LXL04_012590 | RubberDandelionOmics

Gene overview

LXL04_012590

Reference: OH-1004 Chr: Chr03 Coordinates: 15197359-15200658 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1110 bp · LXL04_012590|LXL04_012590|OH1004|cDNA

ATGGCTGGAAAAGATTCGGACTACCGTATATTTGTAGGAGGGCTCTCATGGGACGTTACTGATCGTCAGCTTGAAGACGCCTTTAGTCGTTTCGGAAAAATTATCGACTCTCAGTTAATGACTCTTAAGTGGAAGTTAGTTGCACAGAACATATGTCTGGTTGTTCAGCTGGTTAAGAAGAGTGTGCTCCCCAAGTTCCTTGTTGCCCACATTGATCGAAAGATAATGCTTGAAAGAGACACGGGGCGTCCACGTGGATT...

CDS

Download CDS FASTA

1110 bp · LXL04_012590|LXL04_012590|OH1004|CDS

ATGGCTGGAAAAGATTCGGACTACCGTATATTTGTAGGAGGGCTCTCATGGGACGTTACTGATCGTCAGCTTGAAGACGCCTTTAGTCGTTTCGGAAAAATTATCGACTCTCAGTTAATGACTCTTAAGTGGAAGTTAGTTGCACAGAACATATGTCTGGTTGTTCAGCTGGTTAAGAAGAGTGTGCTCCCCAAGTTCCTTGTTGCCCACATTGATCGAAAGATAATGCTTGAAAGAGACACGGGGCGTCCACGTGGATT...

Protein

Download Protein FASTA

369 aa · LXL04_012590|LXL04_012590|OH1004|PROTEIN

MAGKDSDYRIFVGGLSWDVTDRQLEDAFSRFGKIIDSQLMTLKWKLVAQNICLVVQLVKKSVLPKFLVAHIDRKIMLERDTGRPRGFGFITFSDRRGMEDAIREMHGSDLGDRVISVNKAQPKMGGDEADHGYPSGGRGGGGGYGGDTRSMGQDECFKCGRSGHWARDCPSGGGGGGGGGQFSSRPRFGGGGRGDRYADRERYVEDRYDGGRFGDRDRYDSRDSKYVGSRSRYSNERYVPSSGGDRFGGDRYGVPERYPP...

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_012590`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_012590

Location Chr03:15197359-15200658 (+)

Description Similar to RZ1C: Glycine-rich RNA-binding protein RZ1C

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g04280`	Binds RNA and DNA sequences non-specifically.	No verified direct reference in this release
`At1g60650`	Binds RNA and DNA sequences non-specifically.	No verified direct reference in this release
`At3g26420`	Binds RNA and DNA sequences with a preference to single-stranded nucleic acids.	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_012590 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009409 response to cold Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0016070 RNA metabolic process Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

GO:0048026 positive regulation of mRNA splicing, via spliceosome Biological Process

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0016607 nuclear speck Cellular Component

GO:0000166 nucleotide binding Molecular Function

KEGG gene cross-reference

ath:AT1G60650

ath:AT3G26420

ath:AT5G04280

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.

Nucleus0.868

Rank 1 · LXL04_012590 · OH-1004

Cytoplasm0.276

Rank 2 · LXL04_012590 · OH-1004

Cell membrane0.032

Rank 3 · LXL04_012590 · OH-1004

Endoplasmic reticulum0.027

Rank 4 · LXL04_012590 · OH-1004

Mitochondrion0.018

Rank 5 · LXL04_012590 · 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.

PF16367.12RRM_79-35 aa

PF00076.29RRM_110-41 aa

PF00076.29RRM_175-115 aa

PF00098.29zf-CCHC155-171 aa

PF06813.20Nodulin-like310-366 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012590	`PF16367.12`	RRM_7	9	35	9.7e-06	26.2
LXL04_012590	`PF00076.29`	RRM_1	10	41	6.7e-18	65.1
LXL04_012590	`PF00076.29`	RRM_1	75	115	6.7e-18	65.1
LXL04_012590	`PF00098.29`	zf-CCHC	155	171	5.9e-08	33.2
LXL04_012590	`PF06813.20`	Nodulin-like	310	366	4e-13	50.2

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8RWN5`	Arabidopsis thaliana	Glycine-rich RNA-binding protein RZ1C	48.125%	Swiss-Prot	moderate database homology
`O22703`	Arabidopsis thaliana	Glycine-rich RNA-binding protein RZ1B	44.272%	Swiss-Prot	moderate database homology
`Q9LIN3`	Arabidopsis thaliana	Glycine-rich RNA-binding protein RZ1A	36.782%	Swiss-Prot	moderate database homology

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