LXL04_023875 | RubberDandelionOmics

Gene overview

LXL04_023875

Reference: OH-1004 Chr: Chr05 Coordinates: 72125272-72127571 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1040 bp · LXL04_023875|LXL04_023875|OH1004|cDNA

AAGAACTCACGCTTTTCACACACACTCCCTCTCCTTCTTATATCCACCACCAACTCATACTATTCCGGTCATCGGTCCATCTCTAGGGTTTCCAATGGCATATGGCCGTACTGACGCACGCAGACACATGTTCGATGGCGGTGTCAACTTTATCTCCGACCAAAACCCTCACACTGGTTATCAACAGCATCCGCCTCAACGATTTTCCAATGTCGGGATTCATGAATCGATGCGCCATGATTTTGTTCCTGGTGGTTATG...

CDS

Download CDS FASTA

942 bp · LXL04_023875|LXL04_023875|OH1004|CDS

ATGGCATATGGCCGTACTGACGCACGCAGACACATGTTCGATGGCGGTGTCAACTTTATCTCCGACCAAAACCCTCACACTGGTTATCAACAGCATCCGCCTCAACGATTTTCCAATGTCGGGATTCATGAATCGATGCGCCATGATTTTGTTCCTGGTGGTTATGGAAACTGGAGCAGAAACTTCAGCATGCAGCAGTACTACCCTCTCCCAAAATCCGATAAGGTCTGCCTGGTTTTTACCCACACAGGATTTTGTAG...

Protein

Download Protein FASTA

313 aa · LXL04_023875|LXL04_023875|OH1004|PROTEIN

MAYGRTDARRHMFDGGVNFISDQNPHTGYQQHPPQRFSNVGIHESMRHDFVPGGYGNWSRNFSMQQYYPLPKSDKVCLVFTHTGFCSFRDRCRFRHPTPENAQVDAEENKGKPSETESEKSRPVIPCKFYPTGVCKNGEKCKFDHSITEFKQIFNIMGLPIRLGEQDCSFYMRNGTCNFGKSCKFHHPDPIIYHEPDQAYEDYFEYENGASGFTDGEYGIGYPDPNQRYYPQPPVIGNNYQPNFSWNDLIQLSHQQENVP...

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_023875`
TK1151 ID	TkA06G202260
OH-1004 ID	LXL04_023875
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 89.213 / OH-1004 97.764 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

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Basic Information and Functional Annotation

Gene ID LXL04_023875

Location Chr05:72125272-72127571 (+)

Description Similar to At3g48440: Zinc finger CCCH domain-containing protein 43

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g48440`	Zinc finger CCCH domain-containing protein 43.	No verified direct reference in this release
`At5g63260`	Zinc finger CCCH domain-containing protein 67.	No verified direct reference in this release
`At1g04990`	Possesses RNA-binding and ribonuclease activities in vitro.	No verified direct reference in this release
`At2g47850`	Zinc finger CCCH domain-containing protein 32.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0258700`	Zinc finger CCCH domain-containing protein 6.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_023875 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006970 response to osmotic stress Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

GO:0004518 nuclease activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0016787 hydrolase activity Molecular Function

KEGG gene cross-reference

ath:AT1G04990

ath:AT3G48440

ath:AT5G63260

dosa:Os01g0258700

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.

Nucleus0.572

Rank 1 · LXL04_023875 · OH-1004

Cytoplasm0.524

Rank 2 · LXL04_023875 · OH-1004

Cell membrane0.041

Rank 3 · LXL04_023875 · OH-1004

Endoplasmic reticulum0.036

Rank 4 · LXL04_023875 · OH-1004

Mitochondrion0.029

Rank 5 · LXL04_023875 · 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.

PF16131.12Torus115-152 aa

PF00642.31zf-CCCH126-146 aa

PF18044.8zf-CCCH_4126-145 aa

PF25585.2zf-CCCH_DUS3L127-150 aa

PF18345.8zf_CCCH_4127-145 aa

PF00642.31zf-CCCH165-188 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_023875	`PF16131.12`	Torus	115	152	3.5e-09	37.9
LXL04_023875	`PF00642.31`	zf-CCCH	126	146	6.2e-17	61.8
LXL04_023875	`PF18044.8`	zf-CCCH_4	126	145	3.4e-09	37.0
LXL04_023875	`PF25585.2`	zf-CCCH_DUS3L	127	150	1.2e-11	45.0
LXL04_023875	`PF18345.8`	zf_CCCH_4	127	145	2.7e-09	37.5
LXL04_023875	`PF00642.31`	zf-CCCH	165	188	6.2e-17	61.8

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
`Q9STM4`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 43	41.379%	Swiss-Prot	weak database homology
`Q5RJC5`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 67	39.130%	Swiss-Prot	weak database homology
`Q94AD9`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 3	30.693%	Swiss-Prot	moderate database homology
`Q84W91`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 32	34.591%	Swiss-Prot	weak database homology
`Q5NAW2`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 6	38.462%	Swiss-Prot	weak database homology

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