LXL04_025842 | RubberDandelionOmics

Gene overview

LXL04_025842

Reference: OH-1004 Chr: Chr05 Coordinates: 117551341-117552171 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

831 bp · LXL04_025842|LXL04_025842|OH1004|cDNA

ATGTCAGTTTGTATTGATGAAAGCATCACGATCCGAGAAGTATGGTCTGATAACTTAGAATCCGAGTTTGATTTGATCAGATCTGTAATCGATCATTACCCTTACATCTCCATGGACACCGAGTTCCCGGGTGTTGTATACCGTCAGTCATCGGAGCCTGGAAGATCTTACAAGCATCGGAAGCCATCGGAGCACTACAAGTTTCTTAAGTCAAACGTCGACGCTTTGAACCTCATCCAGCTCGGTCTCACCCTCTCCGA...

CDS

Download CDS FASTA

831 bp · LXL04_025842|LXL04_025842|OH1004|CDS

ATGTCAGTTTGTATTGATGAAAGCATCACGATCCGAGAAGTATGGTCTGATAACTTAGAATCCGAGTTTGATTTGATCAGATCTGTAATCGATCATTACCCTTACATCTCCATGGACACCGAGTTCCCGGGTGTTGTATACCGTCAGTCATCGGAGCCTGGAAGATCTTACAAGCATCGGAAGCCATCGGAGCACTACAAGTTTCTTAAGTCAAACGTCGACGCTTTGAACCTCATCCAGCTCGGTCTCACCCTCTCCGA...

Protein

Download Protein FASTA

276 aa · LXL04_025842|LXL04_025842|OH1004|PROTEIN

MSVCIDESITIREVWSDNLESEFDLIRSVIDHYPYISMDTEFPGVVYRQSSEPGRSYKHRKPSEHYKFLKSNVDALNLIQLGLTLSDASGNLPYINGSHQRFIWQFNFNDFDLTRDAYAPESIDLLKRQGIDFERNRVNGIDSADFAEMMMSSGLVCNESVSWVTFHSAYDFGYLLKILTRRLLPSGLPEFMEALKVFFGDNVYDVKHLMKFCRTGLYGGLDRVASILEVNRVVGKCHQAGSDSLLTWHAFQKMRDVYFV...

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_025842`
TK1151 ID	TkA06G040090
OH-1004 ID	LXL04_025842
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	64.100
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_025842

Location Chr05:117551341-117552171 (-)

Description Similar to CAF1-11: Probable CCR4-associated factor 1 homolog 11

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g22250`	Ubiquitous transcription factor required for a diverse set of processes.	No verified direct reference in this release
`At3g44260`	Ubiquitous transcription factor required for a diverse set of processes.	No verified direct reference in this release
`At1g80780`	Ubiquitous transcription factor required for a diverse set of processes.	No verified direct reference in this release
`At2g32070`	Ubiquitous transcription factor required for a diverse set of processes.	No verified direct reference in this release
`At5g10960`	Ubiquitous transcription factor required for a diverse set of processes.	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_025842 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Biological Process

GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening Biological Process

GO:0002213 defense response to insect Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0009611 response to wounding Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0000932 P-body Cellular Component

GO:0005634 nucleus Cellular Component

GO:0030015 CCR4-NOT core complex Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0004535 poly(A)-specific ribonuclease activity Molecular Function

GO:0008408 3'-5' exonuclease activity Molecular Function

KEGG gene cross-reference

ath:AT1G80780

ath:AT2G32070

ath:AT3G44260

ath:AT5G10960

ath:AT5G22250

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_025842 · OH-1004

Cytoplasm0.559

Rank 2 · LXL04_025842 · OH-1004

Cell membrane0.058

Rank 3 · LXL04_025842 · OH-1004

Endoplasmic reticulum0.041

Rank 4 · LXL04_025842 · OH-1004

Lysosome / Vacuole0.034

Rank 5 · LXL04_025842 · 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.

PF04857.27CAF114-141 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025842	`PF04857.27`	CAF1	14	141	1.3e-21	77.9

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9FMS6`	Arabidopsis thaliana	Probable CCR4-associated factor 1 homolog 11	67.033%	Swiss-Prot	strong database homology
`Q9LXM2`	Arabidopsis thaliana	Probable CCR4-associated factor 1 homolog 9	66.296%	Swiss-Prot	strong database homology
`Q9SAI2`	Arabidopsis thaliana	Probable CCR4-associated factor 1 homolog 6	55.926%	Swiss-Prot	strong database homology
`Q9SKZ2`	Arabidopsis thaliana	Probable CCR4-associated factor 1 homolog 7	55.762%	Swiss-Prot	strong database homology
`Q9LEU4`	Arabidopsis thaliana	Probable CCR4-associated factor 1 homolog 10	53.532%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card