SM00320 | WD40_4 | 320 | 359 | 9.8E-11 | IPR001680 |
| SMART | SM00320 | WD40_4 | 276 | 316 | 7.1E-9 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 545 | 578 | 8.861059 | - |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 413 | 445 | 10.495596 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 545 | 578 | 8.870959 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 327 | 364 | 11.681953 | - |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 283 | 317 | 10.943775 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 413 | 445 | 12.613797 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 283 | 317 | 13.181907 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 327 | 368 | 15.554599 | IPR001680 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 303 | 317 | - | IPR019775 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 432 | 446 | 1.4E-5 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 346 | 360 | 1.4E-5 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 303 | 317 | 1.4E-5 | IPR020472 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 186 | 208 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 157 | 176 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 157 | 208 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 224 | 254 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 13 | 30 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 39 | - | - |
| Coils | Coil | Coil | 154 | 174 | - | - |
Gene Ontology
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT1G10580.1 | Transducin/WD40 repeat-like superfamily protein. | 0 |
| RefSeq | XP_017236247.1 | PREDICTED: pre-mRNA-processing factor 17 isoform X1 [Daucus carota subsp. sativus] | 0 |
| Q9DC48 | Pre-mRNA-processing factor 17 OS=Mus musculus OX=10090 GN=Cdc40 PE=1 SV=1 | 0 | |
| TrEMBL | A0A162AUX5 | WD_REPEATS_REGION domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_007090 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 30.950201 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 27.92466 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 30.18438 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 30.806614 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 30.740183 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 29.355396 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 32.475487 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 24.364746 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 47.226078 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 50.195435 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 51.136665 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 60.595501 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 56.481812 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 49.202477 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 13.453729 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 14.124617 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 14.23173 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 16.954599 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 14.775957 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 17.217371 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 14.059711 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 20.696596 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 19.861837 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 14.271856 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 20.225651 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 19.668346 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 17.51433 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 17.637157 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 18.882662 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 14.91622 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 17.451912 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 17.60055 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 35.570946 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 30.117489 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 43.458721 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 25.780622 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 18.379911 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 20.347412 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 24.523802 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 15.549358 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 11.742317 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 24.298826 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 18.138384 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 23.441204 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 22.532701 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 24.022375 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 17.56934 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 24.807825 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 25.754158 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 24.180763 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg9462 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_18136 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah013553 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_6g148920 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg42936, Sbi_jg45548 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg11394 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00002406 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl35361, Sgl40715 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000000484, gene:ENSEOMG00000012586 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.6AG0005420, CQ.Regalona.r1.6BG0005650 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30222460 |
| Apiaceae | Apium graveolens | 2 | Ag1G01332, Ag6G00331 |
| Arecaceae | Cocos nucifera | 1 | COCNU_09G004460 |
| Arecaceae | Phoenix dactylifera | 2 | gene-LOC103719239, gene-LOC103722596 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_07.2668.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri13G30231 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT1G10580.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10007215m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 2 | Sp1g09240.v2.2, Sp4g02400.v2.2 |
| Brassicaceae | Brassica nigra | 1 | BniB04g029020.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq07G0805 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl07G0859 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno15g02700 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0324s00009.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate01g02430 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG05.496 |
| Plantaginaceae | Plantago ovata | 3 | Pov_00022407, Pov_00036359, Pov_00036379 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb1G06529 |
| Poaceae | Echinochloa crus-galli | 1 | CH01.3977 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_3AG0251290, gene-QOZ80_3BG0277070 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.4HG0370350.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_059173 |
| Poaceae | Oryza coarctata | 2 | Oco05G015340, Oco06G015840 |
| Poaceae | Oryza sativa | 1 | LOC_Os03g27970.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_01G336700 |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0105195 |
| Poaceae | Sporobolus alterniflorus | 3 | Chr01G024650, Chr04G012940, Chr07G012400 |
| Poaceae | Thinopyrum elongatum | 1 | Tel4E01G265700 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC4AG025020, gene_TRIDC4BG027160 |
| Poaceae | Triticum aestivum | 3 | TraesCS4A02G160700.1, TraesCS4B02G157400.1 ... |
| Poaceae | Zea mays | 2 | Zm00001eb019350_P001, Zm00001eb392750_P001 |
| Poaceae | Zoysia japonica | 2 | nbis-gene-12064, nbis-gene-43535 |
| Poaceae | Zoysia macrostachya | 2 | Zma_g1056, Zma_g3413 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG03.398, evm.TU.LG12.1309 |
| Posidoniaceae | Posidonia oceanica | 3 | gene.Posoc01g00430, gene.Posoc01g00440, gene.Posoc01g00450 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_17_RagTag.246 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-23087 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-11676 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-14775 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000013l.171 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00006623 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-7078 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-15851 |
| Salicaceae | Populus euphratica | 2 | populus_peu07578, populus_peu21612 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132623630 |
| Solanaceae | Solanum chilense | 1 | SOLCI002314700 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107011665 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.9170_chr03_+ |
| Zosteraceae | Zostera marina | 1 | Zosma01g19950.v3.1 |