LXL04_032063 | RubberDandelionOmics

Gene overview

LXL04_032063

Reference: OH-1004 Chr: Chr07 Coordinates: 15845986-15855174 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

7110 bp · LXL04_032063|LXL04_032063|OH1004|cDNA

ATGTGGAATAGTAACAACGGGCAAGAGATGTGGAATAACAACGGTATGATTGCCCCTCCTGGAACTGGTGGAGTACCACCGCTAGCGCCTCCGGGGACTGGAGGTGCTGGTGGCTCAATACCACCGCCGCCTGCTGCGCAACCTTCCTACACTGTTCTGCCGTCTCCAGCTGAAGCGGAGGCGAGGTTGGAAGAAAAAGCGAGGAAATGGATGCAGTTGAACTCGAAGCGATATGGAGATAAACGGAAATTTGGTTTCGT...

CDS

Download CDS FASTA

7110 bp · LXL04_032063|LXL04_032063|OH1004|CDS

ATGTGGAATAGTAACAACGGGCAAGAGATGTGGAATAACAACGGTATGATTGCCCCTCCTGGAACTGGTGGAGTACCACCGCTAGCGCCTCCGGGGACTGGAGGTGCTGGTGGCTCAATACCACCGCCGCCTGCTGCGCAACCTTCCTACACTGTTCTGCCGTCTCCAGCTGAAGCGGAGGCGAGGTTGGAAGAAAAAGCGAGGAAATGGATGCAGTTGAACTCGAAGCGATATGGAGATAAACGGAAATTTGGTTTCGT...

Protein

Download Protein FASTA

2369 aa · LXL04_032063|LXL04_032063|OH1004|PROTEIN

MWNSNNGQEMWNNNGMIAPPGTGGVPPLAPPGTGGAGGSIPPPPAAQPSYTVLPSPAEAEARLEEKARKWMQLNSKRYGDKRKFGFVETQKEDMPPEHVRKIIRDHGDMSSKKYRHDKRVYLGALKFVPHAVYKLLENMPMPWEQVRDVKVLYHITGAITFVNEIPWVVEPIYLAQWGTMWIMMRREKRDRRHFKRMRFPPFDDEEPPLDYADNLLDVDPLEPIQLDLEEDEDSAVYTWFYDHKPLVKTKLINGPSYRKW...

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_032063`
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_032063

Location Chr07:15845986-15855174 (+)

Description Similar to PRP8A: Pre-mRNA-processing-splicing factor 8A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g80070`	Functions as a scaffold that mediates the ordered assembly of spliceosomal proteins and snRNAs.	No verified direct reference in this release
`At4g38780`	Functions as a scaffold that mediates the ordered assembly of spliceosomal proteins and snRNAs.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_032063 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000244 spliceosomal tri-snRNP complex assembly Biological Process

GO:0000375 RNA splicing, via transesterification reactions Biological Process

GO:0000380 alternative mRNA splicing, via spliceosome Biological Process

GO:0000387 spliceosomal snRNP assembly Biological Process

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

GO:0000393 spliceosomal conformational changes to generate catalytic conformation Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0006397 mRNA processing Biological Process

GO:0008380 RNA splicing Biological Process

GO:0045292 mRNA cis splicing, via spliceosome Biological Process

GO:0048025 negative regulation of mRNA splicing, via spliceosome Biological Process

GO:0071222 cellular response to lipopolysaccharide Biological Process

KEGG gene cross-reference

ath:AT1G80070

ath:AT4G38780

cel:CELE_C50C3.6

hsa:10594

mmu:192159

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.

Nucleus0.420

Rank 1 · LXL04_032063 · OH-1004

Cytoplasm0.282

Rank 2 · LXL04_032063 · OH-1004

Mitochondrion0.220

Rank 3 · LXL04_032063 · OH-1004

Cell membrane0.063

Rank 4 · LXL04_032063 · OH-1004

Endoplasmic reticulum0.044

Rank 5 · LXL04_032063 · 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.

PF08082.17PRO8NT91-242 aa

PF08083.17PROCN429-834 aa

PF10598.15RRM_41019-1109 aa

PF10597.15U5_2-snRNA_bdg1271-1406 aa

PF10596.15U6-snRNA_bdg1476-1634 aa

PF12134.14PRP8_domainIV1794-2023 aa

PF01398.27JAB2134-2232 aa

PF08084.17PROCT2246-2366 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032063	`PF08082.17`	PRO8NT	91	242	2.2e-84	281.7
LXL04_032063	`PF08083.17`	PROCN	429	834	3.5e-236	784.2
LXL04_032063	`PF10598.15`	RRM_4	1019	1109	5.8e-47	158.7
LXL04_032063	`PF10597.15`	U5_2-snRNA_bdg	1271	1406	2.7e-75	251.6
LXL04_032063	`PF10596.15`	U6-snRNA_bdg	1476	1634	2.6e-89	297.8
LXL04_032063	`PF12134.14`	PRP8_domainIV	1794	2023	2.7e-129	430.3
LXL04_032063	`PF01398.27`	JAB	2134	2232	2.9e-11	43.9
LXL04_032063	`PF08084.17`	PROCT	2246	2366	5.3e-50	169.2

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9SSD2`	Arabidopsis thaliana	Pre-mRNA-processing-splicing factor 8A	93.934%	Swiss-Prot	strong database homology
`Q9T0I6`	Arabidopsis thaliana	Pre-mRNA-processing-splicing factor 8B	90.599%	Swiss-Prot	strong database homology

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