Rice gene details
Searching for LOC_Os09g04890 [histone-lysine N-methyltransferase, H3 lysine-4 specific ATX1, putative, expressed ]
Basic information [Pfam DB] Graphical representation of the protein domains
S. No. Locus Id Protein Length Doman Start Domain End Pfam ID Domain Name
1 LOC_Os09g04890.1 1023 261 340 PF00855.9 PWWP
2 LOC_Os09g04890.1 1023 407 460 PF05964.6 FYRN
3 LOC_Os09g04890.1 1023 465 548 PF05965.6 FYRC
4 LOC_Os09g04890.1 1023 566 615 PF00628.21 PHD
5 LOC_Os09g04890.1 1023 855 986 PF00856.20 SET
  The basic information is from RGAP and Pfam/InterPro databases

Gene model (download)
IR64 N22
Gene Expression (RNASeq data) in two varieties N22 & IR64 [FC=Fold Change]
N22 Flag-leaf FC
  1
N22InfloresenceFC
  -1
N22 Root FC
  3
IR64 Flag-leaf FC
  3
IR64InfloresenceFC
  -1
IR64 Root FC
  1

Functional details
Molecular Function
S. No. GO Id GO Description
1 GO:0042054 histone methyltransferase activity  
2 GO:0042393 histone binding  
3 GO:0003677 DNA binding (RGAP)
4 GO:0016740 transferase activity (RGAP)
Biological process
S. No. GO Id GO Description
1 GO:0016571 histone methylation  
2 GO:2000028 "regulation of photoperiodism, flowering"  
3 GO:0009058 biosynthetic process (RGAP)
4 GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolic process (RGAP)
5 GO:0016043 cellular component organization (RGAP)
6 GO:0006464 protein modification process (RGAP)
Cellular component
S. No. GO Id GO Description
1 GO:0005634 nucleus (RGAP)

Environment details
S. No. EO Id EO Description Presence(+) or absence(-) of gene expression /activity
1 EO:0007196 light regimen (+)
2 MCE:1000203 dark regimen (+)

Metabolic Pathway details
Not found

QTL details
S. No. QTL Id QTL Associated Trait
1 AQEK010 iron sensitivity
2 AQGB064 chalkiness of endosperm
3 AQGB065 chalkiness of endosperm
4 AQGB066 chalkiness of endosperm
5 AQGB067 chalkiness of endosperm
6 AQGB068 chalkiness of endosperm
7 AQGB069 chalkiness of endosperm
8 AQGB070 chalkiness of endosperm
9 AQGB071 chalkiness of endosperm
10 AQGB085 chalkiness of endosperm
11 AQGB086 chalkiness of endosperm
12 AQGB087 chalkiness of endosperm
13 AQGB096 chalkiness of endosperm
14 AQGB097 chalkiness of endosperm
15 AQGB098 chalkiness of endosperm
16 AQGB099 chalkiness of endosperm
17 AQGB100 chalkiness of endosperm
18 AQGB101 chalkiness of endosperm
19 AQGB102 chalkiness of endosperm
20 AQFF030 spikelet number
21 AQFF032 spikelet number
22 AQFF034 spikelet number
23 AQFF037 spikelet number
24 AQFT016 basal root thickness
25 AQFT041 penetrated root thickness
26 CQH29 basal root thickness
27 AQBM008 albino plantlet differentiation frequency
28 AQBY003 root length
29 AQBR002 days to heading
30 AQBK037 spikelet number
31 AQAQ005 blast disease resistance
32 AQAQ014 blast disease resistance
33 AQAQ022 blast disease resistance
34 AQCU149 panicle length
35 AQCU206 plant height
36 AQCU258 spikelet fertility
37 AQFW027 spikelet number
38 AQFW178 spikelet number
39 AQAC016 total biomass yield
40 AQAC023 biomass yield
41 AQCY023 grain yield
42 AQAI067 large vascular bundle number to spikelet number ratio
43 CQAW27 root number

Plant developmental stage / tissue details
Plant development stage
S. No. PO Id PO Description Presence(+) or absence(-) of gene expression /activity
1 MCP:1000518 seedling development stage (+)
2 PO:0007010 6 ripening (+)
3 PO:0007041 inflorescence emergence from flag leaf sheath (+)
Plant tissue/organ
S. No. PO Id PO Description Presence(+) or absence(-) of gene expression /activity
1 MCP:1000412 first leaf from top (+)
2 PO:0000003 whole plant (+)
3 PO:0020039 leaf lamina (+)
4 PO:0025034 leaf (+)
Others
S. No. PO Id PO Description Presence(+) or absence(-) of gene expression /activity
Not found

Trait details
S. No. TO Id TO Description Presence(+) or absence(-) of gene expression /activity
1 TO:0000344 days to flower (+)

Physical interaction details
Interaction type: protein-protein
S. No. Primary rice gene loci

Interacting rice gene loci

Experiment type

Id

Domain name/N or C term

 Amino acid involved in interaction

Id

Domain name/N or C term

 Amino acid involved in interaction
1 LOC_Os09g04890 - --- LOC_Os08g01420 - --- Protein-protein interaction analysis : Co-immunoprecipitation
2 LOC_Os09g04890 - 561-749 LOC_Os08g01420 - --- Protein-protein interaction analysis : Co-immunoprecipitation
Interaction type: protein-DNA
Not found
Related publications [Sorted by year]

1  Choi Sang Chul; Lee Shinyoung; Kim Sung-Ryul; Lee Yang-Seok; Liu Chunyan; Cao Xiaofeng; An Gynheung; Trithorax Group Protein Oryza sativa Trithorax1 Controls Flowering Time in Rice via Interaction with Early heading date3. Plant physiology 2014:164
PMID [24420930]


Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi-110021, India