TkAUNG088770 | RubberDandelionOmics

Gene overview

TkAUNG088770

Reference: TK1151 Chr: ChrUn Coordinates: 25195969-25198079 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2067 bp · TkAUNG088770|TK1151|cDNA

ATGCAAGCTCTGAGTGTATGGCCAACAAACACTGATATTTTCTTGAACCTTGACTCCGCCCCTCATTTTGTGGGGAGAAAAGGTAGAAACCCTAGTATTTCGAGGGGTTTTAGAAGTAGGTTTGGTTTCAGGGAGACGAGTGATGATTTACGACATGGCGTACCTTGCAGATGCTCTCGAGTTAATCGTCATGTGTTTTGGCGGCCAAAGAAGCGTTCATTTTGTTCGTCAGTTGTCCCCTTGGCTTTGGCATTTGAAGA...

CDS

Download CDS FASTA

2067 bp · TkAUNG088770|TK1151|CDS

ATGCAAGCTCTGAGTGTATGGCCAACAAACACTGATATTTTCTTGAACCTTGACTCCGCCCCTCATTTTGTGGGGAGAAAAGGTAGAAACCCTAGTATTTCGAGGGGTTTTAGAAGTAGGTTTGGTTTCAGGGAGACGAGTGATGATTTACGACATGGCGTACCTTGCAGATGCTCTCGAGTTAATCGTCATGTGTTTTGGCGGCCAAAGAAGCGTTCATTTTGTTCGTCAGTTGTCCCCTTGGCTTTGGCATTTGAAGA...

Protein

Download Protein FASTA

688 aa · TkAUNG088770|TK1151|PROTEIN

MQALSVWPTNTDIFLNLDSAPHFVGRKGRNPSISRGFRSRFGFRETSDDLRHGVPCRCSRVNRHVFWRPKKRSFCSSVVPLALAFEEQVVVDKPDSNSDGENKREDEKSLGETKEKRVNTRELAWSLRDAKTAEDVEMVLGDKSDLPLQVYSSMIRGFGKDKRVNSAMALVNWLKVKKHDSKSPPGPNLFIYNSLLGAMKQAEEFNHVDKIMEDMALEGVSPNVVTYNTLMGIHLAQGHEAKALELFKEIQTKGLSPSPA...

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	`TkAUNG088770`
TK1151 ID	TkAUNG088770
OH-1004 ID	LXL04_013252
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	100.000
Protein coverage (%)	TK1151 70.203 / OH-1004 71.029 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 TkAUNG088770

Location ChrUn:25195969-25198079 (-)

Description Similar to LPE1: Protein LOW PHOTOSYNTHETIC EFFICIENCY 1, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g46610`	Required for light-regulated photosystem II (PSII) biogenesis and grana thylakoids formation by binding to the 5' UTR of PSII subunit mRNAs (e.g. psbJ, psbN and psbA) in a light-dependent manner through a redox-based mechanism, and facilitating the association of HCF173 with target mRNAs, which encodes PSII reaction center proteins (e.g. J, N and D1), thus regulating its expression by modulating ribosome loading.	LOW PHOTOSYNTHETIC EFFICIENCY 1 is required for light-regulated photosystem II biogenesis in Arabidopsis.2018 · DOI: 10.1073/pnas.1807364115 The Arabidopsis pentatricopeptide repeat protein LPE1 and its maize ortholog are required for translation of the chloroplast psbJ RNA.2019 · DOI: 10.1111/tpj.14308

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_013252 · 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:0006413 translational initiation Biological Process

GO:0009416 response to light stimulus Biological Process

GO:0010207 photosystem II assembly Biological Process

GO:0032544 plastid translation Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009535 chloroplast thylakoid membrane Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

GO:0008494 translation activator activity Molecular Function

KEGG gene cross-reference

ath:AT1G62930

ath:AT1G63080

ath:AT3G46610

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.

Plastid0.825

Rank 1 · TkAUNG088770 · TK1151

Mitochondrion0.113

Rank 2 · TkAUNG088770 · TK1151

Nucleus0.046

Rank 3 · TkAUNG088770 · TK1151

Cytoplasm0.015

Rank 4 · TkAUNG088770 · TK1151

Cell membrane0.010

Rank 5 · TkAUNG088770 · 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.

PF19189Mtf2115-234 aa

PF23276TPR_24129-250 aa

PF29070MSC6_N133-273 aa

PF17177PPR_long149-204 aa

PF13041PPR_2150-178 aa

PF01535PPR150-171 aa

PF12854PPR_1151-172 aa

PF13041PPR_2187-231 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkAUNG088770	`PF19189`	Mtf2	115	234	0.1	13.0
TkAUNG088770	`PF23276`	TPR_24	129	250	4.4e-16	59.7
TkAUNG088770	`PF29070`	MSC6_N	133	273	6.5e-17	62.4
TkAUNG088770	`PF17177`	PPR_long	149	204	7.4e-28	98.1
TkAUNG088770	`PF13041`	PPR_2	150	178	4e-58	194.0
TkAUNG088770	`PF01535`	PPR	150	171	1.6e-41	138.3
TkAUNG088770	`PF12854`	PPR_1	151	172	4.7e-22	78.1
TkAUNG088770	`PF13041`	PPR_2	187	231	4e-58	194.0
TkAUNG088770	`PF13812`	PPR_3	187	233	3.5e-41	139.8
TkAUNG088770	`PF12854`	PPR_1	187	196	4.7e-22	78.1
TkAUNG088770	`PF28753`	RMD9_N	188	207	0.11	13.1
TkAUNG088770	`PF23436`	RabGap-TBC_2	189	220	0.087	13.2
TkAUNG088770	`PF01535`	PPR	191	220	1.6e-41	138.3
TkAUNG088770	`PF17177`	PPR_long	203	275	7.4e-28	98.1
TkAUNG088770	`PF28771`	RMD9_mid	208	253	0.063	13.7
TkAUNG088770	`PF13812`	PPR_3	210	267	3.5e-41	139.8

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
`Q9SNB7`	Arabidopsis thaliana	sp\|Q9SNB7\|PP264_ARATH Protein LOW PHOTOSYNTHETIC EFFICIENCY 1, chloroplastic	60.200%	Swiss-Prot	Medium

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