LXL04_025985 | RubberDandelionOmics

Gene overview

LXL04_025985

Reference: OH-1004 Chr: Chr05 Coordinates: 119382403-119384729 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1323 bp · LXL04_025985|LXL04_025985|OH1004|cDNA

ATGGAGATGTCACAGTCCGATCCGGTTACTGAATGGAGCACATCCGGTGGCCAAACAGGGCTCGAAGAGCCTATGTGGCAATTAGGGTTGGGAGGTGGGTTGGATTCATACCCTCAACGGCCGGATGAAGCCGATTGTATCTATTATTTGAGGACAGGGTTTTGTGGGTACGGTTCTCGCTGTCGGTTCAACCATCCTCGTGATCGTAGTTCGGTGGTCGGAGCTATGAGGTCCACCGGAGGAGAATACCCAGAACGGAT...

CDS

Download CDS FASTA

1323 bp · LXL04_025985|LXL04_025985|OH1004|CDS

ATGGAGATGTCACAGTCCGATCCGGTTACTGAATGGAGCACATCCGGTGGCCAAACAGGGCTCGAAGAGCCTATGTGGCAATTAGGGTTGGGAGGTGGGTTGGATTCATACCCTCAACGGCCGGATGAAGCCGATTGTATCTATTATTTGAGGACAGGGTTTTGTGGGTACGGTTCTCGCTGTCGGTTCAACCATCCTCGTGATCGTAGTTCGGTGGTCGGAGCTATGAGGTCCACCGGAGGAGAATACCCAGAACGGAT...

Protein

Download Protein FASTA

440 aa · LXL04_025985|LXL04_025985|OH1004|PROTEIN

MEMSQSDPVTEWSTSGGQTGLEEPMWQLGLGGGLDSYPQRPDEADCIYYLRTGFCGYGSRCRFNHPRDRSSVVGAMRSTGGEYPERIGQPVCQYYMRTGMCKFGASCKYHHPRHGIGSSNQVSLNMSGYPLRPGEKECSYYVKTGQCKFGVTCKFHHPQPVGITPPPPPPPPPDQSSMASVMQSPVASSQQYGVYSGNWQLPVARPPPPPLLPGSYLAGTYGPPMILAPGMVPFPGWNPYHESVNQNTNVGAGSIYTMAP...

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_025985`
TK1151 ID	TkA06G039210
OH-1004 ID	LXL04_025985
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.800
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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_025985

Location Chr05:119382403-119384729 (-)

Description Similar to At2g47850: Zinc finger CCCH domain-containing protein 32

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g47850`	Zinc finger CCCH domain-containing protein 32.	No verified direct reference in this release
`At5g18550`	Zinc finger CCCH domain-containing protein 58.	No verified direct reference in this release
`At3g06410`	Zinc finger CCCH domain-containing protein 34.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0257400`	Zinc finger CCCH domain-containing protein 5.	No verified direct reference in this release
`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_025985 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0005634 nucleus Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT2G47850

ath:AT3G06410

ath:AT5G18550

dosa:Os01g0257400

dosa:Os01g0258700

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.

Nucleus0.846

Rank 1 · LXL04_025985 · OH-1004

Cytoplasm0.208

Rank 2 · LXL04_025985 · OH-1004

Cell membrane0.034

Rank 3 · LXL04_025985 · OH-1004

Endoplasmic reticulum0.022

Rank 4 · LXL04_025985 · OH-1004

Golgi apparatus0.014

Rank 5 · LXL04_025985 · 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.

PF00642.31zf-CCCH42-67 aa

PF00642.31zf-CCCH89-113 aa

PF18044.8zf-CCCH_490-112 aa

PF18345.8zf_CCCH_492-111 aa

PF00642.31zf-CCCH134-159 aa

PF00642.31zf-CCCH285-311 aa

PF14608.13zf-CCCH_2290-310 aa

PF00642.31zf-CCCH332-357 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025985	`PF00642.31`	zf-CCCH	42	67	4.6e-47	157.8
LXL04_025985	`PF00642.31`	zf-CCCH	89	113	4.6e-47	157.8
LXL04_025985	`PF18044.8`	zf-CCCH_4	90	112	2.2e-17	63.1
LXL04_025985	`PF18345.8`	zf_CCCH_4	92	111	4.3e-20	71.8
LXL04_025985	`PF00642.31`	zf-CCCH	134	159	4.6e-47	157.8
LXL04_025985	`PF00642.31`	zf-CCCH	285	311	4.6e-47	157.8
LXL04_025985	`PF14608.13`	zf-CCCH_2	290	310	6.2e-19	68.4
LXL04_025985	`PF00642.31`	zf-CCCH	332	357	4.6e-47	157.8
LXL04_025985	`PF18044.8`	zf-CCCH_4	334	356	2.2e-17	63.1
LXL04_025985	`PF18345.8`	zf_CCCH_4	336	355	4.3e-20	71.8

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q84W91`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 32	53.047%	Swiss-Prot	strong database homology
`Q6NPN3`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 58	55.294%	Swiss-Prot	strong database homology
`Q9SQU4`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 34	52.656%	Swiss-Prot	strong database homology
`Q5NAV3`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 5	50.110%	Swiss-Prot	strong database homology
`Q5NAW2`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 6	49.095%	Swiss-Prot	moderate database homology

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