LXL04_007640 | RubberDandelionOmics

Gene overview

LXL04_007640

Reference: OH-1004 Chr: Chr02 Coordinates: 54947970-54950781 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1815 bp · LXL04_007640|LXL04_007640|OH1004|cDNA

ATGCCGGTAATGGAAAGATCAGAAATCGGAATTCCGATTTGGCCAGTGAACCCCTCAACCGGTAATCGCCGGAGAGGACCGCTCAGGAGCAGGACTGTTGACACACTTCTTCATATACTGTCCATTTGCTATGCCGATTCTTCTCATATCACTCAAAATTCAGATAAGAGCCACACTCTTGAAGAATCAGTCACAAAAGATGATTCAGTAGATAAAGAAGAAACAAATGTGGATGAAACAAAAGTAATTTTAGGTACTCA...

CDS

Download CDS FASTA

1815 bp · LXL04_007640|LXL04_007640|OH1004|CDS

ATGCCGGTAATGGAAAGATCAGAAATCGGAATTCCGATTTGGCCAGTGAACCCCTCAACCGGTAATCGCCGGAGAGGACCGCTCAGGAGCAGGACTGTTGACACACTTCTTCATATACTGTCCATTTGCTATGCCGATTCTTCTCATATCACTCAAAATTCAGATAAGAGCCACACTCTTGAAGAATCAGTCACAAAAGATGATTCAGTAGATAAAGAAGAAACAAATGTGGATGAAACAAAAGTAATTTTAGGTACTCA...

Protein

Download Protein FASTA

604 aa · LXL04_007640|LXL04_007640|OH1004|PROTEIN

MPVMERSEIGIPIWPVNPSTGNRRRGPLRSRTVDTLLHILSICYADSSHITQNSDKSHTLEESVTKDDSVDKEETNVDETKVILGTQEEEFCNTHVEPVEQDHNISEERKDLSSPHLVTDKDVEEGEIAGEFLNLIPEDDVASVDKTGSEHEDFVGIESEFEKNNSLTSLSIDTVDDIGKGMAVVVSKTKRNLVDYSEIALQSNITKSATKNQDFASPVKNNGTQNNKKRPGSCTVEKRTNKKARKSVDQSTCPQDLTTN...

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_007640`
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_007640

Location Chr02:54947970-54950781 (-)

Description Similar to EMB1789: Zinc finger CCCH domain-containing protein 65

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g56930`	Possesses RNA-binding and ribonuclease activities in vitro.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0572100`	Zinc finger CCCH domain-containing protein 7.	No verified direct reference in this release

Functional annotation source

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Functional annotation source: OH1004 · LXL04_007640 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006353 DNA-templated transcription termination Biological Process

GO:0032785 negative regulation of DNA-templated transcription, elongation Biological Process

GO:0071027 nuclear RNA surveillance Biological Process

GO:0110064 lncRNA catabolic process Biological Process

GO:0140744 negative regulation of lncRNA transcription Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005694 chromosome Cellular Component

GO:0005829 cytosol Cellular Component

GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific Molecular Function

GO:0003677 DNA binding Molecular Function

GO:0003682 chromatin binding Molecular Function

KEGG gene cross-reference

ath:AT5G56930

dosa:Os01g0572100

hsa:23211

mmu:330474

osa:4326353

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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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.

Nucleus0.956

Rank 1 · LXL04_007640 · OH-1004

Cytoplasm0.116

Rank 2 · LXL04_007640 · OH-1004

Cell membrane0.021

Rank 3 · LXL04_007640 · OH-1004

Mitochondrion0.012

Rank 4 · LXL04_007640 · OH-1004

Endoplasmic reticulum0.010

Rank 5 · LXL04_007640 · 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.

PF18345.8zf_CCCH_4329-347 aa

PF18345.8zf_CCCH_4383-402 aa

PF22623.3zf-CCCH_9383-412 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_007640	`PF18345.8`	zf_CCCH_4	329	347	5.8e-09	36.4
LXL04_007640	`PF18345.8`	zf_CCCH_4	383	402	5.8e-09	36.4
LXL04_007640	`PF22623.3`	zf-CCCH_9	383	412	2.9e-08	34.0

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
`Q9LTS7`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 65	37.778%	Swiss-Prot	weak database homology
`Q657B3`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 7	44.958%	Swiss-Prot	weak database homology

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