LXL04_029639 | RubberDandelionOmics

Gene overview

LXL04_029639

Reference: OH-1004 Chr: Chr06 Coordinates: 96125490-96130171 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2031 bp · LXL04_029639|LXL04_029639|OH1004|cDNA

ATGGGGAAGGCCTCGAAATTCTTCAAATCACTCCTGGGATTCAGGACCACCGAAGCTCCCGCCAAACAATCGGCACGTTCAGAGGCTAAACAACCAAAGCGACGGTGGAGTTTTGCAAAATCGTACAGAGGAATTTCCCAGCGTCGTCTCCGGGACACTTCCAGTTCTTTCGACGGCACCTCACTCCACCATTATCATCGTAATCCAACTGACAATGAAGATCCCAATGAGCACGCGATTGCGCTTGTTGCGGCCACCGC...

CDS

Download CDS FASTA

2031 bp · LXL04_029639|LXL04_029639|OH1004|CDS

ATGGGGAAGGCCTCGAAATTCTTCAAATCACTCCTGGGATTCAGGACCACCGAAGCTCCCGCCAAACAATCGGCACGTTCAGAGGCTAAACAACCAAAGCGACGGTGGAGTTTTGCAAAATCGTACAGAGGAATTTCCCAGCGTCGTCTCCGGGACACTTCCAGTTCTTTCGACGGCACCTCACTCCACCATTATCATCGTAATCCAACTGACAATGAAGATCCCAATGAGCACGCGATTGCGCTTGTTGCGGCCACCGC...

Protein

Download Protein FASTA

676 aa · LXL04_029639|LXL04_029639|OH1004|PROTEIN

MGKASKFFKSLLGFRTTEAPAKQSARSEAKQPKRRWSFAKSYRGISQRRLRDTSSSFDGTSLHHYHRNPTDNEDPNEHAIALVAATAAVVDAAVAAAQAAAEVVRITSRSCRTTAYGVREDLAAVKIQSCFRAYLARRALKALKALVKLQAVVRGHILRKQTADMMRRLQALHRAQARARALRSLSTSSHFHHHEPQTPEKIEQFPRNKHDHRSISMKSSSKSYTRDVIAHENDKIVEVDMGQPVITTKGKKLFQHEQIN...

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_029639`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_029639

Location Chr06:96125490-96130171 (-)

Description Similar to MIZ1: Protein MIZU-KUSSEI 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g23060`	May be involved in cooperative interactions with calmodulins or calmodulin-like proteins (By similarity).	No verified direct reference in this release
`At2g41660`	Plays a role in lateral root development by maintaining auxin levels.	A gene essential for hydrotropism in roots.2007 · DOI: 10.1073/pnas.0609929104 Hormonal regulation of lateral root development in Arabidopsis modulated by MIZ1 and requirement of GNOM activity for MIZ1 function.2011 · DOI: 10.1104/pp.111.186270 MIZ1, an essential protein for root hydrotropism, is associated with the cytoplasmic face of the endoplasmic reticulum membrane in Arabidopsis root cells.2012 · DOI: 10.1016/j.febslet.2012.01.008 Light and abscisic acid signalling are integrated by MIZ1 gene expression and regulate hydrotropic response in roots of Arabidopsis thaliana.2012 · DOI: 10.1111/j.1365-3040.2012.02493.x Overexpression of MIZU-KUSSEI1 enhances the root hydrotropic response by retaining cell viability under hydrostimulated conditions in Arabidopsis thaliana.2012 · DOI: 10.1093/pcp/pcs129
`At5g07240`	May be involved in cooperative interactions with calmodulins or calmodulin-like proteins (By similarity).	No verified direct reference in this release
`At5g62070`	May be involved in cooperative interactions with calmodulins or calmodulin-like proteins (By similarity).	No verified direct reference in this release
`At4g14750`	May be involved in cooperative interactions with calmodulins or calmodulin-like proteins (By similarity).	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_029639 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009658 chloroplast organization Biological Process

GO:0009739 response to gibberellin Biological Process

GO:0010091 trichome branching Biological Process

GO:0010274 hydrotropism Biological Process

GO:0051592 response to calcium ion Biological Process

GO:1901020 negative regulation of calcium ion transmembrane transporter activity Biological Process

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005783 endoplasmic reticulum Cellular Component

GO:0005789 endoplasmic reticulum membrane Cellular Component

KEGG gene cross-reference

ath:AT2G41660

ath:AT4G14750

ath:AT4G23060

ath:AT5G07240

ath:AT5G62070

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.

Cell membrane0.450

Rank 1 · LXL04_029639 · OH-1004

Nucleus0.339

Rank 2 · LXL04_029639 · OH-1004

Cytoplasm0.326

Rank 3 · LXL04_029639 · OH-1004

Endoplasmic reticulum0.058

Rank 4 · LXL04_029639 · OH-1004

Plastid0.042

Rank 5 · LXL04_029639 · 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.

PF00612.34IQ123-141 aa

PF13178.12DUF4005283-341 aa

PF04759.19DUF617517-675 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_029639	`PF00612.34`	IQ	123	141	3.8e-09	36.2
LXL04_029639	`PF13178.12`	DUF4005	283	341	4.9e-11	43.8
LXL04_029639	`PF04759.19`	DUF617	517	675	8.7e-62	208.6

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q2NNE0`	Arabidopsis thaliana	Protein IQ-DOMAIN 22	37.223%	Swiss-Prot	moderate database homology
`O22227`	Arabidopsis thaliana	Protein MIZU-KUSSEI 1	44.681%	Swiss-Prot	weak database homology
`Q9LYP2`	Arabidopsis thaliana	Protein IQ-DOMAIN 24	38.079%	Swiss-Prot	weak database homology
`Q9FIT1`	Arabidopsis thaliana	Protein IQ-DOMAIN 23	36.997%	Swiss-Prot	moderate database homology
`A0A1P8B590`	Arabidopsis thaliana	Protein IQ-DOMAIN 19	29.167%	Swiss-Prot	weak database homology

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