LXL04_013838 | RubberDandelionOmics

Gene overview

LXL04_013838

Reference: OH-1004 Chr: Chr03 Coordinates: 36678809-36680856 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

909 bp · LXL04_013838|LXL04_013838|OH1004|cDNA

ATGCATTGTTGGTTTGATGTACTTCCTTCCCTACACCTTCTTTCAGCGACACACTATTTTACTCTCTTGTGGGTAAACAATACGCCAACCGTGACTAAACCCGTGAGCCTTTCAAACCCTCTCTGCATCTTTCAATCTCAATATACACCTGAAGTTCTTTCCAGAAATCTCTTAGCAACTGATTCAGAAATGGAGTTTTTCACACACTCTTCTCATCCTCCCCGTTCGTCTTCACAGACTTCTGAGTTTTCGTTTGGAAA...

CDS

Download CDS FASTA

909 bp · LXL04_013838|LXL04_013838|OH1004|CDS

ATGCATTGTTGGTTTGATGTACTTCCTTCCCTACACCTTCTTTCAGCGACACACTATTTTACTCTCTTGTGGGTAAACAATACGCCAACCGTGACTAAACCCGTGAGCCTTTCAAACCCTCTCTGCATCTTTCAATCTCAATATACACCTGAAGTTCTTTCCAGAAATCTCTTAGCAACTGATTCAGAAATGGAGTTTTTCACACACTCTTCTCATCCTCCCCGTTCGTCTTCACAGACTTCTGAGTTTTCGTTTGGAAA...

Protein

Download Protein FASTA

302 aa · LXL04_013838|LXL04_013838|OH1004|PROTEIN

MHCWFDVLPSLHLLSATHYFTLLWVNNTPTVTKPVSLSNPLCIFQSQYTPEVLSRNLLATDSEMEFFTHSSHPPRSSSQTSEFSFGNLASKVRDFLCSAVSVIVGNVFSAIFTFFFASVGTLLGALTGALIGQETESGFVRGAAVGAISGAVFSIEVFESSLHLWQSDESGIGCLLYLIDVIVSLISGRLVRERIGPAMLSAVQSQMGAVETNFDEVQNIFDIGGCKGLPKYSVEKIPKITVTSDNNVDCSGEKVLCSVC...

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_013838`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_013838

Location Chr03:36678809-36680856 (-)

Description Similar to NIP2: NEP1-interacting protein 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g17730`	Intrinsic thylakoid membrane protein that fixes RPOT2 on the stromal side of the thylakoid membrane.	No verified direct reference in this release
`At4g35840`	Intrinsic thylakoid membrane protein that fixes RPOT2 on the stromal side of the thylakoid membrane.	No verified direct reference in this release
`At5g66070`	May be involved in the early steps of the plant defense signaling pathway.	No verified direct reference in this release
`At1g74410`	May be involved in the early steps of the plant defense signaling pathway.	No verified direct reference in this release
`At2g17450`	E3 ubiquitin-protein ligase that possess E3 ubiquitin ligase activity in vitro and mediates protein monoubiquitination.	Ligand-induced monoubiquitination of BIK1 regulates plant immunity.2020 · DOI: 10.1038/s41586-020-2210-3

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_013838 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006513 protein monoubiquitination Biological Process

GO:0006952 defense response Biological Process

GO:0009416 response to light stimulus Biological Process

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

GO:0016567 protein ubiquitination Biological Process

GO:0051865 protein autoubiquitination Biological Process

GO:0005634 nucleus Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009535 chloroplast thylakoid membrane Cellular Component

GO:0016020 membrane Cellular Component

GO:0042170 plastid membrane Cellular Component

KEGG gene cross-reference

ath:AT1G74410

ath:AT2G17450

ath:AT2G17730

ath:AT4G35840

ath:AT5G66070

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

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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.

Endoplasmic reticulum0.372

Rank 1 · LXL04_013838 · OH-1004

Cytoplasm0.239

Rank 2 · LXL04_013838 · OH-1004

Nucleus0.234

Rank 3 · LXL04_013838 · OH-1004

Golgi apparatus0.164

Rank 4 · LXL04_013838 · OH-1004

Cell membrane0.135

Rank 5 · LXL04_013838 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

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

PF13441.13Gly-zipper_YMGG118-152 aa

PF13639.13zf-RING_2257-299 aa

PF17123.12zf-RING_11257-285 aa

PF13923.13zf-C3HC4_2257-298 aa

PF12678.14zf-rbx1270-299 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013838	`PF13441.13`	Gly-zipper_YMGG	118	152	4.8e-06	27.2
LXL04_013838	`PF13639.13`	zf-RING_2	257	299	2.7e-13	50.7
LXL04_013838	`PF17123.12`	zf-RING_11	257	285	1.1e-08	35.3
LXL04_013838	`PF13923.13`	zf-C3HC4_2	257	298	1e-06	29.1
LXL04_013838	`PF12678.14`	zf-rbx1	270	299	2e-07	31.9

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8GT74`	Arabidopsis thaliana	NEP1-interacting protein 2	73.272%	Swiss-Prot	strong database homology
`Q8GT75`	Arabidopsis thaliana	NEP1-interacting protein 1	73.059%	Swiss-Prot	strong database homology
`Q9FKX5`	Arabidopsis thaliana	NEP1-interacting protein-like 1	74.057%	Swiss-Prot	strong database homology
`Q8LBA0`	Arabidopsis thaliana	NEP1-interacting protein-like 2	36.321%	Swiss-Prot	moderate database homology
`O22755`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase ATL44	45.000%	Swiss-Prot	weak database homology

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