TkA01G399800 | RubberDandelionOmics

Gene overview

TkA01G399800

Reference: TK1151 Chr: Chr01 Coordinates: 99782290-99783124 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

507 bp · TkA01G399800|TK1151|cDNA

ATGGAAGTGCGCCAGAGCATTCTGTTGGCAGTTCAAGAGCTTGAGAAACGGTTCCCTCAAGGCCTTCCAAAACTTAATCCTATCAAGGATATAGGGATAGAAGAACCTCAGTTTGTAGACCTGGTAAATCAAATTGAGAAACTTGAACAACAATTGCTTTCTCACCCACTAAACAAGTCTCAAGACGAAAGCCAGATCCAATGTTTCCAGAGGAAAGCGGAAGTGAATCATGAAATTCAACAGTTGAAAACAAAAATGCG...

CDS

Download CDS FASTA

507 bp · TkA01G399800|TK1151|CDS

ATGGAAGTGCGCCAGAGCATTCTGTTGGCAGTTCAAGAGCTTGAGAAACGGTTCCCTCAAGGCCTTCCAAAACTTAATCCTATCAAGGATATAGGGATAGAAGAACCTCAGTTTGTAGACCTGGTAAATCAAATTGAGAAACTTGAACAACAATTGCTTTCTCACCCACTAAACAAGTCTCAAGACGAAAGCCAGATCCAATGTTTCCAGAGGAAAGCGGAAGTGAATCATGAAATTCAACAGTTGAAAACAAAAATGCG...

Protein

Download Protein FASTA

168 aa · TkA01G399800|TK1151|PROTEIN

MEVRQSILLAVQELEKRFPQGLPKLNPIKDIGIEEPQFVDLVNQIEKLEQQLLSHPLNKSQDESQIQCFQRKAEVNHEIQQLKTKMRDSQLQKFRDELKNRSRVLKKLGHIDADSIVQVKGRAACLIDTGDELLVTELMFNGTFNEYETMEEIGKLNPQARQWLESHY

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	`TkA01G399800`
TK1151 ID	TkA01G399800
OH-1004 ID	LXL04_001312
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	37.300
Protein coverage (%)	TK1151 93.452 / OH-1004 16.084 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA01G399800

Location Chr01:99782290-99783124 (+)

Description Similar to MTR4: DExH-box ATP-dependent RNA helicase DExH9

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g06990`	ATP-dependent RNA helicase that associates with the RNA exosome complex, with the cap binding complex (CBC) and with the NEXT- like complex.	The RNA helicases AtMTR4 and HEN2 target specific subsets of nuclear transcripts for degradation by the nuclear exosome in Arabidopsis thaliana.2014 · DOI: 10.1371/journal.pgen.1004564

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_001312 · 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:0000292 RNA fragment catabolic process Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0000460 maturation of 5.8S rRNA Biological Process

GO:0000467 exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Biological Process

GO:0006364 rRNA processing Biological Process

GO:0006397 mRNA processing Biological Process

GO:0006401 RNA catabolic process Biological Process

GO:0006974 DNA damage response Biological Process

GO:0008380 RNA splicing Biological Process

GO:0016075 rRNA catabolic process Biological Process

GO:0016076 snRNA catabolic process Biological Process

GO:0031125 rRNA 3'-end processing Biological Process

KEGG gene cross-reference

ath:AT1G59760

hsa:23517

mmu:72198

sce:YJL050W

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.

Cytoplasm0.559

Rank 1 · TkA01G399800 · TK1151

Nucleus0.456

Rank 2 · TkA01G399800 · TK1151

Mitochondrion0.076

Rank 3 · TkA01G399800 · TK1151

Cell membrane0.035

Rank 4 · TkA01G399800 · TK1151

Endoplasmic reticulum0.025

Rank 5 · TkA01G399800 · TK1151

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.

PF13234MTR4_beta-barrel3-88 aa

PF06292MUN9-121 aa

PF03568Separin_C42-106 aa

PF07817GLE144-100 aa

PF08148DSHCT66-93 aa

PF30413Tnp_IS1634_N94-114 aa

PF13234MTR4_beta-barrel113-167 aa

PF08148DSHCT115-150 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G399800	`PF13234`	MTR4_beta-barrel	3	88	1.4e-21	78.4
TkA01G399800	`PF06292`	MUN	9	121	0.021	14.5
TkA01G399800	`PF03568`	Separin_C	42	106	0.11	12.3
TkA01G399800	`PF07817`	GLE1	44	100	0.2	11.6
TkA01G399800	`PF08148`	DSHCT	66	93	5.3e-09	36.8
TkA01G399800	`PF30413`	Tnp_IS1634_N	94	114	0.046	14.3
TkA01G399800	`PF13234`	MTR4_beta-barrel	113	167	1.4e-21	78.4
TkA01G399800	`PF08148`	DSHCT	115	150	5.3e-09	36.8
TkA01G399800	`PF03568`	Separin_C	117	164	0.11	12.3

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
`Q9ZVW2`	Arabidopsis thaliana	sp\|Q9ZVW2\|HEN2_ARATH DExH-box ATP-dependent RNA helicase DExH10	77.400%	Swiss-Prot	High

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