Basic Information
Locus ID:
Ag11G03296
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
SNF2 domain-containing protein helicase domain-containing protein RING finger domain-containing protein
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr11 | 9268482 | 9278567 | - | Ag11G03296 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 8.04 | 104,352.26 Da | 43.29 | 78.64 | -0.51 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd18793 | SF2_C_SNF | 749 | 881 | 9.30187E-56 | - |
| CDD | cd18008 | DEXDc_SHPRH-like | 203 | 574 | 2.25182E-80 | - |
| Pfam | PF00176 | SNF2 family N-terminal domain | 219 | 504 | 5.2E-46 | IPR000330 |
| Pfam | PF13923 | Zinc finger, C3HC4 type (RING finger) | 672 | 711 | 1.7E-6 | - |
| Pfam | PF00271 | Helicase conserved C-terminal domain | 758 | 870 | 9.0E-14 | IPR001650 |
| SUPERFAMILY | SSF57850 | RING/U-box | 665 | 716 | 4.01E-14 | - |
| SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 159 | 574 | 1.69E-43 | IPR027417 |
| SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 445 | 924 | 1.83E-57 | IPR027417 |
| Gene3D | G3DSA:3.40.50.300 | - | 596 | 924 | 2.0E-64 | IPR027417 |
| Gene3D | G3DSA:3.40.50.10810 | - | 397 | 595 | 3.4E-26 | IPR038718 |
| Gene3D | G3DSA:3.40.50.10810 | - | 205 | 348 | 3.5E-24 | IPR038718 |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 664 | 738 | 2.6E-12 | IPR013083 |
| SMART | SM00487 | ultradead3 | 199 | 519 | 2.5E-28 | IPR014001 |
| SMART | SM00184 | ring_2 | 672 | 711 | 9.7E-6 | IPR001841 |
| SMART | SM00490 | helicmild6 | 787 | 870 | 8.5E-17 | IPR001650 |
| ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 216 | 501 | 14.627331 | IPR014001 |
| ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 672 | 712 | 12.061441 | IPR001841 |
| ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 752 | 916 | 14.422738 | IPR001650 |
| ProSitePatterns | PS00387 | Inorganic pyrophosphatase signature. | 26 | 32 | - | - |
| ProSitePatterns | PS00518 | Zinc finger RING-type signature. | 687 | 696 | - | IPR017907 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 44 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 18 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 72 | 110 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 378 | 414 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 19 | 40 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 374 | 425 | - | - |
Gene Ontology
Molecular Function:
KEGG Pathway
KO Term:
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT1G05120.1 | Helicase protein with RING/U-box domain. | 0 |
| RefSeq | XP_017258149.1 | PREDICTED: DNA repair protein RAD16-like [Daucus carota subsp. sativus] | 0 |
| P79051 | ATP-dependent helicase rhp16 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=rhp16 PE=3 SV=2 | 0 | |
| TrEMBL | A0A5B7BR46 | Putative DNA repair protein RAD16 OS=Davidia involucrata OX=16924 GN=Din_039802 PE=3 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 55.939899 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 38.343494 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 40.135105 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 41.008224 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 45.020752 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 45.069344 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 42.219166 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 35.945835 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 43.38036 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 42.134739 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 45.511311 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 52.365726 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 50.720753 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 41.756943 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 16.8575 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 20.410034 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 16.710407 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 32.919632 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 30.403172 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 37.80352 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 37.884613 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 23.519548 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 29.504148 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 26.577486 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 31.564409 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 28.395077 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 18.097208 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 23.37468 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 26.50214 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 58.901829 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 34.290638 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 26.27523 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 39.802902 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 26.671848 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 43.144707 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 37.905052 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 31.588345 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 40.37756 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 23.228157 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 19.280716 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 15.796033 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 88.502083 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 100.743736 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 154.159622 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 134.822525 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 67.716637 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 104.498428 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 33.772194 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 42.440769 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 42.386787 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 2 | jg18987, jg18989 |
| Aizoaceae | Mesembryanthemum crystallinum | 2 | gene_14750, gene_25783 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah037464 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_9g208500 |
| Amaranthaceae | Salicornia bigelovii | 3 | Sbi_jg29553, Sbi_jg41818, Sbi_jg48299 |
| Amaranthaceae | Salicornia europaea | 2 | Seu_jg15841, Seu_jg27638 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00028477 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl79171, Sgl81626 |
| Amaranthaceae | Chenopodium album | 2 | gene:ENSEOMG00000037857, gene:ENSEOMG00000052877 |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.9AG0006380, CQ.Regalona.r1.9BG0016040 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30018310 |
| Apiaceae | Apium graveolens | 1 | Ag11G03296 |
| Arecaceae | Cocos nucifera | 2 | COCNU_06G012040, contig69363763G000010 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103717783 |
| Asparagaceae | Asparagus officinalis | 2 | AsparagusV1_03.1174.V1.1, AsparagusV1_03.1175.V1.1 |
| Asteraceae | Flaveria trinervia | 2 | Ftri14G27109, Ftri7G21753 |
| Brassicaceae | Arabidopsis thaliana | 2 | AT1G02670.1, AT1G05120.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10006803m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp1g03980.v2.2 |
| Brassicaceae | Brassica nigra | 3 | BniB03g001220.2N, BniB06g045550.2N, BniB06g045570.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq02G2401 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl02G2476 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno17g00500 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0215s00007.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate01g18950 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG04.2082 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00004420 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb5G28281 |
| Poaceae | Echinochloa crus-galli | 3 | AH03.3136, BH03.3321, CH03.3511 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_7AG0568870, gene-QOZ80_7BG0600540 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.2HG0141740.1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_041052 |
| Poaceae | Oryza coarctata | 2 | Oco13G008410, Oco14G008870 |
| Poaceae | Paspalum vaginatum | 2 | gene-BS78_02G291200, gene-BS78_03G027200 |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0304165 |
| Poaceae | Sporobolus alterniflorus | 2 | Chr08G018520, Chr28G007680 |
| Poaceae | Thinopyrum elongatum | 1 | Tel2E01G417600 |
| Poaceae | Triticum dicoccoides | 3 | gene_TRIDC1BG009870, gene_TRIDC2AG030000 ... |
| Poaceae | Triticum aestivum | 4 | TraesCS1B02G074500.2, TraesCS2A02G224300.1 ... |
| Poaceae | Zea mays | 5 | Zm00001eb046950_P001, Zm00001eb092190_P001 ... |
| Poaceae | Zoysia japonica | 1 | nbis-gene-910 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g6505 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG13.374, evm.TU.LG21.76 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc10g13000 |
| Rhizophoraceae | Bruguiera sexangula | 2 | evm.TU.60414.8, evm.TU.Scaffold_9_RagTag.1591 |
| Rhizophoraceae | Carallia pectinifolia | 2 | nbisL1-mrna-20411, nbisL1-mrna-20488 |
| Rhizophoraceae | Ceriops tagal | 1 | nbisL1-mrna-8822 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-21352 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000003l.844 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-1214 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-4715 |
| Salicaceae | Populus euphratica | 1 | populus_peu27014 |
| Solanaceae | Lycium barbarum | 5 | gene-LOC132617992, gene-LOC132618790, gene-LOC132618966 ... |
| Solanaceae | Solanum chilense | 8 | SOLCI000188200, SOLCI001125800, SOLCI001356700 ... |
| Solanaceae | Solanum pennellii | 7 | gene-LOC107001711, gene-LOC107006318, gene-LOC107018510 ... |
| Tamaricaceae | Reaumuria soongarica | 1 | gene_13800 |
| Tamaricaceae | Tamarix chinensis | 1 | TC01G2324 |