Basic Information
Locus ID:
Ag3G00776
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
U4 U6 small nuclear ribonucleoprotein PRP4-like protein
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr3 | 23113927 | 23119085 | - | Ag3G00776 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.58 | 66,920.07 Da | 44.74 | 83.36 | -0.40 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd00200 | WD40 | 311 | 589 | 1.19452E-88 | - |
| Pfam | PF00400 | WD domain, G-beta repeat | 383 | 420 | 5.2E-5 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 469 | 504 | 1.3E-9 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 431 | 462 | 3.6E-4 | IPR001680 |
| Pfam | PF08799 | pre-mRNA processing factor 4 (PRP4) like | 175 | 203 | 1.4E-11 | IPR014906 |
| Pfam | PF00400 | WD domain, G-beta repeat | 344 | 379 | 2.8E-5 | IPR001680 |
| Pfam | PF00400 | WD domain, G-beta repeat | 552 | 589 | 1.4E-5 | IPR001680 |
| SUPERFAMILY | SSF158230 | PRP4-like | 153 | 206 | 1.31E-14 | IPR036285 |
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 306 | 588 | 1.05E-84 | IPR036322 |
| Gene3D | G3DSA:2.130.10.10 | - | 286 | 471 | 5.4E-49 | IPR015943 |
| Gene3D | G3DSA:4.10.280.110 | - | 144 | 215 | 2.2E-13 | IPR036285 |
| Gene3D | G3DSA:2.130.10.10 | - | 472 | 602 | 1.6E-38 | IPR015943 |
| SMART | SM00320 | WD40_4 | 298 | 337 | 0.074 | IPR001680 |
| SMART | SM00320 | WD40_4 | 507 | 547 | 1.5E-4 | IPR001680 |
| SMART | SM00320 | WD40_4 | 465 | 504 | 4.8E-11 | IPR001680 |
| SMART | SM00320 | WD40_4 | 381 | 420 | 2.2E-7 | IPR001680 |
| SMART | SM00320 | WD40_4 | 550 | 589 | 2.1E-8 | IPR001680 |
| SMART | SM00500 | pr04_2 | 170 | 223 | 3.6E-16 | IPR014906 |
| SMART | SM00320 | WD40_4 | 340 | 379 | 6.7E-8 | IPR001680 |
| SMART | SM00320 | WD40_4 | 423 | 462 | 4.4E-7 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 388 | 425 | 11.075592 | - |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 430 | 467 | 10.943775 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 514 | 556 | 11.510997 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 388 | 429 | 14.217871 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 347 | 379 | 10.864685 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 430 | 471 | 14.284707 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 472 | 513 | 16.891327 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 557 | 589 | 10.337415 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 557 | 598 | 12.74747 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 514 | 547 | 9.045603 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 347 | 379 | 13.081652 | IPR001680 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 472 | 506 | 13.184673 | - |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 407 | 421 | - | IPR019775 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 491 | 505 | - | IPR019775 |
| ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 449 | 463 | - | IPR019775 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 491 | 505 | 4.9E-6 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 366 | 380 | 4.9E-6 | IPR020472 |
| PRINTS | PR00320 | G protein beta WD-40 repeat signature | 407 | 421 | 4.9E-6 | IPR020472 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 99 | 146 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 119 | 146 | - | - |
Gene Ontology
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT2G41500.1 | WD-40 repeat family protein / small nuclear ribonucleoprotein Prp4p-related. Encodes LACHESIS (LIS), a protein with seven WD40 repeats. LIS is homologous to the yeast splicing factor PRP4 which is associated with the U4/U6 complex of the spliceosome. LIS is involved in a mechanism that prevents accessory cells from adopting gametic cell fate: lis mutant forms supernumerary egg cells. | 0 |
| RefSeq | XP_017248386.1 | PREDICTED: U4/U6 small nuclear ribonucleoprotein PRP4-like protein [Daucus carota subsp. sativus] | 0 |
| O22212 | U4/U6 small nuclear ribonucleoprotein PRP4-like protein OS=Arabidopsis thaliana OX=3702 GN=LIS PE=2 SV=1 | 0 | |
| TrEMBL | A0A165XXA1 | SFM domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_014011 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 38.627014 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 23.850185 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 18.527451 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 18.895033 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 20.751741 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 17.514166 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 19.582424 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 17.611362 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 32.025414 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 32.244953 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 33.612885 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 36.248878 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 32.301746 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 33.033375 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 13.240837 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 13.39908 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 14.898477 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 13.318892 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 12.987327 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 14.016007 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 15.536383 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 20.253702 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 23.128763 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 20.754877 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 19.384459 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 19.107058 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 15.723554 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 16.153345 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 20.811289 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 5.247871 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 9.708556 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 8.001884 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 16.424454 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 13.919382 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 12.712505 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 9.07105 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 6.848598 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 6.634198 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 21.075247 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 8.342134 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 3.90195 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 12.163117 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 14.36565 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 43.35445 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 31.94887 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 18.857107 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 22.304764 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 26.801107 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 22.740202 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 27.503183 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg4297 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_4616 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah022013 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_3g062190 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg59422, Sbi_jg63224 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg23667 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00020750 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl02801, Sgl07928 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000015868, gene:ENSEOMG00000031830 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.3AG0021940, CQ.Regalona.r1.3BG0022730 |
| Anacardiaceae | Pistacia vera | 2 | pistato.v30185870, pistato.v30185920 |
| Apiaceae | Apium graveolens | 1 | Ag3G00776 |
| Arecaceae | Cocos nucifera | 2 | COCNU_04G008580, COCNU_04G008590 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103697000 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_07.1547.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri11G20849 |
| Brassicaceae | Arabidopsis thaliana | 2 | AT2G05720.1, AT2G41500.1 |
| Brassicaceae | Eutrema salsugineum | 2 | Thhalv10000860m.g.v1.0, Thhalv10016457m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp4g23770.v2.2 |
| Brassicaceae | Brassica nigra | 2 | BniB01g004030.2N, BniB06g000680.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq04G0988 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl04G1119 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno10g04910 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0142s00002.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate02g01260 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG01.2511 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00024221 |
| Plumbaginaceae | Limonium bicolor | 4 | Lb2G09059, Lb2G09065, Lb3G21066, Lb4G23346 |
| Poaceae | Echinochloa crus-galli | 3 | AH01.3617, BH01.3965, CH01.4233 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_3AG0248450, gene-QOZ80_3BG0279810 |
| Poaceae | Hordeum vulgare | 2 | HORVU.MOREX.r3.2HG0127160.1.CDS1 ... |
| Poaceae | Lolium multiflorum | 2 | gene-QYE76_003868, gene-QYE76_067869 |
| Poaceae | Oryza coarctata | 2 | Oco05G013690, Oco06G012690 |
| Poaceae | Oryza sativa | 1 | LOC_Os03g23935.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_01G352500 |
| Poaceae | Sporobolus alterniflorus | 4 | Chr01G034800, Chr04G011460, Chr07G010890, Chr12G004840 |
| Poaceae | Thinopyrum elongatum | 2 | Tel2E01G344100, Tel4E01G250400 |
| Poaceae | Triticum dicoccoides | 4 | gene_TRIDC2AG022360, gene_TRIDC2BG025830 ... |
| Poaceae | Triticum aestivum | 6 | TraesCS2A02G175200.1, TraesCS2B02G201600.1.cds1 ... |
| Poaceae | Zea mays | 2 | Zm00001eb017050_P005, Zm00001eb344450_P001 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-3317 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g3655 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG07.432, evm.TU.LG15.511 |
| Posidoniaceae | Posidonia oceanica | 2 | gene.Posoc06g21700, gene.Posoc07g10130 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_1_RagTag.1126 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-6486 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-16593 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-21088 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000016l.830 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00016797 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-11016 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-13329 |
| Salicaceae | Populus euphratica | 2 | populus_peu10900, populus_peu26220 |
| Solanaceae | Lycium barbarum | 2 | gene-LOC132612576, gene-LOC132613932 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107017856 |
| Tamaricaceae | Reaumuria soongarica | 1 | gene_5107 |
| Tamaricaceae | Tamarix chinensis | 1 | TC06G2514 |
| Zosteraceae | Zostera marina | 1 | Zosma05g18040.v3.1 |