LXL04_024946 | RubberDandelionOmics

Gene overview

LXL04_024946

Reference: OH-1004 Chr: Chr05 Coordinates: 102615440-102618754 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1305 bp · LXL04_024946|LXL04_024946|OH1004|cDNA

ATGGCTGGACCATCATGGGTGGTTGACAAGAACAGAATTGCAACAAAGATTAGAAGCGCATCTGGTTCATGTGATCCTGAACATATCAATTGGAAAAGCAACCCCACTAAAACATGCCCTAATTGCCACCATGTGGTCGATAATAGTGATGTTAATCAAGCATGGCCCGGGTTGCCCCGTGGGGTGAAATTCGACCCACTGGATCATGAAATTATGTGGCATTTACTTGCCAAAAGTGGCGTACACAATTTTCCACCTCA...

CDS

Download CDS FASTA

1305 bp · LXL04_024946|LXL04_024946|OH1004|CDS

ATGGCTGGACCATCATGGGTGGTTGACAAGAACAGAATTGCAACAAAGATTAGAAGCGCATCTGGTTCATGTGATCCTGAACATATCAATTGGAAAAGCAACCCCACTAAAACATGCCCTAATTGCCACCATGTGGTCGATAATAGTGATGTTAATCAAGCATGGCCCGGGTTGCCCCGTGGGGTGAAATTCGACCCACTGGATCATGAAATTATGTGGCATTTACTTGCCAAAAGTGGCGTACACAATTTTCCACCTCA...

Protein

Download Protein FASTA

434 aa · LXL04_024946|LXL04_024946|OH1004|PROTEIN

MAGPSWVVDKNRIATKIRSASGSCDPEHINWKSNPTKTCPNCHHVVDNSDVNQAWPGLPRGVKFDPLDHEIMWHLLAKSGVHNFPPHPFIDEFIPTVEEDDGICYTHPQKLPGVQQDGSVSHFFHRAIKAYQTGTRKRRKIHGDDFGYFRWHKTGRTKPVILDNIQRGCKKIMVLYVSPVKGGKSEKTNWVMHQYHLGTGEDEKEGDYVISKVFYQQQSQSQLQSVKSNGKDDDVIIEEVNVPVEKVDPVTPTSVTPEPP...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`LXL04_024946`
TK1151 ID	TkA06G094470
OH-1004 ID	LXL04_024946
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.500
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_024946

Location Chr05:102615440-102618754 (+)

Description Similar to SOG1: SUPPRESSOR OF GAMMA RESPONSE 1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g25580`	Transcription factor regulating the transcriptional activation response to gamma irradiation.	Suppressor of gamma response 1 (SOG1) encodes a putative transcription factor governing multiple responses to DNA damage.2009 · DOI: 10.1073/pnas.0810304106 A shared DNA-damage-response pathway for induction of stem-cell death by UVB and by gamma irradiation.2010 · DOI: 10.1016/j.dnarep.2010.06.006 Arabidopsis casein kinase 2 triggers stem cell exhaustion under Al toxicity and phosphate deficiency through activating the DNA damage response pathway.2021 · DOI: 10.1093/plcell/koab005
`At4g29230`	Transcription activator involved in xylem formation.	No verified direct reference in this release
`At1g28470`	Transcriptional activator that plays a regulatory role in the development of secondary cell wall fibers.	A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis.2008 · DOI: 10.1105/tpc.108.061325
`At4g28500`	Transcriptional activator that plays a regulatory role in the development of secondary cell wall fibers.	A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis.2008 · DOI: 10.1105/tpc.108.061325 SND2, a NAC transcription factor gene, regulates genes involved in secondary cell wall development in Arabidopsis fibres and increases fibre cell area in Eucalyptus.2011 · DOI: 10.1186/1471-2229-11-173
`At1g01720`	NAC domain-containing protein 2.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_024946 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000077 DNA damage checkpoint signaling Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0009611 response to wounding Biological Process

GO:0009788 negative regulation of abscisic acid-activated signaling pathway Biological Process

GO:0010321 regulation of vegetative phase change Biological Process

GO:0010332 response to gamma radiation Biological Process

GO:0040020 regulation of meiotic nuclear division Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

GO:0071456 cellular response to hypoxia Biological Process

GO:0071555 cell wall organization Biological Process

GO:1905177 tracheary element differentiation Biological Process

KEGG gene cross-reference

ath:AT1G01720

ath:AT1G25580

ath:AT1G28470

ath:AT4G28500

ath:AT4G29230

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene

Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Nucleus0.955

Rank 1 · LXL04_024946 · OH-1004

Cytoplasm0.118

Rank 2 · LXL04_024946 · OH-1004

Cell membrane0.033

Rank 3 · LXL04_024946 · OH-1004

Endoplasmic reticulum0.027

Rank 4 · LXL04_024946 · OH-1004

Plastid0.014

Rank 5 · LXL04_024946 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF02365.21NAM59-197 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_024946	`PF02365.21`	NAM	59	197	1.6e-23	84.2

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q6NQK2`	Arabidopsis thaliana	SUPPRESSOR OF GAMMA RESPONSE 1	57.018%	Swiss-Prot	strong database homology
`Q9M0F8`	Arabidopsis thaliana	NAC domain-containing protein 75	58.333%	Swiss-Prot	weak database homology
`F4HY61`	Arabidopsis thaliana	NAC domain-containing protein 10	52.036%	Swiss-Prot	weak database homology
`O49459`	Arabidopsis thaliana	NAC domain-containing protein 73	50.000%	Swiss-Prot	moderate database homology
`Q39013`	Arabidopsis thaliana	NAC domain-containing protein 2	33.803%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card