LXL04_014967 | RubberDandelionOmics

Gene overview

LXL04_014967

Reference: OH-1004 Chr: Chr03 Coordinates: 60563173-60564429 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

531 bp · LXL04_014967|LXL04_014967|OH1004|cDNA

ATGCCGCTGGGAAAATACCACTGTGACTACTGCGATAAGCAGTTCCAGGACACCCCTTTCCACCGGAAACGCCATATTCAGGGCCTTCAGCACCAGAAAGCCAAAGCTCTCTGGTACGCCTCCATACCGCGAGATCCCAATCAGGTATCTCTACAATCATCTACTGTTGGACTCTGCAATCGCTTCATCAGGACGGGCTCATGCCCATATGGTGATTCATGCAAATATGTTCATCCCAATCAAAACTTTCCAAACATGAA...

CDS

Download CDS FASTA

531 bp · LXL04_014967|LXL04_014967|OH1004|CDS

ATGCCGCTGGGAAAATACCACTGTGACTACTGCGATAAGCAGTTCCAGGACACCCCTTTCCACCGGAAACGCCATATTCAGGGCCTTCAGCACCAGAAAGCCAAAGCTCTCTGGTACGCCTCCATACCGCGAGATCCCAATCAGGTATCTCTACAATCATCTACTGTTGGACTCTGCAATCGCTTCATCAGGACGGGCTCATGCCCATATGGTGATTCATGCAAATATGTTCATCCCAATCAAAACTTTCCAAACATGAA...

Protein

Download Protein FASTA

176 aa · LXL04_014967|LXL04_014967|OH1004|PROTEIN

MPLGKYHCDYCDKQFQDTPFHRKRHIQGLQHQKAKALWYASIPRDPNQVSLQSSTVGLCNRFIRTGSCPYGDSCKYVHPNQNFPNMNMQGFPGAYIFFYLISFKYLLPVIYCSSQLQIAWKLNCQVSQGVSPLKDPHYQARGMVVDRMGVMLGNVPPSLRPPPEGGYPPIPFVDWG

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_014967`
TK1151 ID	TkA02G380460
OH-1004 ID	LXL04_014967
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	72.700
Protein coverage (%)	TK1151 90.968 / OH-1004 93.750 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_014967

Location Chr03:60563173-60564429 (+)

Description Similar to Os01g0252200: Zinc finger CCCH domain-containing protein 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

No hit for this species in the current source table.

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0252200`	Zinc finger CCCH domain-containing protein 3.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_014967 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000388 spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0006397 mRNA processing Biological Process

GO:0008380 RNA splicing Biological Process

GO:0005654 nucleoplasm Cellular Component

GO:0005681 spliceosomal complex Cellular Component

GO:0005689 U12-type spliceosomal complex Cellular Component

GO:0034693 U11/U12 snRNP Cellular Component

GO:0071016 U12-type precatalytic spliceosome Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

bta:616095

dosa:Os01g0252200

dre:445314

hsa:55954

mmu:67178

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.

Nucleus0.564

Rank 1 · LXL04_014967 · OH-1004

Cytoplasm0.483

Rank 2 · LXL04_014967 · OH-1004

Mitochondrion0.065

Rank 3 · LXL04_014967 · OH-1004

Endoplasmic reticulum0.040

Rank 4 · LXL04_014967 · OH-1004

Cell membrane0.032

Rank 5 · LXL04_014967 · 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.

PF06220.19zf-U15-37 aa

PF25585.2zf-CCCH_DUS3L57-78 aa

PF00642.31zf-CCCH58-79 aa

PF18345.8zf_CCCH_459-78 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_014967	`PF06220.19`	zf-U1	5	37	1.4e-08	35.1
LXL04_014967	`PF25585.2`	zf-CCCH_DUS3L	57	78	3.4e-06	27.6
LXL04_014967	`PF00642.31`	zf-CCCH	58	79	9.7e-09	35.6
LXL04_014967	`PF18345.8`	zf_CCCH_4	59	78	1.4e-06	28.9

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
`Q0JP11`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 3	40.625%	Swiss-Prot	moderate database homology

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