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- Pseudotsuga menziesii
- Sequence
- PSME_00009907-RA
PSME_00009907-RA
Description : (at2g25170 : 144.0) 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.; PICKLE (PKL); CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF1087 (InterPro:IPR009463), Zinc finger, RING-type (InterPro:IPR001841), Zinc finger, PHD-type, conserved site (InterPro:IPR019786), Zinc finger, PHD-type (InterPro:IPR001965), Protein of unknown function DUF1086 (InterPro:IPR009462), Chromo domain (InterPro:IPR000953), SNF2-related (InterPro:IPR000330), DEAD-like helicase, N-terminal (InterPro:IPR014001), Chromo domain-like (InterPro:IPR016197), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Zinc finger, FYVE/PHD-type (InterPro:IPR011011), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021), Zinc finger, PHD-finger (InterPro:IPR019787); BEST Arabidopsis thaliana protein match is: chromatin remodeling factor, putative (TAIR:AT4G31900.1); Has 20234 Blast hits to 17178 proteins in 1958 species: Archae - 161; Bacteria - 5176; Metazoa - 5098; Fungi - 4334; Plants - 1876; Viruses - 134; Other Eukaryotes - 3455 (source: NCBI BLink). & (reliability: 288.0) & (original description: no original description)
Expression Profile
Attention: This gene has low abundance.
Note:Only the main profile, including all conditions, is shown. Additional statistics and tissue specific profiles are available here.
Co-expression Networks
| Type | Description | Actions |
| Neighborhood | Pseudotsuga release: PSME_00009907-RA | |
Expression Context Conservation (ECC)
| Target | Alias | Description | ECC score | Gene Family Method | Actions |
| 164481 | No alias | P-loop containing nucleoside triphosphate hydrolases... | 0.02 | Orthogroups_2024-Update | |
| 440203 | No alias | chromatin-remodeling protein 11 | 0.01 | Orthogroups_2024-Update | |
| At2g44980 | No alias | Probable helicase CHR10 [Source:UniProtKB/Swiss-Prot;Acc:F4IV45] | 0.03 | Orthogroups_2024-Update | |
| At5g44800 | No alias | PKR1 [Source:UniProtKB/TrEMBL;Acc:A0A178UKW2] | 0.01 | Orthogroups_2024-Update | |
| Bradi1g18910 | No alias | chromatin remodeling 5 | 0.01 | Orthogroups_2024-Update | |
| Brara.J01708.1 | No alias | ATPase component *(CHR11/CHR17) of ISWI chromatin... | 0.02 | Orthogroups_2024-Update | |
| Cre03.g158550 | No alias | chromatin remodeling factor CHD3 (PICKLE) | 0.01 | Orthogroups_2024-Update | |
| Glyma.04G062400 | No alias | chromatin remodeling factor CHD3 (PICKLE) | 0.01 | Orthogroups_2024-Update | |
| Glyma.07G252100 | No alias | P-loop containing nucleoside triphosphate hydrolases... | 0.01 | Orthogroups_2024-Update | |
| Glyma.11G004100 | No alias | Homeotic gene regulator | 0.02 | Orthogroups_2024-Update | |
| Glyma.17G022300 | No alias | P-loop containing nucleoside triphosphate hydrolases... | 0.01 | Orthogroups_2024-Update | |
| HORVU1Hr1G021540.17 | No alias | ATPase component *(CHR11/CHR17) of ISWI chromatin... | 0.02 | Orthogroups_2024-Update | |
| LOC_Os03g01200 | No alias | SNF2 family N-terminal domain containing protein, expressed | 0.01 | Orthogroups_2024-Update | |
| LOC_Os07g31450 | No alias | CHR4/MI-2-LIKE, putative, expressed | 0.01 | Orthogroups_2024-Update | |
| PSME_00001767-RA | No alias | (at5g66750 : 797.0) Protein is similar to SWI2/SNF2... | 0.02 | Orthogroups_2024-Update | |
| Pp1s223_99V6 | No alias | chromodomain helicase dna binding protein 5 | 0.03 | Orthogroups_2024-Update | |
| Pp1s235_76V6 | No alias | chromatin remodeling complex subunit | 0.02 | Orthogroups_2024-Update | |
| Sobic.010G065300.1 | No alias | CHD3-type chromatin remodeling factor *(PKL/PKR) | 0.01 | Orthogroups_2024-Update | |
| Solyc02g068560 | No alias | CHD3-type chromatin-remodeling factor PICKLE (AHRD V3.3... | 0.01 | Orthogroups_2024-Update | |
| Solyc06g065730 | No alias | chromatin remodeling factor CHD3 (PICKLE) (AHRD V3.3 ***... | 0.02 | Orthogroups_2024-Update | |
| Solyc08g029130 | No alias | chromatin remodeling factor CHD3 (PICKLE) (AHRD V3.3 ***... | 0.01 | Orthogroups_2024-Update | |
| evm.model.tig00021623.13 | No alias | (at2g25170 : 464.0) Encodes a SWI/SWF nuclear-localized... | 0.02 | Orthogroups_2024-Update | |
Functional Annotation
| Type | GO Term | Name | Evidence | Source |
| MF | GO:0000166 | nucleotide binding | None | Extended |
| MF | GO:0003674 | molecular_function | None | Extended |
| MF | GO:0005488 | binding | None | Extended |
| MF | GO:0005524 | ATP binding | IEA | InterProScan predictions |
| MF | GO:0008144 | drug binding | None | Extended |
| MF | GO:0017076 | purine nucleotide binding | None | Extended |
| MF | GO:0030554 | adenyl nucleotide binding | None | Extended |
| MF | GO:0032553 | ribonucleotide binding | None | Extended |
| MF | GO:0032555 | purine ribonucleotide binding | None | Extended |
| MF | GO:0032559 | adenyl ribonucleotide binding | None | Extended |
| MF | GO:0035639 | purine ribonucleoside triphosphate binding | None | Extended |
| MF | GO:0036094 | small molecule binding | None | Extended |
| MF | GO:0043167 | ion binding | None | Extended |
| MF | GO:0043168 | anion binding | None | Extended |
| MF | GO:0097159 | organic cyclic compound binding | None | Extended |
| MF | GO:0097367 | carbohydrate derivative binding | None | Extended |
| MF | GO:1901265 | nucleoside phosphate binding | None | Extended |
| MF | GO:1901363 | heterocyclic compound binding | None | Extended |
| Type | GO Term | Name | Evidence | Source |
| CC | GO:0000148 | 1,3-beta-D-glucan synthase complex | IEP | Predicted GO |
| BP | GO:0000271 | polysaccharide biosynthetic process | IEP | Predicted GO |
| MF | GO:0003843 | 1,3-beta-D-glucan synthase activity | IEP | Predicted GO |
| BP | GO:0005976 | polysaccharide metabolic process | IEP | Predicted GO |
| BP | GO:0006073 | cellular glucan metabolic process | IEP | Predicted GO |
| BP | GO:0006074 | (1->3)-beta-D-glucan metabolic process | IEP | Predicted GO |
| BP | GO:0006075 | (1->3)-beta-D-glucan biosynthetic process | IEP | Predicted GO |
| MF | GO:0008194 | UDP-glycosyltransferase activity | IEP | Predicted GO |
| BP | GO:0009250 | glucan biosynthetic process | IEP | Predicted GO |
| BP | GO:0016051 | carbohydrate biosynthetic process | IEP | Predicted GO |
| BP | GO:0033692 | cellular polysaccharide biosynthetic process | IEP | Predicted GO |
| BP | GO:0034637 | cellular carbohydrate biosynthetic process | IEP | Predicted GO |
| MF | GO:0035251 | UDP-glucosyltransferase activity | IEP | Predicted GO |
| BP | GO:0044042 | glucan metabolic process | IEP | Predicted GO |
| BP | GO:0044262 | cellular carbohydrate metabolic process | IEP | Predicted GO |
| BP | GO:0044264 | cellular polysaccharide metabolic process | IEP | Predicted GO |
| CC | GO:0044459 | plasma membrane part | IEP | Predicted GO |
| MF | GO:0046527 | glucosyltransferase activity | IEP | Predicted GO |
| BP | GO:0051273 | beta-glucan metabolic process | IEP | Predicted GO |
| BP | GO:0051274 | beta-glucan biosynthetic process | IEP | Predicted GO |
| CC | GO:0098796 | membrane protein complex | IEP | Predicted GO |
| CC | GO:0098797 | plasma membrane protein complex | IEP | Predicted GO |
| CC | GO:1902494 | catalytic complex | IEP | Predicted GO |
| CC | GO:1990234 | transferase complex | IEP | Predicted GO |
| InterPro domains | Description | Start | Stop |
| IPR000330 | SNF2_N | 42 | 112 |
