LXL04_033003 | RubberDandelionOmics

Gene overview

LXL04_033003

Reference: OH-1004 Chr: Chr07 Coordinates: 33168273-33172479 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2502 bp · LXL04_033003|LXL04_033003|OH1004|cDNA

ATGTTATCGCTTCGGTCGTGCTGTTACAGTGTGACTcacaccaacaccataaccaCCGCACTCTGTCATCCTATTAAACATTCTCTTCTTGAATTGTCATTTCCTCTCTTCTTTCTCACGAAACTAAAAATGTCATCATCTCGTCCCTCCGCCTTCGATGCACTCATGTCGAATGCTCGTGCTGCTGCCGCGAAGAAGAAAACCACGGAATCTTCCGCTTCCCCTAAGAAGCGCAAAACCCTAGAATCAAAACCCCCAAT...

CDS

Download CDS FASTA

2502 bp · LXL04_033003|LXL04_033003|OH1004|CDS

ATGTTATCGCTTCGGTCGTGCTGTTACAGTGTGACTCACACCAACACCATAACCACCGCACTCTGTCATCCTATTAAACATTCTCTTCTTGAATTGTCATTTCCTCTCTTCTTTCTCACGAAACTAAAAATGTCATCATCTCGTCCCTCCGCCTTCGATGCACTCATGTCGAATGCTCGTGCTGCTGCCGCGAAGAAGAAAACCACGGAATCTTCCGCTTCCCCTAAGAAGCGCAAAACCCTAGAATCAAAACCCCCAAT...

Protein

Download Protein FASTA

833 aa · LXL04_033003|LXL04_033003|OH1004|PROTEIN

MLSLRSCCYSVTHTNTITTALCHPIKHSLLELSFPLFFLTKLKMSSSRPSAFDALMSNARAAAAKKKTTESSASPKKRKTLESKPPISLTPISEAKVAEVSPKPDKPLDTNAKKKTSVSSSSPKKRKTLDSKPPIKSTPVSEDKVAEVSPKPEKTLDTNQIKDETNVSNGITEAQPKLDVVSSEEKPASKKPPAIDVDESMIQLKKKPANFKPEKAAFWGEGERVPFLFLCRVFDAISKESGRILITEIVCNMLRTVIKT...

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	`LXL04_033003`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_033003

Location Chr07:33168273-33172479 (+)

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.

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.

Nucleus0.779

Rank 1 · LXL04_033003 · OH-1004

Cytoplasm0.240

Rank 2 · LXL04_033003 · OH-1004

Mitochondrion0.046

Rank 3 · LXL04_033003 · OH-1004

Cell membrane0.030

Rank 4 · LXL04_033003 · OH-1004

Endoplasmic reticulum0.025

Rank 5 · LXL04_033003 · OH-1004

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.

PF04675.20DNA_ligase_A_N226-401 aa

PF01068.27DNA_ligase_A_M461-665 aa

PF09414.16RNA_ligase481-664 aa

PF04679.22DNA_ligase_A_C692-801 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_033003	`PF04675.20`	DNA_ligase_A_N	226	401	8.5e-54	183.1
LXL04_033003	`PF01068.27`	DNA_ligase_A_M	461	665	2.2e-68	230.7
LXL04_033003	`PF09414.16`	RNA_ligase	481	664	4.8e-07	30.8
LXL04_033003	`PF04679.22`	DNA_ligase_A_C	692	801	9.6e-21	74.7

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q42572`	Arabidopsis thaliana	DNA ligase 1	64.330%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card