LXL04_022958 | RubberDandelionOmics

Gene overview

LXL04_022958

Reference: OH-1004 Chr: Chr05 Coordinates: 15140563-15145030 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2829 bp · LXL04_022958|LXL04_022958|OH1004|cDNA

ATGGCTGGGAGTTCTAGTGAAGAGTCTGGGGTTAGCAGATCATTAGAAGGATTATCAAATGGGCAGCAGCGTTCTGGTGAAGCATTGGCTGAATGGAGGTCTTCTGAGCAAGTTGAGAATGGAATCACTTCAACTTCACCTCCTTACTGGGATactgatgatgatgatgattgtGGACCAAAGCCTTCTGAGTTATATGGAAAGTATACATGGAAGATAGACAAGTTCTCACAAATTAACAAGAGAGAGCTTCGTAGCAA...

CDS

Download CDS FASTA

2829 bp · LXL04_022958|LXL04_022958|OH1004|CDS

ATGGCTGGGAGTTCTAGTGAAGAGTCTGGGGTTAGCAGATCATTAGAAGGATTATCAAATGGGCAGCAGCGTTCTGGTGAAGCATTGGCTGAATGGAGGTCTTCTGAGCAAGTTGAGAATGGAATCACTTCAACTTCACCTCCTTACTGGGATACTGATGATGATGATGATTGTGGACCAAAGCCTTCTGAGTTATATGGAAAGTATACATGGAAGATAGACAAGTTCTCACAAATTAACAAGAGAGAGCTTCGTAGCAA...

Protein

Download Protein FASTA

942 aa · LXL04_022958|LXL04_022958|OH1004|PROTEIN

MAGSSSEESGVSRSLEGLSNGQQRSGEALAEWRSSEQVENGITSTSPPYWDTDDDDDCGPKPSELYGKYTWKIDKFSQINKRELRSNAFEVGGYKWYILIYPQGCDVCNHLSLFLCVANHDKLLPGWSHFAQFTIAVVNKDPKKSKYSDTLHRFWKKEHDWGWKKFMELSKVLDGFVDADTLIIKAQVQVIRERADRPFRCLDCQYRRELVRVYLSNVEQICRRFVEERRGRLGKLIEDKVRWSSFCGFWSGIDQNSRRR...

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_022958`
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_022958

Location Chr05:15140563-15145030 (+)

Description Similar to TRAF1B: TNF receptor-associated factor homolog 1b

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g04300`	Functions redundantly with TRAF1A in the regulation of plant immune response.	TRAF Family Proteins Regulate Autophagy Dynamics by Modulating AUTOPHAGY PROTEIN6 Stability in Arabidopsis.2017 · DOI: 10.1105/tpc.17.00056
`At5g43560`	Functions redundantly with TRAF1B in the regulation of plant immune response.	TRAF Family Proteins Regulate Autophagy Dynamics by Modulating AUTOPHAGY PROTEIN6 Stability in Arabidopsis.2017 · DOI: 10.1105/tpc.17.00056
`At3g11910`	Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin.	No verified direct reference in this release
`At5g06600`	Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin.	No verified direct reference in this release
`At3g58210`	MATH domain and coiled-coil domain-containing protein At3g58210.	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_022958 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006508 proteolysis Biological Process

GO:0009867 jasmonic acid mediated signaling pathway Biological Process

GO:0010078 maintenance of root meristem identity Biological Process

GO:0016579 protein deubiquitination Biological Process

GO:0031647 regulation of protein stability Biological Process

GO:0045087 innate immune response Biological Process

GO:0070646 protein modification by small protein removal Biological Process

GO:1905037 autophagosome organization Biological Process

GO:2000280 regulation of root development Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT1G04300

ath:AT3G11910

ath:AT3G58210

ath:AT5G06600

ath:AT5G43560

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.

Cytoplasm0.464

Rank 1 · LXL04_022958 · OH-1004

Nucleus0.446

Rank 2 · LXL04_022958 · OH-1004

Cell membrane0.273

Rank 3 · LXL04_022958 · OH-1004

Endoplasmic reticulum0.057

Rank 4 · LXL04_022958 · OH-1004

Golgi apparatus0.044

Rank 5 · LXL04_022958 · 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.

PF22486.3MATH_268-188 aa

PF00917.33MATH73-190 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022958	`PF22486.3`	MATH_2	68	188	1.6e-33	116.6
LXL04_022958	`PF00917.33`	MATH	73	190	3.9e-22	79.4

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
`A8MQL1`	Arabidopsis thaliana	TNF receptor-associated factor homolog 1b	45.438%	Swiss-Prot	moderate database homology
`Q8RY18`	Arabidopsis thaliana	TNF receptor-associated factor homolog 1a	47.680%	Swiss-Prot	moderate database homology
`Q84WU2`	Arabidopsis thaliana	Ubiquitin C-terminal hydrolase 13	44.094%	Swiss-Prot	weak database homology
`Q9FPT1`	Arabidopsis thaliana	Ubiquitin C-terminal hydrolase 12	44.094%	Swiss-Prot	weak database homology
`Q9M2J5`	Arabidopsis thaliana	MATH domain and coiled-coil domain-containing protein At3g58210	39.231%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card