LXL04_021687 | RubberDandelionOmics

Gene overview

LXL04_021687

Reference: OH-1004 Chr: Chr04 Coordinates: 135159498-135163738 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

618 bp · LXL04_021687|LXL04_021687|OH1004|cDNA

ATGCAACGAAACTCCATCAAATCTGGAGCACGAGACCGAAGGCATGAAGTCACTGAAGCAGCTCAAGCTCTCTGTTCCTACTCAAGATGCTCCGATTACCAGCTTCTTATAATGCTTGAAAGAGACACGGGGCGTCCACGTGGATTTGGTTTCATAACATTTTCAGACCGCCGAGGCATGGAAGACGCCATCAGGGAAATGCACGGAAGTGATCTCGGTGACCGTGTCATCTCCGTCAACAAAGCCCAGCCTAAAATGGG...

CDS

Download CDS FASTA

618 bp · LXL04_021687|LXL04_021687|OH1004|CDS

ATGCAACGAAACTCCATCAAATCTGGAGCACGAGACCGAAGGCATGAAGTCACTGAAGCAGCTCAAGCTCTCTGTTCCTACTCAAGATGCTCCGATTACCAGCTTCTTATAATGCTTGAAAGAGACACGGGGCGTCCACGTGGATTTGGTTTCATAACATTTTCAGACCGCCGAGGCATGGAAGACGCCATCAGGGAAATGCACGGAAGTGATCTCGGTGACCGTGTCATCTCCGTCAACAAAGCCCAGCCTAAAATGGG...

Protein

Download Protein FASTA

205 aa · LXL04_021687|LXL04_021687|OH1004|PROTEIN

MQRNSIKSGARDRRHEVTEAAQALCSYSRCSDYQLLIMLERDTGRPRGFGFITFSDRRGMEDAIREMHGSDLGDRVISVNKAQPKMGGDEAYHGYGGGYPSGGRGGGGYGGDTRSMGQDECFKCGRSGHWARDCPSAGAGGGGGGGGGGRGGGQCSSRPRFGGGRGDRYADRERYVEDRYDGGRFDLTWVYIVTVMSYLMIIMDS

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_021687`
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_021687

Location Chr04:135159498-135163738 (-)

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
`At4g39260`	Plays a role in RNA transcription or processing during stress.	Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis.2008 · DOI: 10.1093/nar/gkn847 Quantitative analysis of single-molecule RNA-protein interaction.2009 · DOI: 10.1016/j.bpj.2009.03.022 An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with transcripts in Arabidopsis thaliana.2012 · DOI: 10.1093/nar/gks873

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021687 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000380 alternative mRNA splicing, via spliceosome Biological Process

GO:0006858 extracellular transport Biological Process

GO:0009409 response to cold Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0010043 response to zinc ion Biological Process

GO:0016070 RNA metabolic process Biological Process

GO:0045087 innate immune response Biological Process

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

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

GO:0050658 RNA transport Biological Process

GO:0050688 regulation of defense response to virus Biological Process

GO:1990428 miRNA transport Biological Process

KEGG gene cross-reference

ath:AT1G60650

ath:AT3G26420

ath:AT4G39260

ath:AT5G04280

bna:106438956

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.

Nucleus0.728

Rank 1 · LXL04_021687 · OH-1004

Cytoplasm0.460

Rank 2 · LXL04_021687 · OH-1004

Endoplasmic reticulum0.039

Rank 3 · LXL04_021687 · OH-1004

Cell membrane0.035

Rank 4 · LXL04_021687 · OH-1004

Extracellular0.034

Rank 5 · LXL04_021687 · 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.

PF00076.29RRM_139-77 aa

PF00098.29zf-CCHC120-136 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021687	`PF00076.29`	RRM_1	39	77	6.1e-09	36.3
LXL04_021687	`PF00098.29`	zf-CCHC	120	136	2.7e-08	34.2

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	55.618%	Swiss-Prot	strong database homology
`O22703`	Arabidopsis thaliana	Glycine-rich RNA-binding protein RZ1B	59.434%	Swiss-Prot	moderate database homology
`Q9LIN3`	Arabidopsis thaliana	Glycine-rich RNA-binding protein RZ1A	37.267%	Swiss-Prot	moderate database homology
`Q03251`	Arabidopsis thaliana	Glycine-rich RNA-binding protein 8	57.447%	Swiss-Prot	weak database homology

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