Difference between revisions of "Os04g0541700"

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(→‎Evolution)
(→‎Evolution)
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===Evolution===
 
===Evolution===
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Oshox22 belongs to the homeodomain-leucine zipper (HD-Zip) family I of transcription factors. The HD-Zip genes, are an abundant group of transcription factors that are exclusively found in plants<ref name="ref 1"/>The NJ tree (Fig. 5) shows that the HD-Zip genes of family I can be divided into nine clades  as ''α'', ''β''1, ''β''2, ''γ'', ''δ'', ''ε'', ''ζ'', ''φ''1 and ''φ''2<ref name="ref 2"/>. Subfamilies IB, IC and ID all have an intron at the same position in the Zip region. ''Oshox22''belongs to subfamily IB.[[File:HD-ZIP tree.jpg|200px|thumb|left|Fig. 5 Phylogenetic tree showing the predicted relationship between HD-ZIP I, II and III genes from rice, Arabidopsis and C. plantagineum. The tree was created with the PAUP program using Neighbour-joining methods on an amino acid alignment of the complete HD-Zip domains as in Supplemental Figure 2. Family I is subdivided in clades ''α'', ''β''1, ''β''2, ''γ'', ''δ'', ''ε'', ''ζ'', ''φ''1 and ''φ''2<ref name="ref 2"/>. After each gene, the intron subfamily is indicated with a box (family I), circle (family II) and triangle (family III), respectively, in different grey tones or patterns. Below: Subfamily division based on exon-intron organization. The exon-intron pattern is divided into seven subfamilies for family I (IA, IB, IC, ID, IE, IF and IG), and both family II (IIA, IIB, IIC and IID) and III (IIIA, IIIB, IIIC and IIID) have four subfamilies. Open and filled boxes represent coding and conserved domains, respectively. The HD, Zip and START
+
Oshox22 belongs to the homeodomain-leucine zipper (HD-Zip) family I of transcription factors. The HD-Zip genes, are an abundant group of transcription factors that are exclusively found in plants<ref name="ref 1"/>The NJ tree (Fig. 5) shows that the HD-Zip genes of family I can be divided into nine clades  as ''α'', ''β''1, ''β''2, ''γ'', ''δ'', ''ε'', ''ζ'', ''φ''1 and ''φ''2<ref name="ref 2"/>. Subfamilies IB, IC and ID all have an intron at the same position in the Zip region. ''Oshox22''belongs to subfamily IB.[[File:HD-ZIP tree.jpg|200px|frame|left|Fig. 5 Phylogenetic tree showing the predicted relationship between HD-ZIP I, II and III genes from rice, Arabidopsis and C. plantagineum. The tree was created with the PAUP program using Neighbour-joining methods on an amino acid alignment of the complete HD-Zip domains as in Supplemental Figure 2. Family I is subdivided in clades ''α'', ''β''1, ''β''2, ''γ'', ''δ'', ''ε'', ''ζ'', ''φ''1 and ''φ''2<ref name="ref 2"/>. After each gene, the intron subfamily is indicated with a box (family I), circle (family II) and triangle (family III), respectively, in different grey tones or patterns. Below: Subfamily division based on exon-intron organization. The exon-intron pattern is divided into seven subfamilies for family I (IA, IB, IC, ID, IE, IF and IG), and both family II (IIA, IIB, IIC and IID) and III (IIIA, IIIB, IIIC and IIID) have four subfamilies. Open and filled boxes represent coding and conserved domains, respectively. The HD, Zip and START
 
domains are indicated in light grey, dark grey and black, respectively. The position of the introns is shown with black arrowheads. The white arrowhead and star (*) refers to an alternative transcript occurring with Oshox6 in subfamily IB]]
 
domains are indicated in light grey, dark grey and black, respectively. The position of the introns is shown with black arrowheads. The white arrowhead and star (*) refers to an alternative transcript occurring with Oshox6 in subfamily IB]]
  

Revision as of 02:44, 6 June 2014

Gene Os04g0541700,namely Oshox22,means Homeobox-leucine zipper protein HOX22.

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Annotated Information

Function

Please input function information here.

Expression

Expressed in seedlings, roots, stems, leaf sheaths and blades and panicles.

Evolution

Oshox22 belongs to the homeodomain-leucine zipper (HD-Zip) family I of transcription factors. The HD-Zip genes, are an abundant group of transcription factors that are exclusively found in plants[1]The NJ tree (Fig. 5) shows that the HD-Zip genes of family I can be divided into nine clades as α, β1, β2, γ, δ, ε, ζ, φ1 and φ2[2]. Subfamilies IB, IC and ID all have an intron at the same position in the Zip region. Oshox22belongs to subfamily IB.
Fig. 5 Phylogenetic tree showing the predicted relationship between HD-ZIP I, II and III genes from rice, Arabidopsis and C. plantagineum. The tree was created with the PAUP program using Neighbour-joining methods on an amino acid alignment of the complete HD-Zip domains as in Supplemental Figure 2. Family I is subdivided in clades α, β1, β2, γ, δ, ε, ζ, φ1 and φ2[2]. After each gene, the intron subfamily is indicated with a box (family I), circle (family II) and triangle (family III), respectively, in different grey tones or patterns. Below: Subfamily division based on exon-intron organization. The exon-intron pattern is divided into seven subfamilies for family I (IA, IB, IC, ID, IE, IF and IG), and both family II (IIA, IIB, IIC and IID) and III (IIIA, IIIB, IIIC and IIID) have four subfamilies. Open and filled boxes represent coding and conserved domains, respectively. The HD, Zip and START domains are indicated in light grey, dark grey and black, respectively. The position of the introns is shown with black arrowheads. The white arrowhead and star (*) refers to an alternative transcript occurring with Oshox6 in subfamily IB

Labs working on this gene

Please input related labs here.

References

Please input cited references here.

Structured Information

Gene Name

Os04g0541700

Description

Homeodomain-like containing protein

Version

NM_001059981.2 GI:297603098 GeneID:4336542

Length

944 bp

Definition

Oryza sativa Japonica Group Os04g0541700, complete gene.

Source

Oryza sativa Japonica Group 

 ORGANISM  Oryza sativa Japonica Group
           Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
           Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
           clade; Ehrhartoideae; Oryzeae; Oryza.
Chromosome

Chromosome 4

Location

Chromosome 4:27522725..27523668

Sequence Coding Region

27522763..27523206,27523324..27523668

Expression

GEO Profiles:Os04g0541700

Genome Context

<gbrowseImage1> name=NC_008397:27522725..27523668 source=RiceChromosome04 preset=GeneLocation </gbrowseImage1>

Gene Structure

<gbrowseImage2> name=NC_008397:27522725..27523668 source=RiceChromosome04 preset=GeneLocation </gbrowseImage2>

Coding Sequence

<cdnaseq>atggatcggggtgaccaccaccacctccagcagcagcaccagttcttgatgccaccgcctgcgccggtggtgccgccgcagctgtgcatgccggcgatgatggcggacgagcagtacatggacctgggcggtggcggggcggcggcggcgccggggaggggcggggccggggagaggaagcggcggttcacggaggagcagatacggtcgctggagtccatgttccacgcgcaccacgccaagctggagccccgcgagaaggcggagctggcgcgcgagctgggcctgcagccgcggcaggtggccatctggttccagaacaagcgcgcgcggtggcgctccaagcagctcgagcacgactacgccgcactccgctccaagtacgacgccctccactcccgcgtcgagtccctcaagcaagagaagctcgctctcaccgtccagttgcacgagctaagagagaggctgagggaacgggaggagaggagcggcaacggtggtgccgccacgacggcagcaagcagcagcagctgcaacggatcaggcagcgaggaggtcgacgacgacgacgacaagaggaacgccgccgcggggtgcctggacctcgagccgccggagagctgcgtgctcggcggcgcgacgtgcgccacgccggcggacgtgtcggtggagtcggatcagtgcgacgaccagcttgactacgatgagggcttgttcccggagtccttctgcgccacgccggagctgtgggagccatggccgctcgtcgagtggaatgcggtggcttga</cdnaseq>

Protein Sequence

<aaseq>MDRGDHHHLQQQHQFLMPPPAPVVPPQLCMPAMMADEQYMDLGG GGAAAAPGRGGAGERKRRFTEEQIRSLESMFHAHHAKLEPREKAELARELGLQPRQVA IWFQNKRARWRSKQLEHDYAALRSKYDALHSRVESLKQEKLALTVQLHELRERLRERE ERSGNGGAATTAASSSSCNGSGSEEVDDDDDKRNAAAGCLDLEPPESCVLGGATCATP ADVSVESDQCDDQLDYDEGLFPESFCATPELWEPWPLVEWNAVA</aaseq>

Gene Sequence

<dnaseqindica>39..482#600..944#atggtcgaacacagctagctagctgggctaggatcgccatggatcggggtgaccaccaccacctccagcagcagcaccagttcttgatgccaccgcctgcgccggtggtgccgccgcagctgtgcatgccggcgatgatggcggacgagcagtacatggacctgggcggtggcggggcggcggcggcgccggggaggggcggggccggggagaggaagcggcggttcacggaggagcagatacggtcgctggagtccatgttccacgcgcaccacgccaagctggagccccgcgagaaggcggagctggcgcgcgagctgggcctgcagccgcggcaggtggccatctggttccagaacaagcgcgcgcggtggcgctccaagcagctcgagcacgactacgccgcactccgctccaagtacgacgccctccactcccgcgtcgagtccctcaagcaagagaagctcgctctcaccgtccaggtaattaacgatgaattaagcaagctagcttagctactaatcgtaggaacatgcagatcatgtgttccataattaattcaaacgctaacttgattgctctttgcatgtaatatgcagttgcacgagctaagagagaggctgagggaacgggaggagaggagcggcaacggtggtgccgccacgacggcagcaagcagcagcagctgcaacggatcaggcagcgaggaggtcgacgacgacgacgacaagaggaacgccgccgcggggtgcctggacctcgagccgccggagagctgcgtgctcggcggcgcgacgtgcgccacgccggcggacgtgtcggtggagtcggatcagtgcgacgaccagcttgactacgatgagggcttgttcccggagtccttctgcgccacgccggagctgtgggagccatggccgctcgtcgagtggaatgcggtggcttga</dnaseqindica>

External Link(s)

NCBI Gene:Os04g0541700, RefSeq:Os04g0541700

  1. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named ref_1
  2. ↑ 2.0 2.1 Cite error: Invalid <ref> tag; no text was provided for refs named ref_2
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