LXL04_035173 | RubberDandelionOmics

Gene overview

LXL04_035173

Reference: OH-1004 Chr: Chr08 Coordinates: 16398009-16400958 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1536 bp · LXL04_035173|LXL04_035173|OH1004|cDNA

ATGTCGTCGACGCTGTTAGAGCTGACTCGAGCGGCTCACGAGGAAACTGAGAAGTTGGAGAGACTGATAGTGAAGGATCTGCAGAATGAACCGGCTTCGAACAAGGATCGCCTCTCCCAAAGCCACCGTGTGCGCCATATGATCGACCAAATCACCACCACTACTTACAAGATTATTGAGATTTATGAAGACAAAGACAATGCAAGGAAGGATGAAATTGCAGCCCTTGGTGGACAAACTGCATCTGGGACGACTAATGT...

CDS

Download CDS FASTA

1536 bp · LXL04_035173|LXL04_035173|OH1004|CDS

ATGTCGTCGACGCTGTTAGAGCTGACTCGAGCGGCTCACGAGGAAACTGAGAAGTTGGAGAGACTGATAGTGAAGGATCTGCAGAATGAACCGGCTTCGAACAAGGATCGCCTCTCCCAAAGCCACCGTGTGCGCCATATGATCGACCAAATCACCACCACTACTTACAAGATTATTGAGATTTATGAAGACAAAGACAATGCAAGGAAGGATGAAATTGCAGCCCTTGGTGGACAAACTGCATCTGGGACGACTAATGT...

Protein

Download Protein FASTA

511 aa · LXL04_035173|LXL04_035173|OH1004|PROTEIN

MSSTLLELTRAAHEETEKLERLIVKDLQNEPASNKDRLSQSHRVRHMIDQITTTTYKIIEIYEDKDNARKDEIAALGGQTASGTTNVFSAFYDRLKEIREYHRRHPSARVIDTTDEYEELLQEEPQVEFSGEEAHGRYLDMHELYNDYINSKFGKHLDYTSYLEVFSQPHTIPRKLKMTRQYREYLSKMVEYLVYFIERTEPLQDLDRLFLKVSSEFEEQWANGKVDGWKDEVKDNGHVSDEHTSIDLDYYSTVEELVEL...

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_035173`
TK1151 ID	TkA04G160100
OH-1004 ID	LXL04_035173
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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_035173

Location Chr08:16398009-16400958 (-)

Description Similar to ATO: Splicing factor SF3a60 homolog

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g06160`	Splicing factor homolog to SF3a60 that may be involved in pre-spliceosome formation.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_035173 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000278 mitotic cell cycle Biological Process

GO:0000375 RNA splicing, via transesterification reactions Biological Process

GO:0000387 spliceosomal snRNP assembly Biological Process

GO:0000389 mRNA 3'-splice site recognition Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0006397 mRNA processing Biological Process

GO:0009566 fertilization Biological Process

GO:0045292 mRNA cis splicing, via spliceosome Biological Process

GO:0045694 regulation of embryo sac egg cell differentiation Biological Process

GO:1903241 U2-type prespliceosome assembly Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

KEGG gene cross-reference

ath:AT5G06160

dme:Dmel_CG2925

hsa:10946

mmu:75062

spo:2540932

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.

Nucleus0.901

Rank 1 · LXL04_035173 · OH-1004

Cytoplasm0.175

Rank 2 · LXL04_035173 · OH-1004

Mitochondrion0.023

Rank 3 · LXL04_035173 · OH-1004

Cell membrane0.017

Rank 4 · LXL04_035173 · OH-1004

Endoplasmic reticulum0.009

Rank 5 · LXL04_035173 · 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.

PF12108.14SF3a60_bindingd83-107 aa

PF16837.11SF3A3128-176 aa

PF13297.12SDE2_2C225-305 aa

PF11931.15SF3a60_Prp9_C392-511 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_035173	`PF12108.14`	SF3a60_bindingd	83	107	2.5e-12	47.2
LXL04_035173	`PF16837.11`	SF3A3	128	176	1.4e-16	61.0
LXL04_035173	`PF13297.12`	SDE2_2C	225	305	2.1e-29	102.0
LXL04_035173	`PF11931.15`	SF3a60_Prp9_C	392	511	1.2e-54	184.7

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
`Q9FG01`	Arabidopsis thaliana	Splicing factor SF3a60 homolog	70.874%	Swiss-Prot	strong database homology

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