Basic Information
Locus ID:
Ag5G00446
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
DNA ligase
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr5 | 13813658 | 13825639 | + | Ag5G00446 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.85 | 157,501.03 Da | 42.38 | 85.25 | -0.28 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd07969 | OBF_DNA_ligase_I | 1253 | 1394 | 3.52499E-78 | - |
| CDD | cd16273 | SNM1A-1C-like_MBL-fold | 40 | 188 | 1.15006E-73 | - |
| CDD | cd07900 | Adenylation_DNA_ligase_I_Euk | 1013 | 1247 | 1.41413E-100 | - |
| Pfam | PF04675 | DNA ligase N terminus | 782 | 958 | 2.4E-38 | IPR012308 |
| Pfam | PF04679 | ATP dependent DNA ligase C terminal region | 1270 | 1379 | 6.4E-21 | IPR012309 |
| Pfam | PF07522 | DNA repair metallo-beta-lactamase | 266 | 368 | 6.1E-20 | IPR011084 |
| Pfam | PF01068 | ATP dependent DNA ligase domain | 1024 | 1244 | 1.4E-46 | IPR012310 |
| SUPERFAMILY | SSF56281 | Metallo-hydrolase/oxidoreductase | 65 | 368 | 1.76E-31 | IPR036866 |
| SUPERFAMILY | SSF56091 | DNA ligase/mRNA capping enzyme, catalytic domain | 1018 | 1249 | 3.74E-43 | - |
| SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 1253 | 1397 | 4.11E-41 | IPR012340 |
| SUPERFAMILY | SSF117018 | ATP-dependent DNA ligase DNA-binding domain | 763 | 1007 | 8.37E-74 | IPR036599 |
| Gene3D | G3DSA:3.30.1490.70 | - | 1034 | 1248 | 1.7E-64 | - |
| Gene3D | G3DSA:3.40.50.12650 | - | 191 | 345 | 1.7E-86 | - |
| Gene3D | G3DSA:3.30.470.30 | DNA ligase/mRNA capping enzyme | 1053 | 1184 | 1.7E-64 | - |
| Gene3D | G3DSA:3.60.15.10 | - | 45 | 367 | 1.7E-86 | IPR036866 |
| Gene3D | G3DSA:1.10.3260.10 | - | 762 | 1026 | 2.0E-95 | IPR036599 |
| Gene3D | G3DSA:2.40.50.140 | - | 1249 | 1405 | 7.6E-57 | - |
| TIGRFAM | TIGR00574 | dnl1: DNA ligase I, ATP-dependent (dnl1) | 840 | 1394 | 9.7E-123 | IPR000977 |
| ProSiteProfiles | PS50160 | ATP-dependent DNA ligase family profile. | 1135 | 1282 | 34.840981 | IPR012310 |
| ProSitePatterns | PS00333 | ATP-dependent DNA ligase signature 2. | 1218 | 1244 | - | IPR016059 |
| ProSitePatterns | PS00697 | ATP-dependent DNA ligase AMP-binding site. | 1048 | 1056 | - | IPR016059 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 569 | 588 | - | - |
Gene Ontology
Biological Process:
KEGG Pathway
Pathway:
Reaction:
R00381 (ATP + DNA(n) + 5'-Phospho-DNA(m) <=> AMP + Diphosphate + DNA(n+m))
R00382 (NAD+ + DNA(n) + 5'-Phospho-DNA(m) <=> AMP + Nicotinamide D-ribonucleotide + DNA(n+m))
R10822 (ADP + DNA(n) + 5'-Phospho-DNA(m) <=> AMP + Orthophosphate + DNA(n+m))
R10823 (GTP + DNA(n) + 5'-Phospho-DNA(m) <=> GMP + Diphosphate + DNA(n+m))
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT1G66730.1 | DNA LIGASE 6. Encodes a novel plant specific DNA ligase that is involved in seed germination and DNA repair. | 0 |
| RefSeq | XP_017218765.1 | PREDICTED: DNA ligase 6 isoform X1 [Daucus carota subsp. sativus] | 0 |
| F4HPZ9 | DNA ligase 6 OS=Arabidopsis thaliana OX=3702 GN=LIG6 PE=2 SV=1 | 0 | |
| TrEMBL | A0A164UFC6 | DNA ligase OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_025889 PE=3 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 2.611257 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 3.12534 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 2.534832 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 2.693034 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 3.335999 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 2.404027 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 2.888038 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 2.046954 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 7.257076 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 8.150697 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 8.255819 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 8.100677 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 6.874907 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 6.70692 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 1.875253 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 2.365776 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 2.151128 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 5.072498 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 3.539389 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 3.00706 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 4.500602 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 3.079337 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 2.695455 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 3.295523 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 4.393096 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 5.062338 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 2.420795 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 3.030722 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 4.22043 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 2.133417 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 4.124381 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 2.809836 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 2.726498 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 2.192381 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 1.599678 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 2.007093 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 1.685269 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 2.07987 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 2.061827 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 4.7441 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 4.332433 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 3.638627 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 4.58499 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 7.012573 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 6.600012 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 3.518086 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 4.969203 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 3.940324 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 4.473764 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 3.81813 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 1 | jg39833 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_16634 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah035542 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_2g027400 |
| Amaranthaceae | Salicornia bigelovii | 3 | Sbi_jg20899, Sbi_jg20901, Sbi_jg22882 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg16744 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00008435 |
| Amaranthaceae | Suaeda glauca | 3 | Sgl62191, Sgl62221, Sgl66753 |
| Amaranthaceae | Chenopodium album | 4 | gene:ENSEOMG00000018823, gene:ENSEOMG00000020288 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.2AG0018750, CQ.Regalona.r1.2BG0020440 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30191030 |
| Apiaceae | Apium graveolens | 1 | Ag5G00446 |
| Arecaceae | Cocos nucifera | 1 | COCNU_06G008000 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103705614 |
| Asparagaceae | Asparagus officinalis | 4 | AsparagusV1_01.2163.V1.1, AsparagusV1_04.1989.V1.1 ... |
| Asteraceae | Flaveria trinervia | 1 | Ftri18G06628 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT1G66730.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10018010m.g.v1.0 |
| Brassicaceae | Brassica nigra | 1 | BniB03g043990.2N |
| Casuarinaceae | Casuarina glauca | 1 | Cgl08G0663 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno01g10210 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0865s00004.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate02g36310 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG02.509 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00029645 |
| Plumbaginaceae | Limonium bicolor | 2 | Lb2G15502, Lb6G29725 |
| Poaceae | Echinochloa crus-galli | 3 | AH02.2791, BH02.2921, CH02.3668 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_1BG0079130, gene-QOZ80_1BG0079140 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.3HG0280850.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_054623 |
| Poaceae | Oryza coarctata | 2 | Oco01G017520, Oco02G017750 |
| Poaceae | Oryza sativa | 1 | LOC_Os01g49180.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_03G235400 |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0602385 |
| Poaceae | Sporobolus alterniflorus | 3 | Chr02G012450, Chr03G013700, Chr08G013860 |
| Poaceae | Thinopyrum elongatum | 1 | Tel3E01G440100 |
| Poaceae | Triticum dicoccoides | 3 | gene_TRIDC2BG049630, gene_TRIDC3AG039520 ... |
| Poaceae | Triticum aestivum | 3 | TraesCS3A02G264800.1, TraesCS3B02G298100.1 ... |
| Poaceae | Zea mays | 2 | Zm00001eb156510_P003, Zm00001eb275110_P001 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-12596 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g8446 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG05.760, evm.TU.LG25.564 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc03g19280 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_6_RagTag.1266 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-16235 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-12015 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-1091 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000011l.818 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00007581 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-13482 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-3984 |
| Salicaceae | Populus euphratica | 1 | populus_peu09595 |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132622464 |
| Solanaceae | Solanum chilense | 1 | SOLCI003032800 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107011627 |
| Tamaricaceae | Reaumuria soongarica | 1 | gene_9842 |
| Tamaricaceae | Tamarix chinensis | 1 | TC08G0719 |