TkA01G588920 | RubberDandelionOmics

Gene overview

TkA01G588920

Reference: TK1151 Chr: Chr01 Coordinates: 148158823-148160933 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1650 bp · TkA01G588920|TK1151|cDNA

AAGGATTGGGACCTGTTGAACAAATAGAAGTTCGCTGGGTTTATGAAATTTGAGCTTTAGCTCAAACCCTGCAACCCAGTACCCGACAAGCAACATAAACCCTAAGCAATCGTAAAGGAAAGCGCTTGAAGGGAGAGAAAAAATCATGAAACGATGATGAGAACTCTAGCTTCAATGGTATTTTGCAAATCGAAACAGCTGAAGAATCTCATCTTCACCCCATTTCTATATCGCCAATTTCTTCCCAAGCCAAGTTTCTC...

CDS

Download CDS FASTA

1335 bp · TkA01G588920|TK1151|CDS

ATGATGAGAACTCTAGCTTCAATGGTATTTTGCAAATCGAAACAGCTGAAGAATCTCATCTTCACCCCATTTCTATATCGCCAATTTCTTCCCAAGCCAAGTTTCTCTGATGTTATATACAAGGTTTTGCATGATGAACCAGCTGTTATATCACATGGAAACCAAAGATATATCCCTAGAGGTATCTTCTGGTATAGTTCGGCTCCTATTGACACAGTCATCAAACCACCAGTGAGCCATGTAACCGACACTGTATCCAA...

Protein

Download Protein FASTA

444 aa · TkA01G588920|TK1151|PROTEIN

MMRTLASMVFCKSKQLKNLIFTPFLYRQFLPKPSFSDVIYKVLHDEPAVISHGNQRYIPRGIFWYSSAPIDTVIKPPVSHVTDTVSNGSPEAKPKRKKLKGKRAVVRWLKFFRFKKKKDYERMTAEEKILFKLRKARKKEERLNEALNKIEPKETSETTHDPEILTPEEHFYFLKMGIKSKNYVPVGRRGIYQGVILNMHLHWKKHETLQVIVKTFTPDEVKEMAVELARLSGGIVLDIKDDETIIMYRGKNYSQPPTEI...

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	`TkA01G588920`
TK1151 ID	TkA01G588920
OH-1004 ID	LXL04_000772
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	96.900
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 TkA01G588920

Location Chr01:148158823-148160933 (-)

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
`At3g25440`	Uncharacterized CRM domain-containing protein At3g25440, chloroplastic.	No verified direct reference in this release
`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
`At3g23070`	Binds specific group II introns in chloroplasts and facilitates their splicing.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os11g0592400`	Binds specific group II introns in chloroplasts and facilitates their splicing.	Two CRM protein subfamilies cooperate in the splicing of group IIB introns in chloroplasts.2008 · DOI: 10.1261/rna.1223708

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.

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.

Mitochondrion0.808

Rank 1 · TkA01G588920 · TK1151

Plastid0.120

Rank 2 · TkA01G588920 · TK1151

Nucleus0.072

Rank 3 · TkA01G588920 · TK1151

Cytoplasm0.053

Rank 4 · TkA01G588920 · TK1151

Cell membrane0.013

Rank 5 · TkA01G588920 · 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.

PF14749Acyl-CoA_ox_N113-173 aa

PF01985CRS1_YhbY165-249 aa

PF08753NikR_C195-233 aa

PF14749Acyl-CoA_ox_N277-295 aa

PF14749Acyl-CoA_ox_N330-349 aa

PF14749Acyl-CoA_ox_N389-417 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G588920	`PF14749`	Acyl-CoA_ox_N	113	173	1.6	10.0
TkA01G588920	`PF01985`	CRS1_YhbY	165	249	1.9e-15	57.7
TkA01G588920	`PF08753`	NikR_C	195	233	0.17	12.8
TkA01G588920	`PF14749`	Acyl-CoA_ox_N	277	295	1.6	10.0
TkA01G588920	`PF14749`	Acyl-CoA_ox_N	330	349	1.6	10.0
TkA01G588920	`PF14749`	Acyl-CoA_ox_N	389	417	1.6	10.0

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
`Q67XL4`	Arabidopsis thaliana	sp\|Q67XL4\|Y3544_ARATH Uncharacterized CRM domain-containing protein At3g25440, chloroplastic	58.400%	Swiss-Prot	High
`Q9LT57`	Arabidopsis thaliana	sp\|Q9LT57\|CFM9_ARATH CRM-domain containing factor CFM9, mitochondrial	46.600%	Swiss-Prot	Low
`F4J2U9`	Arabidopsis thaliana	sp\|F4J2U9\|CFM3A_ARATH CRM-domain containing factor CFM3A, chloroplastic/mitochondrial	39.200%	Swiss-Prot	Low
`Q2R1U8`	Oryza sativa subsp. japonica	sp\|Q2R1U8\|CFM3_ORYSJ CRM-domain containing factor CFM3, chloroplastic/mitochondrial	35.400%	Swiss-Prot	Low

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