TkA01G037040 | RubberDandelionOmics

Gene overview

TkA01G037040

Reference: TK1151 Chr: Chr01 Coordinates: 9560815-9565512 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2561 bp · TkA01G037040|TK1151|cDNA

TCCTCTCTGTATCTGGGTCAAAGAAACCATACCTCTCTGCCTCCCCTCATCTCAATCAATCTTCCATATGTGAAGAAGGTCGAAGTTCAAGGGTTTGGGGGTTTCGATTTTGACTGAAATCGACGAATTTGCTGGAAATAGAAATCGTCTGCAACATGCTGAGAACCGTAATCAAGACAACACCCGACGACTTGGTTCCAGTCGTATACCTATTAGCCAATAGAATCGCTCCAGCACACGAAGGTTTAGAGCTTGGAATC...

CDS

Download CDS FASTA

1746 bp · TkA01G037040|TK1151|CDS

ATGCTGAGAACCGTAATCAAGACAACACCCGACGACTTGGTTCCAGTCGTATACCTATTAGCCAATAGAATCGCTCCAGCACACGAAGGTTTAGAGCTTGGAATCGGCGATGCTTCCATTATCAAAGCACTTGCTGAAGCTTGTGGTGCAAAAGAAGTACATATAAAAAAACAATACAAGGAATTGGGAGACTTGGGCCTTGTTGCTAAAGCAAGCCGTTCTTCCCAACCTCTGATGCGTAAACCTCAACCTTTGACAGT...

Protein

Download Protein FASTA

581 aa · TkA01G037040|TK1151|PROTEIN

MLRTVIKTTPDDLVPVVYLLANRIAPAHEGLELGIGDASIIKALAEACGAKEVHIKKQYKELGDLGLVAKASRSSQPLMRKPQPLTVSKVFDTFRVIAKESGKDSQDKKKNHIKGLLVAATDCEPQYLIRLLQTKLRIGLAEQTLLTALGHAIAYTEKHPTDLEEAAKIVKQVYSVISVYDKIVPALLSNGILDLPKTCCFSPGVPVGPMLAKPTKGVSEILDKFQDMEFTCEYKYDGERAQIHYLEDGTVQIYSRNAER...

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	`TkA01G037040`
TK1151 ID	TkA01G037040
OH-1004 ID	LXL04_033003
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.100
Protein coverage (%)	TK1151 100.000 / OH-1004 69.748 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA01G037040

Location Chr01:9560815-9565512 (+)

Description Similar to LIG1: DNA ligase 1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g08130`	Essential protein.	DNA ligase 1 deficient plants display severe growth defects and delayed repair of both DNA single and double strand breaks.2009 · DOI: 10.1186/1471-2229-9-79 DNA LIGASE I exerts a maternal effect on seed development in Arabidopsis thaliana.2010 · DOI: 10.1242/dev.041020

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_033003 · 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:0000012 single strand break repair Biological Process

GO:0006260 DNA replication Biological Process

GO:0006273 lagging strand elongation Biological Process

GO:0006281 DNA repair Biological Process

GO:0006284 base-excision repair Biological Process

GO:0006287 base-excision repair, gap-filling Biological Process

GO:0006298 mismatch repair Biological Process

GO:0006302 double-strand break repair Biological Process

GO:0006303 double-strand break repair via nonhomologous end joining Biological Process

GO:0006310 DNA recombination Biological Process

GO:0009653 anatomical structure morphogenesis Biological Process

GO:0032201 telomere maintenance via semi-conservative replication Biological Process

KEGG gene cross-reference

ath:AT1G08130

ddi:DDB_G0274493

hsa:3978

mmu:16881

xla:397978

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.

Nucleus0.719

Rank 1 · TkA01G037040 · TK1151

Cytoplasm0.334

Rank 2 · TkA01G037040 · TK1151

Mitochondrion0.084

Rank 3 · TkA01G037040 · TK1151

Cell membrane0.024

Rank 4 · TkA01G037040 · TK1151

Endoplasmic reticulum0.016

Rank 5 · TkA01G037040 · 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.

PF04675DNA_ligase_A_N2-149 aa

PF29374EDDM1342-82 aa

PF01068DNA_ligase_A_M209-413 aa

PF09414RNA_ligase229-412 aa

PF29374EDDM13398-418 aa

PF04679DNA_ligase_A_C440-549 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G037040	`PF04675`	DNA_ligase_A_N	2	149	9.6e-45	153.6
TkA01G037040	`PF29374`	EDDM13	42	82	0.24	11.7
TkA01G037040	`PF01068`	DNA_ligase_A_M	209	413	3e-68	230.2
TkA01G037040	`PF09414`	RNA_ligase	229	412	6.6e-07	30.4
TkA01G037040	`PF29374`	EDDM13	398	418	0.24	11.7
TkA01G037040	`PF04679`	DNA_ligase_A_C	440	549	3.5e-21	76.1

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
`Q42572`	Arabidopsis thaliana	sp\|Q42572\|DNLI1_ARATH DNA ligase 1	73.700%	Swiss-Prot	High

JBrowse

View in Genome Browser

Gene Card