Basic Information
Locus ID:
Ag9G00462
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
Polyribonucleotide nucleotidyltransferase
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr9 | 21419601 | 21429265 | - | Ag9G00462 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 6.41 | 108,020.85 Da | 42.36 | 86.41 | -0.34 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd11364 | RNase_PH_PNPase_2 | 377 | 605 | 4.57898E-141 | - |
| CDD | cd11363 | RNase_PH_PNPase_1 | 58 | 285 | 1.18368E-117 | - |
| Pfam | PF03725 | 3' exoribonuclease family, domain 2 | 199 | 261 | 6.6E-10 | IPR015847 |
| Pfam | PF01138 | 3' exoribonuclease family, domain 1 | 377 | 510 | 8.2E-23 | IPR001247 |
| Pfam | PF00575 | S1 RNA binding domain | 680 | 751 | 1.9E-13 | IPR003029 |
| Pfam | PF01138 | 3' exoribonuclease family, domain 1 | 66 | 196 | 6.1E-19 | IPR001247 |
| Pfam | PF03726 | Polyribonucleotide nucleotidyltransferase, RNA binding domain | 294 | 373 | 1.5E-15 | IPR015848 |
| SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 902 | 981 | 6.19E-6 | IPR012340 |
| SUPERFAMILY | SSF55666 | Ribonuclease PH domain 2-like | 190 | 283 | 7.72E-21 | IPR036345 |
| SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 55 | 196 | 1.11E-40 | IPR020568 |
| SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 345 | 549 | 4.71E-48 | IPR020568 |
| SUPERFAMILY | SSF54791 | Eukaryotic type KH-domain (KH-domain type I) | 612 | 677 | 5.61E-6 | IPR036612 |
| SUPERFAMILY | SSF55666 | Ribonuclease PH domain 2-like | 504 | 606 | 1.83E-23 | IPR036345 |
| SUPERFAMILY | SSF46915 | Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | 278 | 380 | 8.24E-22 | IPR036456 |
| SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 670 | 754 | 2.68E-17 | IPR012340 |
| Gene3D | G3DSA:3.30.230.70 | - | 289 | 610 | 6.4E-120 | IPR027408 |
| Gene3D | G3DSA:2.40.50.140 | - | 680 | 754 | 1.7E-21 | - |
| Gene3D | G3DSA:3.30.1370.10 | K Homology domain, type 1 | 611 | 676 | 5.2E-9 | IPR036612 |
| Gene3D | G3DSA:3.30.230.70 | - | 55 | 288 | 2.1E-72 | IPR027408 |
| SMART | SM00322 | kh_6 | 596 | 677 | 0.0023 | IPR004087 |
| SMART | SM00316 | S1_6 | 681 | 751 | 1.5E-19 | IPR022967 |
| SMART | SM00316 | S1_6 | 919 | 982 | 0.015 | IPR022967 |
| TIGRFAM | TIGR03591 | polynuc_phos: polyribonucleotide nucleotidyltransferase | 64 | 752 | 1.2E-236 | IPR012162 |
| ProSiteProfiles | PS50084 | Type-1 KH domain profile. | 614 | 672 | 8.365987 | - |
| ProSiteProfiles | PS50126 | S1 domain profile. | 683 | 751 | 18.243748 | IPR003029 |
| Hamap | MF_01595 | Polyribonucleotide nucleotidyltransferase [pnp]. | 56 | 754 | 25.566389 | IPR012162 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 766 | 865 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 830 | 862 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 803 | 817 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 887 | 914 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 784 | 802 | - | - |
Gene Ontology
Biological Process:
KEGG Pathway
Pathway:
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT5G14580.1 | polyribonucleotide nucleotidyltransferase, putative. | 0 |
| RefSeq | XP_017214738.1 | PREDICTED: polyribonucleotide nucleotidyltransferase 2, mitochondrial isoform X1 [Daucus carota subsp. sativus] | 0 |
| Q9S7G6 | Polyribonucleotide nucleotidyltransferase 2, mitochondrial OS=Arabidopsis thaliana OX=3702 GN=PNP2 PE=1 SV=1 | 0 | |
| TrEMBL | A0A164VVL7 | polyribonucleotide nucleotidyltransferase OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_021710 PE=3 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 5.767147 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 2.953662 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 2.746423 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 2.909292 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 3.097861 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 2.088813 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 1.743457 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 2.389599 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 8.817291 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 8.380648 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 9.917187 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 10.650944 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 8.283814 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 7.557675 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 0.632499 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 2.101888 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 2.058991 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 1.653761 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 1.911466 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 2.640403 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 3.384522 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 3.596327 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 2.980161 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 3.960412 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 4.314581 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 3.161085 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 2.029645 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 2.365413 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 3.976886 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 0.263484 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 0.916387 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 0.891853 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 2.25556 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 3.244857 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 1.854436 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 1.519825 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 0.664481 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 0.321316 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 1.452235 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 1.082076 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 0.335031 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 0.790382 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 0.605648 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 4.53175 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 2.405864 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 2.519098 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 1.630575 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 7.395275 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 6.26651 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 6.638333 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 2 | jg17778, jg40385 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_9801 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah016421 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg40668, Sbi_jg50675 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg2229 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00016587 |
| Amaranthaceae | Suaeda glauca | 4 | Sgl44071, Sgl44073, Sgl48837, Sgl48838 |
| Amaranthaceae | Chenopodium album | 1 | gene:ENSEOMG00000035234 |
| Amaranthaceae | Chenopodium quinoa | 1 | CQ.Regalona.r1.8AG0011440 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30022740 |
| Apiaceae | Apium graveolens | 1 | Ag9G00462 |
| Arecaceae | Cocos nucifera | 1 | COCNU_13G000400 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103711579 |
| Asparagaceae | Asparagus officinalis | 2 | AsparagusV1_08.711.V1.1, AsparagusV1_09.1432.V1.1 |
| Asteraceae | Flaveria trinervia | 1 | Ftri18G02407 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT5G14580.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10012572m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp6g29450.v2.2 |
| Brassicaceae | Brassica nigra | 2 | BniB02g048170.2N, BniB08g007020.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq02G1854 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl02G1935 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno09g07460 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.1098s00001.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate01g15940 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG05.331 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00027857 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb7G34570 |
| Poaceae | Echinochloa crus-galli | 2 | AH07.2622, CH07.2504 |
| Poaceae | Eleusine coracana subsp. coracana | 3 | gene-QOZ80_2AG0137560, gene-QOZ80_2BG0193190 ... |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.6HG0595200.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_023634 |
| Poaceae | Oryza coarctata | 2 | Oco03G015400, Oco04G016040 |
| Poaceae | Oryza sativa | 1 | LOC_Os02g40460.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_04G198400 |
| Poaceae | Puccinellia tenuiflora | 2 | Pt_Chr0204177, Pt_Chr0204677 |
| Poaceae | Sporobolus alterniflorus | 5 | Chr09G025780, Chr0G011210, Chr12G023980, Chr13G007380 ... |
| Poaceae | Thinopyrum elongatum | 1 | Tel6E01G431400 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC6AG034660, gene_TRIDC6BG041310 |
| Poaceae | Triticum aestivum | 3 | TraesCS6A02G228100.1, TraesCS6B02G253600.1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb247190_P001 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-9473 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g13902 |
| Portulacaceae | Portulaca oleracea | 3 | evm.TU.LG05.1564, evm.TU.LG07.1233, evm.TU.LG20.795 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc04g05760 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_3_RagTag.1907 |
| Rhizophoraceae | Carallia pectinifolia | 7 | nbisL1-mrna-2354, nbisL1-mrna-2364, nbisL1-mrna-2368 ... |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-6759 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-3076 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000019l.75 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00002093 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-12047 |
| Salicaceae | Populus euphratica | 1 | populus_peu01056 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132621839 |
| Solanaceae | Solanum chilense | 1 | SOLCI001041000 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107008916 |
| Tamaricaceae | Reaumuria soongarica | 1 | gene_14705 |
| Tamaricaceae | Tamarix chinensis | 1 | TC01G3599 |
| Zosteraceae | Zostera marina | 1 | Zosma06g07070.v3.1 |