LXL04_021981 | RubberDandelionOmics

Gene overview

LXL04_021981

Reference: OH-1004 Chr: Chr04 Coordinates: 141832699-141836683 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3639 bp · LXL04_021981|LXL04_021981|OH1004|cDNA

ATGTATCTCTACAATCTCACCCTCCAACAAGCCACCGGCATCGTCTGTGCCATCAACGGTAGCTTCTCCGGCGGTAACAAGTCCCAAGAAATAGTCGTCGCCCGCGGAAAAGTCCTCGAACTCCTACGCCCCGACGAAAACGGTAAGATCCAGACTATCCTTTCCGTTGATGTTTTCGGTGCTATTAGATCCCTAGCGCAGTTTAGGTTAACCGGTGCCCAAAAGGATTACATCGTTGTCGGTTCTGATTCCGGCCGTAT...

CDS

Download CDS FASTA

3639 bp · LXL04_021981|LXL04_021981|OH1004|CDS

ATGTATCTCTACAATCTCACCCTCCAACAAGCCACCGGCATCGTCTGTGCCATCAACGGTAGCTTCTCCGGCGGTAACAAGTCCCAAGAAATAGTCGTCGCCCGCGGAAAAGTCCTCGAACTCCTACGCCCCGACGAAAACGGTAAGATCCAGACTATCCTTTCCGTTGATGTTTTCGGTGCTATTAGATCCCTAGCGCAGTTTAGGTTAACCGGTGCCCAAAAGGATTACATCGTTGTCGGTTCTGATTCCGGCCGTAT...

Protein

Download Protein FASTA

1212 aa · LXL04_021981|LXL04_021981|OH1004|PROTEIN

MYLYNLTLQQATGIVCAINGSFSGGNKSQEIVVARGKVLELLRPDENGKIQTILSVDVFGAIRSLAQFRLTGAQKDYIVVGSDSGRIVILEYNKEKNVFDKIHQETFGKSGSRRIVPGQYLAIDPKGRAVMIGACEKQKLVYVLNRDTAARLTISSPLEAHKSHTITYSITGVDCGFDNPIFAAIELDYSEADQDSTGQAANEAQKHLTFYELDLGLNHVSRKWSEQVDNGANMLVTVPGGGDGPSGVLVCAENFVIYKN...

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_021981`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_021981

Location Chr04:141832699-141836683 (+)

Description Similar to SAP130B: Spliceosome-associated protein 130 B

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g55220`	Subunit of the splicing factor SF3B required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA.	AtSAP130/AtSF3b-3 function is required for reproduction in Arabidopsis thaliana.2011 · DOI: 10.1093/pcp/pcr077
`At3g55200`	Subunit of the splicing factor SF3B required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA.	AtSAP130/AtSF3b-3 function is required for reproduction in Arabidopsis thaliana.2011 · DOI: 10.1093/pcp/pcr077

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021981 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000375 RNA splicing, via transesterification reactions 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:0000398 mRNA splicing, via spliceosome Biological Process

GO:0006282 regulation of DNA repair Biological Process

GO:0008380 RNA splicing Biological Process

GO:0009555 pollen development Biological Process

GO:0009846 pollen germination Biological Process

GO:0042177 negative regulation of protein catabolic process Biological Process

GO:0043484 regulation of RNA splicing Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

GO:0048481 plant ovule development Biological Process

KEGG gene cross-reference

ath:AT3G55200

ath:AT3G55220

bta:504962

hsa:23450

mmu:101943

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.

Nucleus0.806

Rank 1 · LXL04_021981 · OH-1004

Cytoplasm0.217

Rank 2 · LXL04_021981 · OH-1004

Cell membrane0.036

Rank 3 · LXL04_021981 · OH-1004

Lysosome / Vacuole0.031

Rank 4 · LXL04_021981 · OH-1004

Endoplasmic reticulum0.030

Rank 5 · LXL04_021981 · 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.

PF10433.16Beta-prop_RSE1_1st14-368 aa

PF23726.2Beta-prop_RSE1_2nd443-763 aa

PF03178.22CPSF_A859-1178 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021981	`PF10433.16`	Beta-prop_RSE1_1st	14	368	2.3e-121	405.8
LXL04_021981	`PF23726.2`	Beta-prop_RSE1_2nd	443	763	6.1e-91	305.9
LXL04_021981	`PF03178.22`	CPSF_A	859	1178	1.2e-94	318.0

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
`P0DKL6`	Arabidopsis thaliana	Spliceosome-associated protein 130 B	86.337%	Swiss-Prot	strong database homology
`P0DKL4`	Arabidopsis thaliana	Spliceosome-associated protein 130 A	86.337%	Swiss-Prot	strong database homology

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