LXL04_038790 | RubberDandelionOmics

Gene overview

LXL04_038790

Reference: OH-1004 Chr: Chr09 Coordinates: 50698724-50700455 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1465 bp · LXL04_038790|LXL04_038790|OH1004|cDNA

TGCAGAATTCATGGCACATAGGATACTAAGAGATGTTGAAGCTGATGGTTGGGAACGCTCTGATTTTCCAATCATATGTGAATCATGCCTAGGTGACAATCCATACATTCGGATGACAAAATCAGATTATGACAAGGAGTGCAAGATCTGCACCAGGCCATTCACGGTCTTCAGGTGGAGACCTGGTCGTGATGCAAGATACAAGAAGACCGAGATCTGCCAAACTTGCAGCAAATTGAAAAACGTTTGCCAAGTCTGTC...

CDS

Download CDS FASTA

1455 bp · LXL04_038790|LXL04_038790|OH1004|CDS

ATGGCACATAGGATACTAAGAGATGTTGAAGCTGATGGTTGGGAACGCTCTGATTTTCCAATCATATGTGAATCATGCCTAGGTGACAATCCATACATTCGGATGACAAAATCAGATTATGACAAGGAGTGCAAGATCTGCACCAGGCCATTCACGGTCTTCAGGTGGAGACCTGGTCGTGATGCAAGATACAAGAAGACCGAGATCTGCCAAACTTGCAGCAAATTGAAAAACGTTTGCCAAGTCTGTCTTCTAGATCT...

Protein

Download Protein FASTA

484 aa · LXL04_038790|LXL04_038790|OH1004|PROTEIN

MAHRILRDVEADGWERSDFPIICESCLGDNPYIRMTKSDYDKECKICTRPFTVFRWRPGRDARYKKTEICQTCSKLKNVCQVCLLDLEYGLPVQVRDTALSITSHDSIPKSDVNREYFAEEHDRKARAGLDYESSYGKARPNDTILKLQRTTPYYKRNRAHVCSFFIRGECTRGAECPYRHEMPETGELSQQNIKDRYYGVNDPVALKLLSKAGEMPSLEPPDDESIRTLYVGGLDERVSEQDLRDNFYTHGEIESVKMV...

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_038790`
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_038790

Location Chr09:50698724-50700455 (+)

Description Similar to Os06g0170500: Zinc finger CCCH domain-containing protein 40

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g07360`	Zinc finger CCCH domain-containing protein 4.	No verified direct reference in this release
`At2g29580`	Zinc finger CCCH domain-containing protein 25.	No verified direct reference in this release
`At5g07060`	Zinc finger CCCH domain-containing protein 53.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0170500`	Zinc finger CCCH domain-containing protein 40.	No verified direct reference in this release
`Os07g0281000`	Zinc finger CCCH domain-containing protein 49.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_038790 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0042742 defense response to bacterium Biological Process

GO:0000974 Prp19 complex Cellular Component

GO:0005634 nucleus Cellular Component

GO:0071006 U2-type catalytic step 1 spliceosome Cellular Component

GO:0071007 U2-type catalytic step 2 spliceosome Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0003677 DNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0017070 U6 snRNA binding Molecular Function

GO:0036002 pre-mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G07360

ath:AT2G29580

ath:AT5G07060

dosa:Os06g0170500

dosa:Os07g0281000

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.

Nucleus0.788

Rank 1 · LXL04_038790 · OH-1004

Cytoplasm0.363

Rank 2 · LXL04_038790 · OH-1004

Cell membrane0.029

Rank 3 · LXL04_038790 · OH-1004

Endoplasmic reticulum0.021

Rank 4 · LXL04_038790 · OH-1004

Mitochondrion0.018

Rank 5 · LXL04_038790 · 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.

PF21369.4STL11_N20-110 aa

PF16131.12Torus149-193 aa

PF25584.1zf-CCCH_RBM22157-183 aa

PF00076.29RRM_1230-287 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038790	`PF21369.4`	STL11_N	20	110	2.3e-31	109.0
LXL04_038790	`PF16131.12`	Torus	149	193	9.1e-08	33.4
LXL04_038790	`PF25584.1`	zf-CCCH_RBM22	157	183	9.9e-12	45.4
LXL04_038790	`PF00076.29`	RRM_1	230	287	7.1e-13	48.9

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
`Q9LNV5`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 4	77.889%	Swiss-Prot	strong database homology
`Q9ZW36`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 25	67.404%	Swiss-Prot	strong database homology
`Q9FL40`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 53	54.115%	Swiss-Prot	strong database homology
`Q5SNN4`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 40	79.644%	Swiss-Prot	strong database homology
`Q6Z358`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 49	79.795%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card