LXL04_000221 | RubberDandelionOmics

Gene overview

LXL04_000221

Reference: OH-1004 Chr: Chr01 Coordinates: 4189854-4192599 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2607 bp · LXL04_000221|LXL04_000221|OH1004|cDNA

ATGAAAATCCCCTATCAAACAACAAAAATTCAAACAATAGTCGGTCTGGCTAAAACCCTCGCTGCCTCGCCCACAGAAACTGTATTTTCCAGAAACAAGGGGATGAGTTTTGATCGATTACCGCTCGCTTCCATCGAAGATGAAGACCAAGAATTCGAGGAATCATCGTCGTCTACTCCGGCAACCCAGTCTGAAACATTTATGGTGGGTTTCATGGTCGCAAACATTGTCGGTCTGCAATACTATCGCGGCCGGATAAG...

CDS

Download CDS FASTA

2607 bp · LXL04_000221|LXL04_000221|OH1004|CDS

ATGAAAATCCCCTATCAAACAACAAAAATTCAAACAATAGTCGGTCTGGCTAAAACCCTCGCTGCCTCGCCCACAGAAACTGTATTTTCCAGAAACAAGGGGATGAGTTTTGATCGATTACCGCTCGCTTCCATCGAAGATGAAGACCAAGAATTCGAGGAATCATCGTCGTCTACTCCGGCAACCCAGTCTGAAACATTTATGGTGGGTTTCATGGTCGCAAACATTGTCGGTCTGCAATACTATCGCGGCCGGATAAG...

Protein

Download Protein FASTA

868 aa · LXL04_000221|LXL04_000221|OH1004|PROTEIN

MKIPYQTTKIQTIVGLAKTLAASPTETVFSRNKGMSFDRLPLASIEDEDQEFEESSSSTPATQSETFMVGFMVANIVGLQYYRGRISGREMVGLVREPLNAYDSNAIKVVNTRTIQVGHIEKKVASVLAPLLDSNFVHVEGIVPKTPKSAAAYRIPCHIHVFSKMEAFETVKSALRSFLFTPNDPMFSMSDSMVVKEKKKGDLDEIFKLVDDNLRENAVNGVMEPPQDFILPDLFQHQKEGLYWLHHRENSDELPPFWEK...

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_000221`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_000221

Location Chr01:4189854-4192599 (-)

Description Similar to At5g05130: Putative SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3-like 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g05130`	Possesses intrinsic ATP-dependent nucleosome-remodeling activity.	No verified direct reference in this release
`At5g22750`	Functions in error-free postreplication DNA repair or DNA- damage tolerance (DTT) pathway.	A homolog of ScRAD5 is involved in DNA repair and homologous recombination in Arabidopsis.2008 · DOI: 10.1104/pp.108.116806 RAD5A, RECQ4A, and MUS81 have specific functions in homologous recombination and define different pathways of DNA repair in Arabidopsis thaliana.2010 · DOI: 10.1105/tpc.110.078568 RAD5a and REV3 function in two alternative pathways of DNA-damage tolerance in Arabidopsis.2011 · DOI: 10.1016/j.dnarep.2011.04.009 AtRAD5A is a DNA translocase harboring a HIRAN domain which confers binding to branched DNA structures and is required for DNA repair in vivo.2016 · DOI: 10.1111/tpj.13283

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_000221 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000209 protein polyubiquitination Biological Process

GO:0006281 DNA repair Biological Process

GO:0006325 chromatin organization Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006974 DNA damage response Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0042789 mRNA transcription by RNA polymerase II Biological Process

GO:0045944 positive regulation of transcription by RNA polymerase II Biological Process

GO:0070534 protein K63-linked ubiquitination Biological Process

GO:0071168 protein localization to chromatin Biological Process

GO:0071932 replication fork reversal Biological Process

GO:0141119 chromosomal DNA methylation maintenance following DNA replication Biological Process

KEGG gene cross-reference

ath:AT5G05130

hsa:6596

mmu:20585

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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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.

Nucleus0.812

Rank 1 · LXL04_000221 · OH-1004

Cytoplasm0.198

Rank 2 · LXL04_000221 · OH-1004

Mitochondrion0.035

Rank 3 · LXL04_000221 · OH-1004

Cell membrane0.030

Rank 4 · LXL04_000221 · OH-1004

Endoplasmic reticulum0.021

Rank 5 · LXL04_000221 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF08797.17HIRAN70-163 aa

PF00176.30SNF2-rel_dom237-593 aa

PF13920.13zf-C3HC4_3630-677 aa

PF13639.13zf-RING_2632-672 aa

PF00097.32zf-C3HC4633-671 aa

PF13923.13zf-C3HC4_2633-671 aa

PF14634.13zf-RING_5633-672 aa

PF00271.38Helicase_C700-813 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000221	`PF08797.17`	HIRAN	70	163	1.4e-21	76.8
LXL04_000221	`PF00176.30`	SNF2-rel_dom	237	593	2e-71	241.2
LXL04_000221	`PF13920.13`	zf-C3HC4_3	630	677	1.1e-07	32.2
LXL04_000221	`PF13639.13`	zf-RING_2	632	672	5.1e-08	33.8
LXL04_000221	`PF00097.32`	zf-C3HC4	633	671	2.2e-07	31.3
LXL04_000221	`PF13923.13`	zf-C3HC4_2	633	671	2.5e-07	31.1
LXL04_000221	`PF14634.13`	zf-RING_5	633	672	5.2e-07	30.3
LXL04_000221	`PF00271.38`	Helicase_C	700	813	1.9e-19	70.6

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9FF61`	Arabidopsis thaliana	Putative SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3-like 1	59.419%	Swiss-Prot	strong database homology
`Q9FNI6`	Arabidopsis thaliana	DNA repair protein RAD5A	36.000%	Swiss-Prot	moderate database homology

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