TkA05G465930 | RubberDandelionOmics

Gene overview

TkA05G465930

Reference: TK1151 Chr: Chr05 Coordinates: 116802717-116814552 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

6348 bp · TkA05G465930|TK1151|cDNA

GGAGCCGCCTCTCTTTGTGAAATCGTCGCTCGCATCAGTCGCAAGAACACAGACGCCTATCGAAGAAGCTCCGATTCCTCCTCTGTCGCTGCCAGACGCCGATCCCACCTCCGGCCTCCGATTCCACCTCCGGCCTCCGATTCCACCTCCGGCACGCACAGTCAAATTATCAAATTGGAACAACGTTTTATTGGGTACTACGCACCTACGGGTTTGATGGACGCCATCTTATTTTCGAATCAACCAAAAAGAATCAACCA...

CDS

Download CDS FASTA

4824 bp · TkA05G465930|TK1151|CDS

ATGTCTCTCCCGGCTCTGGACTGTAAATACGTGACCGAAGATTGTATTCGTGAATGGAAGAATGGTAGCACTAGCTTTAGACCGCCTTCTCCGGCACCGGTTATTCGATATCTTTATGAACTTTGTTGGAATATCGTTAGAGGTGAGCTACCGGTTCACAAGTGTAAATCAGCACTGGAGTTGGTTGAGTTTTCTGACAGAGTTTCTGATGAAGAAGTGTCTTCAAATTTAGCTGATATTGTTTCCCAAATGGCTCAAGA...

Protein

Download Protein FASTA

1607 aa · TkA05G465930|TK1151|PROTEIN

MSLPALDCKYVTEDCIREWKNGSTSFRPPSPAPVIRYLYELCWNIVRGELPVHKCKSALELVEFSDRVSDEEVSSNLADIVSQMAQDLTMPGESRARLVKLAKWMVEHSVVSLRLFHERCEEEFLWDSEMIKIKATDLKSKEVRVNTRLLYQQTKFNLLREESEGYAKLVTLLCQGSEVCSQNTSAATVGIIKSLIGHFNLDPNRVFDIVLECFELQPDNEVFLNLIPIFPKSNASQILGFKFQYYQRLEVNSSVPFGLY...

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	`TkA05G465930`
TK1151 ID	TkA05G465930
OH-1004 ID	LXL04_022427
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	52.500
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
Source version	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

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Basic Information and Functional Annotation

Gene ID TkA05G465930

Location Chr05:116802717-116814552 (+)

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

View annotation sources

Functional annotation source: OH1004 · LXL04_022427 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

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.

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.

Nucleus0.944

Rank 1 · TkA05G465930 · TK1151

Cytoplasm0.133

Rank 2 · TkA05G465930 · TK1151

Cell membrane0.024

Rank 3 · TkA05G465930 · TK1151

Mitochondrion0.014

Rank 4 · TkA05G465930 · TK1151

Golgi apparatus0.009

Rank 5 · TkA05G465930 · TK1151

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.

PF16134THOC2_N38-410 aa

PF16134THOC2_N420-562 aa

PF11732Thoc2564-639 aa

PF28763ABPF_N612-688 aa

PF29026DUF4350_C659-698 aa

PF11262Tho2883-1178 aa

PF01803LIM_bind901-949 aa

PF29026DUF4350_C918-952 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA05G465930	`PF16134`	THOC2_N	38	410	4.5e-63	214.7
TkA05G465930	`PF16134`	THOC2_N	420	562	4.5e-63	214.7
TkA05G465930	`PF11732`	Thoc2	564	639	1.9e-29	102.2
TkA05G465930	`PF28763`	ABPF_N	612	688	0.036	14.5
TkA05G465930	`PF29026`	DUF4350_C	659	698	0.17	12.9
TkA05G465930	`PF11262`	Tho2	883	1178	2e-98	330.1
TkA05G465930	`PF01803`	LIM_bind	901	949	0.92	9.7
TkA05G465930	`PF29026`	DUF4350_C	918	952	0.17	12.9
TkA05G465930	`PF01803`	LIM_bind	1083	1145	0.92	9.7
TkA05G465930	`PF01803`	LIM_bind	1275	1275	0.92	9.7
TkA05G465930	`PF16134`	THOC2_N	1462	1504	4.5e-63	214.7
TkA05G465930	`PF11262`	Tho2	1483	1513	2e-98	330.1

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	sp\|F4IAT2\|THOC2_ARATH THO complex subunit 2	76.000%	Swiss-Prot	High

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