LXL04_027406 | RubberDandelionOmics

Gene overview

LXL04_027406

Reference: OH-1004 Chr: Chr06 Coordinates: 15028870-15031323 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

678 bp · LXL04_027406|LXL04_027406|OH1004|cDNA

ATGCAACTCTTTGGAAGTTCTGAGATCAGTCCATCTCTGCTGGTACTGACGGCATCATGCAACAATACACACATGATGTATGTGTTGAATAGAAACGACGTTTGTTTGATTTACAGGGAGTGGAATCGCCCTCTTCGTGCCCTCTATTCCAAGCAGGATCATAAGCTCATGTTTGGTGTCCTTTTCTCTCTCAAATCCCTAACCGCAAAGATGGATCCATCTAGGTTTGGTTCAACTTTGTGTCCTGATTATCTCTCACT...

CDS

Download CDS FASTA

678 bp · LXL04_027406|LXL04_027406|OH1004|CDS

ATGCAACTCTTTGGAAGTTCTGAGATCAGTCCATCTCTGCTGGTACTGACGGCATCATGCAACAATACACACATGATGTATGTGTTGAATAGAAACGACGTTTGTTTGATTTACAGGGAGTGGAATCGCCCTCTTCGTGCCCTCTATTCCAAGCAGGATCATAAGCTCATGTTTGGTGTCCTTTTCTCTCTCAAATCCCTAACCGCAAAGATGGATCCATCTAGGTTTGGTTCAACTTTGTGTCCTGATTATCTCTCACT...

Protein

Download Protein FASTA

225 aa · LXL04_027406|LXL04_027406|OH1004|PROTEIN

MQLFGSSEISPSLLVLTASCNNTHMMYVLNRNDVCLIYREWNRPLRALYSKQDHKLMFGVLFSLKSLTAKMDPSRFGSTLCPDYLSLLLKHMTDPLKTLPKDEGVEKVVEFMDAYSINQEDFELQISFLSMLLLDVIPINVNGGDDLGFWIFVISHNNKMEGLKRTIESYSDLRAELLPRKEGPSKAAVFLGNGTEDMTRRTALSVASSWNYAVNNLKAISSGND

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_027406`
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_027406

Location Chr06:15028870-15031323 (-)

Description Similar to RFC1: Replication factor C subunit 1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g22010`	Plays a role as mediator of transcriptional gene silencing (TGS), DNA replication, DNA repair, hypersensitive response (HR) and telomere length regulation.	Arabidopsis replication factor C subunit 1 plays an important role in embryogenesis.2007 · PMID: 17556804 DNA replication factor C1 mediates genomic stability and transcriptional gene silencing in Arabidopsis.2010 · DOI: 10.1105/tpc.110.076349 Replication factor C1 (RFC1) is required for double-strand break repair during meiotic homologous recombination in Arabidopsis.2013 · DOI: 10.1111/tpj.12024 The DNA replication factor RFC1 is required for interference-sensitive meiotic crossovers in Arabidopsis thaliana.2012 · DOI: 10.1371/journal.pgen.1003039

Rice

Reference gene ID	Possible function	Papers / DOI
`Os11g0572100`	May be involved in DNA replication and thus regulate cell proliferation.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_027406 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000712 resolution of meiotic recombination intermediates Biological Process

GO:0006260 DNA replication Biological Process

GO:0006281 DNA repair Biological Process

GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport Biological Process

GO:0006901 vesicle coating Biological Process

GO:0006974 DNA damage response Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

GO:0048208 COPII vesicle coating Biological Process

GO:0051321 meiotic cell cycle Biological Process

GO:0099022 vesicle tethering Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT5G22010

dosa:Os11g0572100

hsa:58485

mmu:245828

rno:287427

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.

Cytoplasm0.331

Rank 1 · LXL04_027406 · OH-1004

Nucleus0.323

Rank 2 · LXL04_027406 · OH-1004

Mitochondrion0.183

Rank 3 · LXL04_027406 · OH-1004

Cell membrane0.118

Rank 4 · LXL04_027406 · OH-1004

Endoplasmic reticulum0.098

Rank 5 · LXL04_027406 · 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.

PF04099.19Sybindin24-79 aa

PF08519.18RFC178-124 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027406	`PF04099.19`	Sybindin	24	79	1.3e-12	48.7
LXL04_027406	`PF08519.18`	RFC1	78	124	2.2e-07	31.8

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
`Q9C587`	Arabidopsis thaliana	Replication factor C subunit 1	64.444%	Swiss-Prot	weak database homology
`Q2R2B4`	Oryza sativa subsp. japonica	Replication factor C subunit 1	70.588%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card