Basic Information
Locus ID:
Pt_Chr0600062
Species & Taxonomic ID:
Puccinellia tenuiflora & 240906
Genome Assembly:
GCA_012064385.1
Description:
Chromatin organization modifier domain
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| Chr06 | 1142190 | 1149636 | - | Pt_Chr0600062 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.38 | 105,292.37 Da | 47.64 | 84.94 | -0.41 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd18793 | SF2_C_SNF | 622 | 733 | 7.95074E-52 | - |
| Pfam | PF00176 | SNF2 family N-terminal domain | 309 | 585 | 1.6E-52 | IPR000330 |
| Pfam | PF00385 | Chromo (CHRromatin Organisation MOdifier) domain | 219 | 252 | 9.6E-7 | IPR023780 |
| Pfam | PF00271 | Helicase conserved C-terminal domain | 609 | 722 | 6.1E-21 | IPR001650 |
| SUPERFAMILY | SSF54160 | Chromo domain-like | 101 | 184 | 2.14E-7 | IPR016197 |
| SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 282 | 516 | 5.67E-53 | IPR027417 |
| SUPERFAMILY | SSF54160 | Chromo domain-like | 195 | 252 | 1.17E-12 | IPR016197 |
| SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 518 | 784 | 2.19E-67 | IPR027417 |
| Gene3D | G3DSA:3.40.50.300 | - | 532 | 806 | 1.6E-92 | IPR027417 |
| Gene3D | G3DSA:2.40.50.40 | - | 130 | 206 | 6.1E-5 | - |
| Gene3D | G3DSA:2.40.50.40 | - | 207 | 265 | 1.8E-7 | - |
| Gene3D | G3DSA:3.40.50.10810 | - | 266 | 531 | 2.2E-81 | IPR038718 |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 78 | 129 | 2.4E-6 | IPR013083 |
| SMART | SM00249 | PHD_3 | 81 | 128 | 7.7E-7 | IPR001965 |
| SMART | SM00298 | chromo_7 | 197 | 268 | 3.9E-5 | IPR000953 |
| SMART | SM00490 | helicmild6 | 638 | 722 | 2.3E-24 | IPR001650 |
| SMART | SM00298 | chromo_7 | 126 | 182 | 11.0 | IPR000953 |
| SMART | SM00487 | ultradead3 | 291 | 491 | 2.0E-32 | IPR014001 |
| ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 82 | 128 | 10.305834 | IPR001841 |
| ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 612 | 769 | 19.685963 | IPR001650 |
| ProSiteProfiles | PS50013 | Chromo and chromo shadow domain profile. | 199 | 275 | 10.5846 | IPR000953 |
| ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 307 | 476 | 20.732395 | IPR014001 |
| ProSitePatterns | PS00690 | DEAH-box subfamily ATP-dependent helicases signature. | 422 | 431 | - | IPR002464 |
| ProSitePatterns | PS01359 | Zinc finger PHD-type signature. | 82 | 127 | - | IPR019786 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 868 | 919 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 14 | 49 | - | - |
Gene Ontology
Molecular Function:
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_047055461.1 | chromodomain-helicase-DNA-binding protein 3-like [Lolium rigidum] | 0 |
| Q9S775 | CHD3-type chromatin-remodeling factor PICKLE OS=Arabidopsis thaliana OX=3702 GN=PKL PE=1 SV=1 | 0 | |
| TrEMBL | A0A453G8A3 | CHD3-type chromatin-remodeling factor PICKLE OS=Aegilops tauschii subsp. strangulata OX=200361 PE=3 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| No sample metadata found. | |||||||
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Asparagaceae | Asparagus officinalis | 1 | AsparagusV1_01.1289.V1.1 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate03g25110 |
| Poaceae | Echinochloa crus-galli | 3 | AH02.4081, BH02.4092, CH02.4119 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.3HG0307470.1 |
| Poaceae | Lolium multiflorum | 2 | gene-QYE76_056785, gene-QYE76_056810 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_03G357300 |
| Poaceae | Puccinellia tenuiflora | 2 | Pt_Chr0600062, Pt_Chr0600096 |
| Poaceae | Sporobolus alterniflorus | 4 | Chr02G003020, Chr05G030190, Chr05G030200, Chr05G030210 |
| Poaceae | Thinopyrum elongatum | 2 | Tel3E01G649400, Tel3E01G649500 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC3AG058130, gene_TRIDC3BG065190 |
| Poaceae | Triticum aestivum | 2 | TraesCS3A02G408500.1, TraesCS3D02G403600.1 |
| Poaceae | Zoysia japonica | 1 | nbis-gene-28559 |
| Poaceae | Zoysia macrostachya | 1 | Zma_g11666 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc01g02460 |
| Zosteraceae | Zostera marina | 1 | Zosma06g19470.v3.1 |