LXL04_026607 | RubberDandelionOmics

Gene overview

LXL04_026607

Reference: OH-1004 Chr: Chr05 Coordinates: 129441575-129447100 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2481 bp · LXL04_026607|LXL04_026607|OH1004|cDNA

ATGGACTCTCTTCCCCTAGAAACCCTAGCTCCCACTTCCACTCCTTACGATACCTTGGATTATACCAATAACTCCAGTCACCAGCATGCGCCTTCTGATTTTGTCTCAGCAGCACCCCCTCCGCCGCCCAATTCCGACCACAATCTTCCTCCTCAACCACAAATCGTATGTGAAACGGATCCCAACCATAATCCAGAACCAGACACAACAGATCCGAAGTCTGACAATGGCGGCGTCAGGAGTGTTACTACGGAAAAGGA...

CDS

Download CDS FASTA

2481 bp · LXL04_026607|LXL04_026607|OH1004|CDS

ATGGACTCTCTTCCCCTAGAAACCCTAGCTCCCACTTCCACTCCTTACGATACCTTGGATTATACCAATAACTCCAGTCACCAGCATGCGCCTTCTGATTTTGTCTCAGCAGCACCCCCTCCGCCGCCCAATTCCGACCACAATCTTCCTCCTCAACCACAAATCGTATGTGAAACGGATCCCAACCATAATCCAGAACCAGACACAACAGATCCGAAGTCTGACAATGGCGGCGTCAGGAGTGTTACTACGGAAAAGGA...

Protein

Download Protein FASTA

826 aa · LXL04_026607|LXL04_026607|OH1004|PROTEIN

MDSLPLETLAPTSTPYDTLDYTNNSSHQHAPSDFVSAAPPPPPNSDHNLPPQPQIVCETDPNHNPEPDTTDPKSDNGGVRSVTTEKDNSGVEEDKSSRRRRRSRWEPPPADGDADQNGGKKRKSRWADDEPKPVFQLPDFMKDFTGGMDMDPEIQALNARLMEISRILQSGQQLDDRPEGGRSPSPDPVYDNMGTRINTREYRARERLNRERQEIISQIIKRNPAFKPPADYRPPKLQKKLYIPMKEYPGYNFIGLIIGP...

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_026607`
TK1151 ID	TkA06G000860
OH-1004 ID	LXL04_026607
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	54.100
Protein coverage (%)	TK1151 96.000 / OH-1004 17.918 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_026607

Location Chr05:129441575-129447100 (+)

Description Similar to SF1: Splicing factor-like protein 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g51300`	Necessary for the splicing of pre-mRNA.	A homolog of splicing factor SF1 is essential for development and is involved in the alternative splicing of pre-mRNA in Arabidopsis thaliana.2014 · DOI: 10.1111/tpj.12491

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_026607 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0008380 RNA splicing Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0045292 mRNA cis splicing, via spliceosome Biological Process

GO:0048024 regulation of mRNA splicing, via spliceosome Biological Process

GO:0000243 commitment complex Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005681 spliceosomal complex Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005829 cytosol Cellular Component

GO:0016607 nuclear speck Cellular Component

KEGG gene cross-reference

afm:AFUA_3G10840

ath:AT5G51300

cnb:CNBD3480

cne:CND02880

ncr:NCU04110

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.

Nucleus0.681

Rank 1 · LXL04_026607 · OH-1004

Cytoplasm0.412

Rank 2 · LXL04_026607 · OH-1004

Cell membrane0.051

Rank 3 · LXL04_026607 · OH-1004

Endoplasmic reticulum0.038

Rank 4 · LXL04_026607 · OH-1004

Mitochondrion0.025

Rank 5 · LXL04_026607 · 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.

PF16275.11SF1-HH122-233 aa

PF22675.3KH-I_KHDC4-BBP247-328 aa

PF00076.29RRM_1489-558 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026607	`PF16275.11`	SF1-HH	122	233	9.6e-29	100.8
LXL04_026607	`PF22675.3`	KH-I_KHDC4-BBP	247	328	1.1e-23	83.6
LXL04_026607	`PF00076.29`	RRM_1	489	558	1.6e-19	70.2

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
`Q9LU44`	Arabidopsis thaliana	Splicing factor-like protein 1	67.377%	Swiss-Prot	moderate database homology

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