LXL04_035553 | RubberDandelionOmics

Gene overview

LXL04_035553

Reference: OH-1004 Chr: Chr08 Coordinates: 24479478-24482308 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1542 bp · LXL04_035553|LXL04_035553|OH1004|cDNA

ATGTCTGCCCTAGAAATCGAAGCTCGCGATGTGATAAAAATAGTTCTTCAATTCTGCAAAGAGAACTCTTTGCATCAAACATTCCAAACATTACAAAGCGAGTGCCAAGTGCCTTTAAACACAGTGGACAGCCTTGAAACATTTGTAGCTGATATCAACAGTGGTAGATGGGATACAATATTACCTCAAGTGGCACAACTTAAGCTTCCTAGAAAGAAACTTGAAGATTTATATGAGCAGATTGTTCTAGAAATGATTGA...

CDS

Download CDS FASTA

1542 bp · LXL04_035553|LXL04_035553|OH1004|CDS

ATGTCTGCCCTAGAAATCGAAGCTCGCGATGTGATAAAAATAGTTCTTCAATTCTGCAAAGAGAACTCTTTGCATCAAACATTCCAAACATTACAAAGCGAGTGCCAAGTGCCTTTAAACACAGTGGACAGCCTTGAAACATTTGTAGCTGATATCAACAGTGGTAGATGGGATACAATATTACCTCAAGTGGCACAACTTAAGCTTCCTAGAAAGAAACTTGAAGATTTATATGAGCAGATTGTTCTAGAAATGATTGA...

Protein

Download Protein FASTA

513 aa · LXL04_035553|LXL04_035553|OH1004|PROTEIN

MSALEIEARDVIKIVLQFCKENSLHQTFQTLQSECQVPLNTVDSLETFVADINSGRWDTILPQVAQLKLPRKKLEDLYEQIVLEMIELRELDTARAILRQTQAMTVMKQEQPERYLRLEHLLVRTYFDPNEAYQESTKEKRRSQIAQGITEEVSVVPPSRLMALIGQALKWQQHQGLLPPGTQFDLFRGTAAMKQDVDDKYPTTLGHTIKFGKKSHPESARFSPDGQFLVSCSVDGFIEVWDHISGKLKKDLQYQAEESF...

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_035553`
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_035553

Location Chr08:24479478-24482308 (-)

Description Similar to SMU1: Suppressor of mec-8 and unc-52 protein homolog 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g73720`	Auxiliary spliceosomal protein involved in splicing of specific pre-mRNAs that affect multiple aspects of development.	Plant SMU-1 and SMU-2 homologues regulate pre-mRNA splicing and multiple aspects of development.2009 · DOI: 10.1104/pp.109.141705

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_035553 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000381 regulation of alternative mRNA splicing, via spliceosome Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0008380 RNA splicing Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0016607 nuclear speck Cellular Component

GO:0071005 U2-type precatalytic spliceosome Cellular Component

GO:0071011 precatalytic spliceosome Cellular Component

GO:0080008 Cul4-RING E3 ubiquitin ligase complex Cellular Component

KEGG gene cross-reference

ath:AT1G73720

bta:540842

cge:100736555

hsa:55234

mmu:74255

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.

Nucleus0.510

Rank 1 · LXL04_035553 · OH-1004

Cytoplasm0.491

Rank 2 · LXL04_035553 · OH-1004

Cell membrane0.063

Rank 3 · LXL04_035553 · OH-1004

Mitochondrion0.048

Rank 4 · LXL04_035553 · OH-1004

Lysosome / Vacuole0.039

Rank 5 · LXL04_035553 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF17814.8LisH_TPL7-37 aa

PF23383.2Beta-prop_IFT140_1st209-295 aa

PF23414.2Beta-prop_EML_2213-300 aa

PF24814.2WD40_Prp19214-322 aa

PF25175.2Beta-prop_WDR5217-512 aa

PF00400.39WD40218-242 aa

PF24796.2WDR55218-301 aa

PF25174.2Beta-prop_THOC3219-303 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_035553	`PF17814.8`	LisH_TPL	7	37	1.3e-15	57.4
LXL04_035553	`PF23383.2`	Beta-prop_IFT140_1st	209	295	5.2e-07	29.4
LXL04_035553	`PF23414.2`	Beta-prop_EML_2	213	300	2.8e-26	93.2
LXL04_035553	`PF24814.2`	WD40_Prp19	214	322	2.4e-36	125.9
LXL04_035553	`PF25175.2`	Beta-prop_WDR5	217	512	4.3e-57	194.3
LXL04_035553	`PF00400.39`	WD40	218	242	6.3e-46	153.6
LXL04_035553	`PF24796.2`	WDR55	218	301	5.4e-26	92.0
LXL04_035553	`PF25174.2`	Beta-prop_THOC3	219	303	9.3e-44	150.2
LXL04_035553	`PF24782.3`	WD40_MABP1-WDR62_2nd	219	328	4e-18	66.2
LXL04_035553	`PF23381.2`	Beta-prop_IFT122_1st	220	332	7.2e-44	150.9
LXL04_035553	`PF25391.2`	WD40_Gbeta	220	336	7e-17	62.1
LXL04_035553	`PF24805.2`	EIF3I	221	303	1e-25	91.3
LXL04_035553	`PF24807.2`	WD40_CDC20-Fz	221	376	2.4e-25	90.1
LXL04_035553	`PF23342.2`	WDR90_beta-prop_4th	221	348	1.5e-11	44.7
LXL04_035553	`PF23098.2`	Beta-prop_NOL10_N	221	367	2.5e-09	37.5
LXL04_035553	`PF23389.2`	Beta-prop_WDR19_1st	224	381	5.4e-07	29.7

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
`Q8W117`	Arabidopsis thaliana	Suppressor of mec-8 and unc-52 protein homolog 1	84.149%	Swiss-Prot	strong database homology

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