TkA03G003990 | RubberDandelionOmics

Gene overview

TkA03G003990

Reference: TK1151 Chr: Chr03 Coordinates: 961414-968436 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1139 bp · TkA03G003990|TK1151|cDNA

GCCCCTCACCTGTTACCTTGATGGAATGACATGGCTGCTGAATTCTCCGGATCAATCTCTAGCCTTGATTTTGGCGGACCATGGTTATGATGTGTGGATTGCCAACACCAGAGGAACCTCCTTTAGTCGACGACATGTTTCTCTTAATCCTGACATGCCCGAATTCTGGAATTGGACATGGGATGAAATCGCGGCTCGTGACTTGCCTGCTGTTATCGCATATATCTTCCAACAAACTAACCAAAAGATCCACTACGTCG...

CDS

Download CDS FASTA

1476 bp · TkA03G003990|TK1151|CDS

ATGTTTGCTACAAAAAACCTTCAAAAGCGCTGCTTTCAAACCATCGCCTCCCGTTTCATTACCGATTGGTCCAGGGATGTGAAGTTGTTAAGTATCCGTAATAATACACCACGGTATGCAATCCATTCGAGTTTTGTGATTAGAGAGGAGACATTGGGAAATTGGTTGGATGGATATCGGGCGTTTTCTACTTGTAAAGGTCGGAGTATGAGGAGTAAAGTGGAGATGCGAATGAAGAAAGAGTCTGGCAAAACCCTAAG...

Protein

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491 aa · TkA03G003990|TK1151|PROTEIN

MFATKNLQKRCFQTIASRFITDWSRDVKLLSIRNNTPRYAIHSSFVIREETLGNWLDGYRAFSTCKGRSMRSKVEMRMKKESGKTLREIRRAKKIQKKLMTDEERLIYNLKRAKKKVALLLQKLKKYELPELPPPRHDPELLTPEQVQALKKIGFRNRNYVPVGVRGVFGGVVQNMHMHWKFHETVQVCCDNFPKEKIKEMATMLARLSGGIVVNIHNVKTIIMFRGRNYRQPKNLIPINTLTKRKALFKARFEQALDSQ...

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	`TkA03G003990`
TK1151 ID	TkA03G003990
OH-1004 ID	LXL04_000772
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	47.700
Protein coverage (%)	TK1151 35.031 / OH-1004 39.101 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

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Basic Information and Functional Annotation

Gene ID TkA03G003990

Location Chr03:961414-968436 (-)

Description Similar to At3g25440: Uncharacterized CRM domain-containing protein At3g25440, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g27550`	Involved in the splicing of group II introns in mitochondria.	CFM9, a Mitochondrial CRM Protein, Is Crucial for Mitochondrial Intron Splicing, Mitochondria Function and Arabidopsis Growth and Stress Responses.2019 · DOI: 10.1093/pcp/pcz147
`At5g14180`	Triacylglycerol (TAG) lipase.	No verified direct reference in this release
`At2g15230`	Triacylglycerol (TAG) lipase active on triolein, trioctanoin, tributyrin and 1,3-Diolein, but not on phospho- and galactolipids.	Identification and characterization of a triacylglycerol lipase in Arabidopsis homologous to mammalian acid lipases.2005 · DOI: 10.1016/j.febslet.2005.09.072
`At3g25440`	Uncharacterized CRM domain-containing protein At3g25440, chloroplastic.	No verified direct reference in this release
`At5g16180`	Required for the splicing of group IIA introns in chloroplasts, by regulating the intron folding.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os08g0360100`	Required for the splicing of group IIA introns in chloroplasts, by regulating the intron folding.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_000772 · 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:0000373 Group II intron splicing Biological Process

GO:0006397 mRNA processing Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0048316 seed development Biological Process

GO:0140040 mitochondrial polycistronic RNA processing 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:0003723 RNA binding Molecular Function

KEGG gene cross-reference

ath:AT3G23070

ath:AT3G25440

ath:AT3G27550

dosa:Os11g0592400

zma:100126360

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.

Mitochondrion0.872

Rank 1 · TkA03G003990 · TK1151

Nucleus0.078

Rank 2 · TkA03G003990 · TK1151

Plastid0.053

Rank 3 · TkA03G003990 · TK1151

Cytoplasm0.041

Rank 4 · TkA03G003990 · TK1151

Cell membrane0.012

Rank 5 · TkA03G003990 · 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.

PF01985CRS1_YhbY142-226 aa

PF01985CRS1_YhbY315-347 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G003990	`PF01985`	CRS1_YhbY	142	226	1.9e-15	57.7
TkA03G003990	`PF01985`	CRS1_YhbY	315	347	1.9e-15	57.7

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
`Q9LT57`	Arabidopsis thaliana	sp\|Q9LT57\|CFM9_ARATH CRM-domain containing factor CFM9, mitochondrial	81.100%	Swiss-Prot	Medium
`Q67ZU1`	Arabidopsis thaliana	sp\|Q67ZU1\|LIP2_ARATH Triacylglycerol lipase 2	63.800%	Swiss-Prot	High
`Q71DJ5`	Arabidopsis thaliana	sp\|Q71DJ5\|LIP1_ARATH Triacylglycerol lipase 1	39.500%	Swiss-Prot	Medium
`Q67XL4`	Arabidopsis thaliana	sp\|Q67XL4\|Y3544_ARATH Uncharacterized CRM domain-containing protein At3g25440, chloroplastic	44.000%	Swiss-Prot	Low
`Q9LF10`	Arabidopsis thaliana	sp\|Q9LF10\|CRS1_ARATH Chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic	33.100%	Swiss-Prot	Low
`Q6YYA3`	Oryza sativa subsp. japonica	sp\|Q6YYA3\|CRS1_ORYSJ Chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic	33.500%	Swiss-Prot	Low

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