Basic Information
Locus ID:
nbisL1-mrna-3742
Species & Taxonomic ID:
Rhizophora apiculata & 106626
Genome Assembly:
GCA_037832385.1
Description:
CHD3-type chromatin-remodeling factor
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr10 | 1945997 | 1965202 | + | nbisL1-mrna-3742 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.46 | 162,939.77 Da | 42.36 | 81.75 | -0.61 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd18660 | CD1_tandem | 102 | 172 | 7.47864E-19 | - |
| CDD | cd18793 | SF2_C_SNF | 604 | 730 | 9.78648E-57 | - |
| CDD | cd18659 | CD2_tandem | 190 | 240 | 7.36952E-18 | - |
| Pfam | PF06461 | Domain of Unknown Function (DUF1086) | 933 | 1063 | 2.0E-52 | IPR009462 |
| Pfam | PF00176 | SNF2 family N-terminal domain | 304 | 582 | 2.4E-64 | IPR000330 |
| Pfam | PF06465 | Domain of Unknown Function (DUF1087) | 841 | 901 | 4.1E-23 | IPR009463 |
| Pfam | PF00271 | Helicase conserved C-terminal domain | 607 | 719 | 2.8E-17 | IPR001650 |
| Pfam | PF00385 | Chromo (CHRromatin Organisation MOdifier) domain | 193 | 240 | 7.6E-12 | IPR023780 |
| Pfam | PF00628 | PHD-finger | 54 | 96 | 1.2E-8 | IPR019787 |
| Pfam | PF00385 | Chromo (CHRromatin Organisation MOdifier) domain | 102 | 157 | 5.8E-10 | IPR023780 |
| SUPERFAMILY | SSF54160 | Chromo domain-like | 186 | 241 | 5.68E-12 | IPR016197 |
| SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 518 | 777 | 2.84E-66 | IPR027417 |
| SUPERFAMILY | SSF54160 | Chromo domain-like | 66 | 176 | 2.2E-19 | IPR016197 |
| SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 273 | 516 | 7.66E-54 | IPR027417 |
| Gene3D | G3DSA:1.10.10.60 | - | 1033 | 1195 | 1.1E-9 | - |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 44 | 97 | 3.4E-14 | IPR013083 |
| Gene3D | G3DSA:2.40.50.40 | - | 98 | 196 | 2.3E-17 | - |
| Gene3D | G3DSA:2.40.50.40 | - | 197 | 240 | 9.3E-13 | - |
| Gene3D | G3DSA:3.40.50.10810 | - | 275 | 525 | 5.6E-198 | IPR038718 |
| Gene3D | G3DSA:3.40.50.300 | - | 526 | 750 | 5.6E-198 | IPR027417 |
| SMART | SM00249 | PHD_3 | 53 | 96 | 6.9E-12 | IPR001965 |
| SMART | SM00298 | chromo_7 | 99 | 168 | 2.7E-7 | IPR000953 |
| SMART | SM00298 | chromo_7 | 190 | 243 | 3.4E-10 | IPR000953 |
| SMART | SM01147 | DUF1087_2 | 840 | 905 | 4.9E-24 | IPR009463 |
| SMART | SM00487 | ultradead3 | 279 | 492 | 9.2E-33 | IPR014001 |
| SMART | SM01146 | DUF1086_2 | 910 | 1066 | 3.8E-70 | IPR009462 |
| SMART | SM00490 | helicmild6 | 635 | 719 | 5.4E-23 | IPR001650 |
| ProSiteProfiles | PS50013 | Chromo and chromo shadow domain profile. | 100 | 182 | 11.507701 | IPR000953 |
| ProSiteProfiles | PS50016 | Zinc finger PHD-type profile. | 51 | 98 | 9.997299 | IPR019787 |
| ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 295 | 481 | 23.002148 | IPR014001 |
| ProSiteProfiles | PS50013 | Chromo and chromo shadow domain profile. | 192 | 250 | 9.154701 | IPR000953 |
| ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 609 | 770 | 18.779713 | IPR001650 |
| ProSiteProfiles | PS50903 | Rubredoxin-like domain profile. | 61 | 105 | 8.11852 | IPR024934 |
| ProSitePatterns | PS01359 | Zinc finger PHD-type signature. | 54 | 95 | - | IPR019786 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1138 | 1159 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1403 | 1427 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 890 | 949 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1341 | 1361 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1341 | 1366 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1405 | 1427 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 901 | 922 | - | - |
Gene Ontology
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT2G25170.1 | chromatin remodeling factor CHD3 (PICKLE). Encodes a SWI/SWF nuclear-localized chromatin remodeling factor of the CHD3 group. Involved in post-germination repression of embryonic development. Acts with GA to establish repression of embryonic genes upon germination. Protein preferentially accumulates in differentiating tissues. Loss of function alleles are associated with expression of embryonic traits in adult plants and derepression of embryonic genes such as PHEROS1. Is an extragenic suppressor of slr2 (SSL2). Mutations in PKL (SSL2) restores lateral root formation in the slr2 mutant slr-1. It was proposed that PKL/SSL2-mediated chromatin remodeling negatively regulates auxin-mediated LR formation in Arabidopsis. | 0 |
| RefSeq | XP_021640843.1 | CHD3-type chromatin-remodeling factor PICKLE-like [Hevea brasiliensis] | 0 |
| Q9S775 | CHD3-type chromatin-remodeling factor PICKLE OS=Arabidopsis thaliana OX=3702 GN=PKL PE=1 SV=1 | 0 | |
| TrEMBL | A0A2P2L862 | CHD3-type chromatin-remodeling factor PICKLE OS=Rhizophora mucronata OX=61149 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| No sample metadata found. | |||||||
Network
No network data available for this species.
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 2 | jg24036, jg36561 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_13270 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah034823 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_2g031220 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg21073, Sbi_jg22724 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg16603 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00018284 |
| Amaranthaceae | Suaeda glauca | 3 | Sgl62396, Sgl66943, Sgl66945 |
| Amaranthaceae | Chenopodium album | 6 | gene:ENSEOMG00000016795, gene:ENSEOMG00000018331 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.1BG0021900, CQ.Regalona.r1.2AG0023680 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30250780 |
| Apiaceae | Apium graveolens | 2 | Ag6G01340, Ag7G01355 |
| Arecaceae | Cocos nucifera | 1 | COCNU_01G005290 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103714226 |
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_08.1846.V1.1 |
| Asteraceae | Flaveria trinervia | 2 | Ftri11G19512, Ftri12G11603 |
| Brassicaceae | Arabidopsis thaliana | 2 | AT2G25170.1, AT4G31900.1 |
| Brassicaceae | Eutrema salsugineum | 2 | Thhalv10000014m.g.v1.0, Thhalv10027006m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 2 | Sp4g04150.v2.2, Sp7g29720.v2.2 |
| Brassicaceae | Brassica nigra | 2 | BniB02g023330.2N, BniB02g085630.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq04G2427 |
| Casuarinaceae | Casuarina glauca | 2 | Cgl04G2631, Cgl04G2660 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno01g06310 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0001s00013.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate04g29410 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG07.1510 |
| Plantaginaceae | Plantago ovata | 2 | Pov_00006955, Pov_00013937 |
| Plumbaginaceae | Limonium bicolor | 1 | Lb3G17059 |
| Poaceae | Echinochloa crus-galli | 2 | BH06.610, CH06.624 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_6AG0511350, gene-QOZ80_6BG0463330 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.7HG0658830.1 |
| Poaceae | Lolium multiflorum | 2 | gene-QYE76_028191, gene-QYE76_028236 |
| Poaceae | Oryza coarctata | 2 | Oco11G003860, Oco12G003850 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_10G065800 |
| Poaceae | Puccinellia tenuiflora | 3 | Pt_Chr0405231, Pt_Chr0405252, Pt_Chr0405255 |
| Poaceae | Sporobolus alterniflorus | 3 | Chr11G021470, Chr14G002860, Chr21G002040 |
| Poaceae | Thinopyrum elongatum | 1 | Tel7E01G299600 |
| Poaceae | Triticum aestivum | 3 | TraesCS7A02G147100.2, TraesCS7B02G050100.3 ... |
| Poaceae | Zoysia japonica | 2 | nbis-gene-34880, nbis-gene-4997 |
| Poaceae | Zoysia macrostachya | 2 | Zma_g29235, Zma_g31473 |
| Portulacaceae | Portulaca oleracea | 4 | evm.TU.LG05.1548, evm.TU.LG07.1217, evm.TU.LG07.596 ... |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc03g12610 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_10_RagTag.892 |
| Rhizophoraceae | Carallia pectinifolia | 1 | nbisL1-mrna-13581 |
| Rhizophoraceae | Ceriops tagal | 2 | nbisL1-mrna-20561, nbisL1-mrna-838 |
| Rhizophoraceae | Ceriops zippeliana | 1 | nbisL1-mrna-9145 |
| Rhizophoraceae | Kandelia candel | 1 | evm.TU.utg000004l.200 |
| Rhizophoraceae | Kandelia obovata | 1 | Maker00003979 |
| Rhizophoraceae | Rhizophora apiculata | 1 | nbisL1-mrna-3742 |
| Rhizophoraceae | Rhizophora mangle | 1 | nbisL1-mrna-7816 |
| Salicaceae | Populus euphratica | 2 | populus_peu04702, populus_peu12984 |
| Solanaceae | Lycium barbarum | 2 | gene-LOC132636060, gene-LOC132643757 |
| Solanaceae | Solanum chilense | 2 | SOLCI006571200, SOLCI006784900 |
| Solanaceae | Solanum pennellii | 2 | gene-LOC107023146, gene-LOC107028501 |
| Tamaricaceae | Reaumuria soongarica | 2 | gene_17290, gene_6399 |
| Tamaricaceae | Tamarix chinensis | 2 | TC01G0997, TC06G0063 |
| Zosteraceae | Zostera marina | 1 | Zosma03g06310.v3.1 |