LXL04_016927 | RubberDandelionOmics

Gene overview

LXL04_016927

Reference: OH-1004 Chr: Chr03 Coordinates: 137063924-137073684 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3633 bp · LXL04_016927|LXL04_016927|OH1004|cDNA

ATGACAGAGGCAAACCATATGAATATAAGCAACCTTGGTGGAGGTTCTAAACATGTGGACAAGCCTACAAAGGACAACTGGTCTCAGCATGCTATAGCACACAATAATTTCTCAAACCAAGATAAATTCTTGAAATCAAGTTTTCTTTTCTCTTTGTCAACACAAAAACCTTGTGTTCAAGGAGCCATGTCAGCAGCTTTAAGATCACTGTCTTCCCAATTTCAAAATGTTACAAATTCACACAGTCCACATGCTGACAA...

CDS

Download CDS FASTA

3633 bp · LXL04_016927|LXL04_016927|OH1004|CDS

ATGACAGAGGCAAACCATATGAATATAAGCAACCTTGGTGGAGGTTCTAAACATGTGGACAAGCCTACAAAGGACAACTGGTCTCAGCATGCTATAGCACACAATAATTTCTCAAACCAAGATAAATTCTTGAAATCAAGTTTTCTTTTCTCTTTGTCAACACAAAAACCTTGTGTTCAAGGAGCCATGTCAGCAGCTTTAAGATCACTGTCTTCCCAATTTCAAAATGTTACAAATTCACACAGTCCACATGCTGACAA...

Protein

Download Protein FASTA

1210 aa · LXL04_016927|LXL04_016927|OH1004|PROTEIN

MTEANHMNISNLGGGSKHVDKPTKDNWSQHAIAHNNFSNQDKFLKSSFLFSLSTQKPCVQGAMSAALRSLSSQFQNVTNSHSPHADKAWQALSNLKLSSRNYIKPGKSRPVANNGGSGSVQDVRKATQQFSSHVNNKNLAQNQSNETNEARHTADRFPPAGTSVTEASGKFGTRFSGGGGYASNPVDASRRNMNGSYNYATNAGHFKGFQETDTGGFDDDDDDILQSLDLDQIVNQHYQSTCTPPSSSTLKFPPVNPAGI...

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_016927`
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_016927

Location Chr03:137063924-137073684 (-)

Description Similar to RECQL4A: ATP-dependent DNA helicase Q-like 4A

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g10930`	DNA helicase involved in DNA repair.	Arabidopsis RecQI4A suppresses homologous recombination and modulates DNA damage responses.2005 · DOI: 10.1111/j.1365-313x.2005.02501.x Two closely related RecQ helicases have antagonistic roles in homologous recombination and DNA repair in Arabidopsis thaliana.2007 · DOI: 10.1073/pnas.0705998104 Topoisomerase 3alpha and RMI1 suppress somatic crossovers and are essential for resolution of meiotic recombination intermediates in Arabidopsis thaliana.2008 · DOI: 10.1371/journal.pgen.1000285 The RecQ helicase AtRECQ4A is required to remove inter-chromosomal telomeric connections that arise during meiotic recombination in Arabidopsis.2011 · DOI: 10.1111/j.1365-313x.2010.04438.x
`At1g60930`	3'-5' DNA helicase that may play a role in the repair of DNA (By similarity).	Two closely related RecQ helicases have antagonistic roles in homologous recombination and DNA repair in Arabidopsis thaliana.2007 · DOI: 10.1073/pnas.0705998104

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_016927 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000079 regulation of cyclin-dependent protein serine/threonine kinase activity Biological Process

GO:0000723 telomere maintenance Biological Process

GO:0000724 double-strand break repair via homologous recombination Biological Process

GO:0000725 recombinational repair Biological Process

GO:0000729 DNA double-strand break processing Biological Process

GO:0006260 DNA replication Biological Process

GO:0006281 DNA repair Biological Process

GO:0006301 DNA damage tolerance Biological Process

GO:0006310 DNA recombination Biological Process

GO:0006974 DNA damage response Biological Process

GO:0007095 mitotic G2 DNA damage checkpoint signaling Biological Process

GO:0010165 response to X-ray Biological Process

KEGG gene cross-reference

ath:AT1G10930

ath:AT1G60930

mmu:12144

spo:2541620

xla:373628

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.

Nucleus0.854

Rank 1 · LXL04_016927 · OH-1004

Cytoplasm0.210

Rank 2 · LXL04_016927 · OH-1004

Mitochondrion0.044

Rank 3 · LXL04_016927 · OH-1004

Cell membrane0.023

Rank 4 · LXL04_016927 · OH-1004

Endoplasmic reticulum0.014

Rank 5 · LXL04_016927 · 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.

PF04851.22ResIII463-629 aa

PF00270.36DEAD467-634 aa

PF00271.38Helicase_C671-778 aa

PF16124.11RecQ_Zn_bind819-870 aa

PF09382.18RQC878-991 aa

PF00570.29HRDC1035-1105 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_016927	`PF04851.22`	ResIII	463	629	4.9e-06	27.3
LXL04_016927	`PF00270.36`	DEAD	467	634	2e-26	93.5
LXL04_016927	`PF00271.38`	Helicase_C	671	778	9.7e-23	81.2
LXL04_016927	`PF16124.11`	RecQ_Zn_bind	819	870	1.1e-13	52.4
LXL04_016927	`PF09382.18`	RQC	878	991	1.4e-21	77.2
LXL04_016927	`PF00570.29`	HRDC	1035	1105	4.4e-11	43.3

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
`Q8L840`	Arabidopsis thaliana	ATP-dependent DNA helicase Q-like 4A	53.522%	Swiss-Prot	strong database homology
`Q9FT70`	Arabidopsis thaliana	ATP-dependent DNA helicase Q-like 4B	51.051%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card