LXL04_022427 | RubberDandelionOmics

Gene overview

LXL04_022427

Reference: OH-1004 Chr: Chr04 Coordinates: 150198828-150214456 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

8856 bp · LXL04_022427|LXL04_022427|OH1004|cDNA

ATGTCTCTCCCGGCTCTGGACTGTAAATACGTGACCGAAGATTGTATTCGTGAATGGAAGAATGGTAGCACTAGCTTTAGACCGCCTTCTCCGGCACCGGTTATTCGATATCTTTATGAACTTTGTTGGAATATCGTTAGAGGTGAGCTACCGGTTCACAAGTGTAAATCAGCACTCGAGTTGGTTGAGTTTACCGACAGAGTTTCTGATGAAGAAGTGTCTTCAAATTTAGCTGATATTGTTTCCCAAATGGCTCAAGA...

CDS

Download CDS FASTA

8856 bp · LXL04_022427|LXL04_022427|OH1004|CDS

ATGTCTCTCCCGGCTCTGGACTGTAAATACGTGACCGAAGATTGTATTCGTGAATGGAAGAATGGTAGCACTAGCTTTAGACCGCCTTCTCCGGCACCGGTTATTCGATATCTTTATGAACTTTGTTGGAATATCGTTAGAGGTGAGCTACCGGTTCACAAGTGTAAATCAGCACTCGAGTTGGTTGAGTTTACCGACAGAGTTTCTGATGAAGAAGTGTCTTCAAATTTAGCTGATATTGTTTCCCAAATGGCTCAAGA...

Protein

Download Protein FASTA

2951 aa · LXL04_022427|LXL04_022427|OH1004|PROTEIN

MSLPALDCKYVTEDCIREWKNGSTSFRPPSPAPVIRYLYELCWNIVRGELPVHKCKSALELVEFTDRVSDEEVSSNLADIVSQMAQDLTMPGESRARLVKLAKWMVEHSVVSLRLFHERCEEEFLWDSEMIKIKATDLKSKEVRVNTRLLYQQTKFNLLREESEGYAKLVTLLCQGSEVCSQNTSAATVGIIKSLIGHFNLDPNRVFDIVLECFELQPDNEVFLNLIPIFPKSNASQILGFKFQYYQRLEVNSSVPFGLY...

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_022427`
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_022427

Location Chr04:150198828-150214456 (+)

Description Similar to THO2: THO complex subunit 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g24706`	Acts as a component of the THO subcomplex of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_022427 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006397 mRNA processing Biological Process

GO:0006406 mRNA export from nucleus Biological Process

GO:0008380 RNA splicing Biological Process

GO:0035196 miRNA processing Biological Process

GO:1990428 miRNA transport Biological Process

GO:0000347 THO complex Cellular Component

GO:0000445 THO complex part of transcription export complex Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0016607 nuclear speck Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G24706

cjc:100399788

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.

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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.

Nucleus0.833

Rank 1 · LXL04_022427 · OH-1004

Cytoplasm0.203

Rank 2 · LXL04_022427 · OH-1004

Cell membrane0.032

Rank 3 · LXL04_022427 · OH-1004

Mitochondrion0.031

Rank 4 · LXL04_022427 · OH-1004

Endoplasmic reticulum0.017

Rank 5 · LXL04_022427 · 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.

PF16134.11THOC2_N38-410 aa

PF16134.11THOC2_N420-562 aa

PF11732.14Thoc2564-639 aa

PF11262.14Tho2883-1104 aa

PF03732.25PEG10_N-capsid1224-1296 aa

PF19259.5Ty3_capsid1246-1373 aa

PF13975.12gag-asp_proteas1496-1586 aa

PF08284.17RVP_21501-1587 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022427	`PF16134.11`	THOC2_N	38	410	1.6e-65	222.7
LXL04_022427	`PF16134.11`	THOC2_N	420	562	1.6e-65	222.7
LXL04_022427	`PF11732.14`	Thoc2	564	639	3.9e-29	101.2
LXL04_022427	`PF11262.14`	Tho2	883	1104	7.8e-90	301.9
LXL04_022427	`PF03732.25`	PEG10_N-capsid	1224	1296	9.1e-08	33.1
LXL04_022427	`PF19259.5`	Ty3_capsid	1246	1373	1.9e-07	31.4
LXL04_022427	`PF13975.12`	gag-asp_proteas	1496	1586	4.4e-06	27.9
LXL04_022427	`PF08284.17`	RVP_2	1501	1587	9.9e-10	39.1
LXL04_022427	`PF30863.1`	PRO_PEG10-RTL1	1507	1603	3.7e-07	31.3
LXL04_022427	`PF00078.33`	RVT_1	1709	1868	3.1e-42	145.5
LXL04_022427	`PF17919.8`	RT_RNaseH_2	1931	2024	2.5e-27	95.6
LXL04_022427	`PF17917.8`	RT_RNaseH	1957	2024	1.4e-17	64.5
LXL04_022427	`PF17921.8`	Integrase_H2C2	2110	2161	2.4e-14	53.9
LXL04_022427	`PF24626.2`	SH3_Tf2-1	2346	2380	8.1e-10	39.4
LXL04_022427	`PF11262.14`	Tho2	2426	2528	7.8e-90	301.9

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
`F4IAT2`	Arabidopsis thaliana	THO complex subunit 2	75.463%	Swiss-Prot	weak database homology

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