LXL04_010956 | RubberDandelionOmics

Gene overview

LXL04_010956

Reference: OH-1004 Chr: Chr02 Coordinates: 155672895-155678504 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2901 bp · LXL04_010956|LXL04_010956|OH1004|cDNA

ATGAGTTACACACATGGGAATGAAGATAGGCTAAGCCATTTACCTGAAGAGATTCTTTCACGTATACTCTCTTCAATCCCTACAAAATTGGCTGTGCGAACAAGCATCTTATCCAAAAAATGGAGGTACAAATGGACGTTAGTCACAATCCTCGACTTTGACGACGATCGCCCTATCGATGCTTTCCATTCCTTGTCGAATTTTGTAAACCGCGCTTTCAAACTCTGCCAAACATCCAAAATCAAGCGATTCCGGTTACG...

CDS

Download CDS FASTA

2901 bp · LXL04_010956|LXL04_010956|OH1004|CDS

ATGAGTTACACACATGGGAATGAAGATAGGCTAAGCCATTTACCTGAAGAGATTCTTTCACGTATACTCTCTTCAATCCCTACAAAATTGGCTGTGCGAACAAGCATCTTATCCAAAAAATGGAGGTACAAATGGACGTTAGTCACAATCCTCGACTTTGACGACGATCGCCCTATCGATGCTTTCCATTCCTTGTCGAATTTTGTAAACCGCGCTTTCAAACTCTGCCAAACATCCAAAATCAAGCGATTCCGGTTACG...

Protein

Download Protein FASTA

966 aa · LXL04_010956|LXL04_010956|OH1004|PROTEIN

MSYTHGNEDRLSHLPEEILSRILSSIPTKLAVRTSILSKKWRYKWTLVTILDFDDDRPIDAFHSLSNFVNRAFKLCQTSKIKRFRLRLSRYGLQTTSEVKSNISNWIKESVRLNVCEVDLHLTPFEMPVTLFTCKTLTKLSLSGWGMEGYVGSNVSIILPLLKTLHITSPINFPGRVSVNSFRLIHSCPMLESLSMEIAMCNNQEDYNFNIATLKRLKLKIVSVLSLNKVILNLPNLESLSFAGLLRSLFVVKDLSSLVD...

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_010956`
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_010956

Location Chr02:155672895-155678504 (-)

Description Similar to SUV3: DExH-box ATP-dependent RNA helicase DExH16, mitochondrial

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g14790`	Major helicase player in mitochondrial RNA metabolism.	No verified direct reference in this release
`At5g39840`	Major helicase player in mitochondrial RNA metabolism.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0746500`	Major helicase player in mitochondrial RNA metabolism.	OsSUV3 dual helicase functions in salinity stress tolerance by maintaining photosynthesis and antioxidant machinery in rice (Oryza sativa L. cv. IR64).2013 · DOI: 10.1111/tpj.12277 OsSUV3 transgenic rice maintains higher endogenous levels of plant hormones that mitigates adverse effects of salinity and sustains crop productivity.2014 · DOI: 10.1186/s12284-014-0017-2
`Os04g0459800`	Major helicase player in mitochondrial RNA metabolism.	No verified direct reference in this release
`UniProt: Q01IJ3`	Major helicase player in mitochondrial RNA metabolism.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_010956 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000965 mitochondrial RNA 3'-end processing Biological Process

GO:0009555 pollen development Biological Process

GO:0009561 megagametogenesis Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009736 cytokinin-activated signaling pathway Biological Process

GO:0009740 gibberellic acid mediated signaling pathway Biological Process

GO:0009939 positive regulation of gibberellic acid mediated signaling pathway Biological Process

GO:0010929 positive regulation of auxin mediated signaling pathway Biological Process

GO:0016070 RNA metabolic process Biological Process

GO:0080038 positive regulation of cytokinin-activated signaling pathway Biological Process

GO:1901002 positive regulation of response to salt stress Biological Process

KEGG gene cross-reference

ath:AT4G14790

ath:AT5G39840

dosa:Os03g0746500

dosa:Os04g0459800

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Nucleus0.612

Rank 1 · LXL04_010956 · OH-1004

Cytoplasm0.186

Rank 2 · LXL04_010956 · OH-1004

Plastid0.178

Rank 3 · LXL04_010956 · OH-1004

Mitochondrion0.061

Rank 4 · LXL04_010956 · OH-1004

Cell membrane0.028

Rank 5 · LXL04_010956 · 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.

PF00646.39F-box11-46 aa

PF24758.2LRR_At5g56370105-242 aa

PF08387.16FBD351-396 aa

PF22527.3DEXQc_Suv3477-630 aa

PF00271.38Helicase_C650-756 aa

PF18147.7Suv3_C_1838-879 aa

PF12513.16SUV3_C904-951 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_010956	`PF00646.39`	F-box	11	46	9e-06	26.1
LXL04_010956	`PF24758.2`	LRR_At5g56370	105	242	1.2e-07	32.3
LXL04_010956	`PF08387.16`	FBD	351	396	1.7e-11	44.5
LXL04_010956	`PF22527.3`	DEXQc_Suv3	477	630	1.4e-65	220.2
LXL04_010956	`PF00271.38`	Helicase_C	650	756	3.2e-12	47.4
LXL04_010956	`PF18147.7`	Suv3_C_1	838	879	6.5e-09	36.3
LXL04_010956	`PF12513.16`	SUV3_C	904	951	6.8e-16	58.5

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
`Q9SMX1`	Arabidopsis thaliana	DExH-box ATP-dependent RNA helicase DExH16, mitochondrial	72.490%	Swiss-Prot	moderate database homology
`F4KFV7`	Arabidopsis thaliana	DExH-box ATP-dependent RNA helicase DExH18, mitochondrial	41.845%	Swiss-Prot	weak database homology
`Q10D00`	Oryza sativa subsp. japonica	ATP-dependent RNA helicase SUV3, mitochondrial	72.817%	Swiss-Prot	moderate database homology
`Q7X745`	Oryza sativa subsp. japonica	ATP-dependent RNA helicase SUV3L, mitochondrial	43.818%	Swiss-Prot	weak database homology
`Q01IJ3`	Oryza sativa subsp. indica	ATP-dependent RNA helicase SUV3L, mitochondrial	43.818%	Swiss-Prot	weak database homology

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