LXL04_026453 | RubberDandelionOmics

Gene overview

LXL04_026453

Reference: OH-1004 Chr: Chr05 Coordinates: 126486676-126493426 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

6648 bp · LXL04_026453|LXL04_026453|OH1004|cDNA

ATGGCACATCTAGGCGGGGGTGCTGAGGCACATGCCCGATTTAAGCAGTATGAATACAGAGCCAACTCGAGTCTTGTGTTGACAACTGATTCTCGGCCACGTGATACACATGAGCCAACCGGAGAGCCTGAGTCTCTGTATGGGAAGATAGACCCTAAGAGTTTTGGTGACCGTGCTTAtagaggaagaccacaagaGCTGGATGAGAAAATCACCAAGtctaagaagaagaaggaacgTGATCCCTCACTTGCTTCTGG...

CDS

Download CDS FASTA

6648 bp · LXL04_026453|LXL04_026453|OH1004|CDS

ATGGCACATCTAGGCGGGGGTGCTGAGGCACATGCCCGATTTAAGCAGTATGAATACAGAGCCAACTCGAGTCTTGTGTTGACAACTGATTCTCGGCCACGTGATACACATGAGCCAACCGGAGAGCCTGAGTCTCTGTATGGGAAGATAGACCCTAAGAGTTTTGGTGACCGTGCTTATAGAGGAAGACCACAAGAGCTGGATGAGAAAATCACCAAGTCTAAGAAGAAGAAGGAACGTGATCCCTCACTTGCTTCTGG...

Protein

Download Protein FASTA

2215 aa · LXL04_026453|LXL04_026453|OH1004|PROTEIN

MAHLGGGAEAHARFKQYEYRANSSLVLTTDSRPRDTHEPTGEPESLYGKIDPKSFGDRAYRGRPQELDEKITKSKKKKERDPSLASGEAGNNRHSKRRRLQEESVLTSTDEGVYQPKTKETRAAYEAMLSVIQTQLGGQPLNIVSGAADEILAVLKSDTLKNPEKKKDIEKLLNPIPNQVFDQLVSIGRLITDFQDAGGDADGSNAANGEDALDDDVGVAVEFEENEEDDEESDLDIVQEDDEDEDDDGLDRDRSKAMQM...

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_026453`
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_026453

Location Chr05:126486676-126493426 (-)

Description Similar to BRR2A: DExH-box ATP-dependent RNA helicase DExH12

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g20960`	RNA helicase that plays an essential role in pre-mRNA splicing as component of the U5 snRNP and U4/U6-U5 tri-snRNP complexes.	No verified direct reference in this release
`At2g42270`	RNA helicase that plays an essential role in pre-mRNA splicing as component of the U5 snRNP and U4/U6-U5 tri-snRNP complexes.	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_026453 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000244 spliceosomal tri-snRNP complex assembly Biological Process

GO:0000354 cis assembly of pre-catalytic 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:0000398 mRNA splicing, via spliceosome Biological Process

GO:0006397 mRNA processing Biological Process

GO:0010228 vegetative to reproductive phase transition of meristem Biological Process

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

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005681 spliceosomal complex Cellular Component

GO:0005682 U5 snRNP Cellular Component

KEGG gene cross-reference

ath:AT1G20960

ath:AT2G42270

hsa:23020

mmu:320632

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.

Nucleus0.923

Rank 1 · LXL04_026453 · OH-1004

Cytoplasm0.142

Rank 2 · LXL04_026453 · OH-1004

Mitochondrion0.023

Rank 3 · LXL04_026453 · OH-1004

Cell membrane0.019

Rank 4 · LXL04_026453 · OH-1004

Endoplasmic reticulum0.011

Rank 5 · LXL04_026453 · 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.

PF21188.3BRR2_plug121-186 aa

PF18149.7Helicase_PWI277-386 aa

PF04851.22ResIII517-692 aa

PF00270.36DEAD519-696 aa

PF00271.38Helicase_C813-895 aa

PF23445.2WHD_SNRNP200926-993 aa

PF02889.22Sec631042-1344 aa

PF00270.36DEAD1388-1562 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026453	`PF21188.3`	BRR2_plug	121	186	8.6e-10	39.6
LXL04_026453	`PF18149.7`	Helicase_PWI	277	386	2.3e-34	118.7
LXL04_026453	`PF04851.22`	ResIII	517	692	8.8e-27	94.7
LXL04_026453	`PF00270.36`	DEAD	519	696	1.3e-67	227.5
LXL04_026453	`PF00271.38`	Helicase_C	813	895	1.4e-14	55.0
LXL04_026453	`PF23445.2`	WHD_SNRNP200	926	993	1.3e-63	211.8
LXL04_026453	`PF02889.22`	Sec63	1042	1344	4.7e-167	554.2
LXL04_026453	`PF00270.36`	DEAD	1388	1562	1.3e-67	227.5
LXL04_026453	`PF04851.22`	ResIII	1388	1526	8.8e-27	94.7
LXL04_026453	`PF23445.2`	WHD_SNRNP200	1792	1873	1.3e-63	211.8
LXL04_026453	`PF02889.22`	Sec63	1880	2199	4.7e-167	554.2

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
`Q9SYP1`	Arabidopsis thaliana	DExH-box ATP-dependent RNA helicase DExH12	76.878%	Swiss-Prot	strong database homology
`O48534`	Arabidopsis thaliana	DExH-box ATP-dependent RNA helicase DExH13	71.293%	Swiss-Prot	strong database homology

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