LXL04_019668 | RubberDandelionOmics

Gene overview

LXL04_019668

Reference: OH-1004 Chr: Chr04 Coordinates: 36609735-36610382 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

648 bp · LXL04_019668|LXL04_019668|OH1004|cDNA

ATGGCTGAAGATGGTGCTAGGAAGTCGGGAACTGTGAAGTGGTTTAGTGATACCAAGGGTTTTGGATTCATTACACCTGATGATGGCGGCGAAGATCTATTTGTTCATCAGTCTTCGATCAGGGCCGAAGGGTTTAGGAGTTTAGGTGATGGTGAGACAGTGGAGTATGTGGTGGAGAACGGATCTGATGGGAGGGCGAAGGCTGCTGATGTTACTGGACCTGAGGAGGGGCCTGTGCAAGGAAGCAGTCGTGGAGGCGG...

CDS

Download CDS FASTA

648 bp · LXL04_019668|LXL04_019668|OH1004|CDS

ATGGCTGAAGATGGTGCTAGGAAGTCGGGAACTGTGAAGTGGTTTAGTGATACCAAGGGTTTTGGATTCATTACACCTGATGATGGCGGCGAAGATCTATTTGTTCATCAGTCTTCGATCAGGGCCGAAGGGTTTAGGAGTTTAGGTGATGGTGAGACAGTGGAGTATGTGGTGGAGAACGGATCTGATGGGAGGGCGAAGGCTGCTGATGTTACTGGACCTGAGGAGGGGCCTGTGCAAGGAAGCAGTCGTGGAGGCGG...

Protein

Download Protein FASTA

215 aa · LXL04_019668|LXL04_019668|OH1004|PROTEIN

MAEDGARKSGTVKWFSDTKGFGFITPDDGGEDLFVHQSSIRAEGFRSLGDGETVEYVVENGSDGRAKAADVTGPEEGPVQGSSRGGGGGGRGGGGGGDRYGGGGGDRYGGGGGDRYGGGGYGSRGGRGGGGYGGGGGGNACYKCGESGHMARDCDQNGGGGGGGGYGGGRGGYGGGRGGGGGGYGGGRGGGGGGGCYNCGEDGHFARECPTASNR

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_019668`
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_019668

Location Chr04:36609735-36610382 (-)

Description Similar to CSP4: Cold shock domain-containing protein 4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g21060`	Chaperone that binds to and unwinds RNA and both single-stranded DNA and double-stranded DNA (ssDNA and dsDNA DNA) (By similarity).	Arabidopsis cold shock domain proteins: relationships to floral and silique development.2009 · DOI: 10.1093/jxb/ern351 Overexpression of AtCSP4 affects late stages of embryo development in Arabidopsis.2011 · DOI: 10.1093/jxb/erq400
`At4g36020`	Chaperone that binds to RNA, single- (ssDNA) and double-stranded (dsDNA) DNA, and unwinds nucleic acid duplex.	Cold shock domain proteins and glycine-rich RNA-binding proteins from Arabidopsis thaliana can promote the cold adaptation process in Escherichia coli.2007 · DOI: 10.1093/nar/gkl1076 Cold shock domain proteins affect seed germination and growth of Arabidopsis thaliana under abiotic stress conditions.2009 · DOI: 10.1093/pcp/pcp037
`At2g17870`	Chaperone that binds to RNA, single- (ssDNA) and double-stranded (dsDNA) DNA, and unwinds nucleic acid duplex.	Cold shock domain protein 3 regulates freezing tolerance in Arabidopsis thaliana.2009 · DOI: 10.1074/jbc.m109.025791
`At4g38680`	Chaperone that binds to RNA, single- (ssDNA) and double- stranded (dsDNA) DNA, and unwinds nucleic acid duplex.	Cold shock domain proteins and glycine-rich RNA-binding proteins from Arabidopsis thaliana can promote the cold adaptation process in Escherichia coli.2007 · DOI: 10.1093/nar/gkl1076 Arabidopsis COLD SHOCK DOMAIN PROTEIN2 is a RNA chaperone that is regulated by cold and developmental signals.2007 · DOI: 10.1016/j.bbrc.2007.10.059 Cold shock domain proteins affect seed germination and growth of Arabidopsis thaliana under abiotic stress conditions.2009 · DOI: 10.1093/pcp/pcp037 Arabidopsis cold shock domain proteins: relationships to floral and silique development.2009 · DOI: 10.1093/jxb/ern351

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_019668 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009269 response to desiccation Biological Process

GO:0009409 response to cold Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009631 cold acclimation Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0009826 unidimensional cell growth Biological Process

GO:0010154 fruit development Biological Process

GO:0010228 vegetative to reproductive phase transition of meristem Biological Process

GO:0043457 regulation of cellular respiration Biological Process

GO:0048316 seed development Biological Process

KEGG gene cross-reference

ath:AT2G17870

ath:AT2G21060

ath:AT4G36020

ath:AT4G38680

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.

Nucleus0.648

Rank 1 · LXL04_019668 · OH-1004

Cytoplasm0.638

Rank 2 · LXL04_019668 · OH-1004

Extracellular0.174

Rank 3 · LXL04_019668 · OH-1004

Endoplasmic reticulum0.062

Rank 4 · LXL04_019668 · OH-1004

Cell membrane0.056

Rank 5 · LXL04_019668 · 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.

PF00313.29CSD9-73 aa

PF00098.29zf-CCHC140-156 aa

PF00098.29zf-CCHC195-210 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_019668	`PF00313.29`	CSD	9	73	7.2e-25	87.4
LXL04_019668	`PF00098.29`	zf-CCHC	140	156	1.2e-16	60.6
LXL04_019668	`PF00098.29`	zf-CCHC	195	210	1.2e-16	60.6

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
`Q38896`	Arabidopsis thaliana	Cold shock domain-containing protein 4	58.537%	Swiss-Prot	strong database homology
`O65639`	Arabidopsis thaliana	Cold shock protein 1	43.836%	Swiss-Prot	moderate database homology
`Q94C69`	Arabidopsis thaliana	Cold shock domain-containing protein 3	47.964%	Swiss-Prot	moderate database homology
`Q41188`	Arabidopsis thaliana	Cold shock protein 2	62.439%	Swiss-Prot	strong database homology

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