TkA04G113000 | RubberDandelionOmics

Gene overview

TkA04G113000

Reference: TK1151 Chr: Chr04 Coordinates: 29332657-29344095 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1450 bp · TkA04G113000|TK1151|cDNA

GCCCAACCCGATCCCGGCCGTTCTTTCCTGGAAGAGACTTTAGGCCTCATCATCCCCTTCCGCCCAGCTTCTCCGCCTCAATCTGAGAAGCAGCCCAGCAAGAGCTGCCACCACCATGAATATTGCGACTGGAATATTATCATCCTCGTCATCTACCCTTTTCAACTTCAATCGATGTCACCAATTTGTTATTTCATCCTTCACGTCATCTTATGAAACCCACATTCGATCTTCTTGGAAAAGGAGGCCCAGCAAGAGCT...

CDS

Download CDS FASTA

906 bp · TkA04G113000|TK1151|CDS

ATGAAACCCACATTCGATCTTCTTGGAAAAGGAGGCCCAGCAAGAGCTGCCACCACCATGAATATTGCGACTGGAATATTATCATCCTCGTCATCTACCCTTTTCAACTTCAATCGATGTCACCAATTTGTTATTTCATCCTTCACGTCATCTTATGAAACCCACATTCGATCTTCTTGGAAAAGGAGGGTCTGCAGGAGCATTTCCATGTTTTCATCATCGTCTTCCCCCTCGTCTTCATCCCTTTATAGCGGTGCATC...

Protein

Download Protein FASTA

301 aa · TkA04G113000|TK1151|PROTEIN

MKPTFDLLGKGGPARAATTMNIATGILSSSSSTLFNFNRCHQFVISSFTSSYETHIRSSWKRRVCRSISMFSSSSSPSSSSLYSGASSSRIEAETIKENNKPPKQHPWLIVGLGNPGKLYNRTRHNVGFEMVDAIAEAEGISMSSVSFKAFFGKGCIGNIPMMLAKPQTFMNVSGESVGAIVSFYKIPPKQVLVIYDDLDLPFGKLRLLPKGGHGGHNGMKSVINHLKGSRDFPRLRIGIGRPPGKMEAAAFVLRRFTKQ...

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	`TkA04G113000`
TK1151 ID	TkA04G113000
OH-1004 ID	LXL04_007077
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	51.200
Protein coverage (%)	TK1151 67.442 / OH-1004 82.857 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 TkA04G113000

Location Chr04:29332657-29344095 (+)

Description Similar to CRS2: Chloroplastic group IIB intron splicing facilitator CRS2, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g18440`	The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis.	No verified direct reference in this release
`At5g19830`	The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis.	No verified direct reference in this release
`At5g16140`	Required for the splicing of group IIB introns in chloroplasts.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0693900`	The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_007077 · 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:0008380 RNA splicing Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:1990904 ribonucleoprotein complex Cellular Component

GO:0000049 tRNA binding Molecular Function

GO:0004045 peptidyl-tRNA hydrolase activity Molecular Function

KEGG gene cross-reference

ath:AT5G16140

ath:AT5G19830

ath:AT5G38290

dosa:Os01g0132800

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.

Plastid0.898

Rank 1 · TkA04G113000 · TK1151

Mitochondrion0.110

Rank 2 · TkA04G113000 · TK1151

Nucleus0.030

Rank 3 · TkA04G113000 · TK1151

Cytoplasm0.020

Rank 4 · TkA04G113000 · TK1151

Cell membrane0.010

Rank 5 · TkA04G113000 · 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.

PF01195Pept_tRNA_hydro39-72 aa

PF10500SR-2552-92 aa

PF01195Pept_tRNA_hydro109-295 aa

PF30685AAA_RNF213_6255-292 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G113000	`PF01195`	Pept_tRNA_hydro	39	72	4.3e-71	239.3
TkA04G113000	`PF10500`	SR-25	52	92	2.7	8.2
TkA04G113000	`PF01195`	Pept_tRNA_hydro	109	295	4.3e-71	239.3
TkA04G113000	`PF30685`	AAA_RNF213_6	255	292	0.15	12.9

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
`Q8GW64`	Arabidopsis thaliana	sp\|Q8GW64\|PTHC_ARATH Peptidyl-tRNA hydrolase, chloroplastic	73.000%	Swiss-Prot	High
`Q6NLS8`	Arabidopsis thaliana	sp\|Q6NLS8\|PTHM_ARATH Peptidyl-tRNA hydrolase, mitochondrial	50.800%	Swiss-Prot	Medium
`Q9LF14`	Arabidopsis thaliana	sp\|Q9LF14\|CRS2B_ARATH Chloroplastic group IIB intron splicing facilitator CRS2-B, chloroplastic	53.800%	Swiss-Prot	Medium
`Q5N9Q7`	Oryza sativa subsp. japonica	sp\|Q5N9Q7\|PTHM_ORYSJ Peptidyl-tRNA hydrolase, mitochondrial	71.600%	Swiss-Prot	Medium

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