LXL04_009622 | RubberDandelionOmics

Gene overview

LXL04_009622

Reference: OH-1004 Chr: Chr02 Coordinates: 129868238-129868888 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

651 bp · LXL04_009622|LXL04_009622|OH1004|cDNA

ATGGCTGATGACGGCGTCAGGAAAACGGGAACGGTGAAGTGGTTTAACGATACCAAGGGTTTCGGCTTCATCTCCCCTGAAGACGGCAGCGAAGATCTGTTTGTTCACCAATCGTCGATTCGGACTGAAGGATTCCGAAGCCTCGGGGATGGCGAAACTGTTGAGTACGTTGTCGAGAACGGATCCGACGGACGAACCAAAGCTGCTGACGTAACTGGTCCTGAAGAGGGTCCTGTACAGGGAAGCAGTCGTGGAGGAGG...

CDS

Download CDS FASTA

651 bp · LXL04_009622|LXL04_009622|OH1004|CDS

ATGGCTGATGACGGCGTCAGGAAAACGGGAACGGTGAAGTGGTTTAACGATACCAAGGGTTTCGGCTTCATCTCCCCTGAAGACGGCAGCGAAGATCTGTTTGTTCACCAATCGTCGATTCGGACTGAAGGATTCCGAAGCCTCGGGGATGGCGAAACTGTTGAGTACGTTGTCGAGAACGGATCCGACGGACGAACCAAAGCTGCTGACGTAACTGGTCCTGAAGAGGGTCCTGTACAGGGAAGCAGTCGTGGAGGAGG...

Protein

Download Protein FASTA

216 aa · LXL04_009622|LXL04_009622|OH1004|PROTEIN

MADDGVRKTGTVKWFNDTKGFGFISPEDGSEDLFVHQSSIRTEGFRSLGDGETVEYVVENGSDGRTKAADVTGPEEGPVQGSSRGGGGGGGGRGGGGDRYGGGGGGYNGGGRGGRGGGGYGGGGGYGGGGGYGGGGSYGGGGGGGNACFKCGESGHMARDCSQSGGGGGGGYGGGGRGGGGYGGGGRGGGGGGGGGCYNCGEDGHFARECPNANNR

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_009622`
TK1151 ID	TkA03G451810
OH-1004 ID	LXL04_009622
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	100.000
Protein coverage (%)	TK1151 98.101 / OH-1004 71.759 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
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_009622

Location Chr02:129868238-129868888 (-)

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_009622 · 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

nsy:104218376

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.

Cytoplasm0.651

Rank 1 · LXL04_009622 · OH-1004

Nucleus0.613

Rank 2 · LXL04_009622 · OH-1004

Extracellular0.186

Rank 3 · LXL04_009622 · OH-1004

Endoplasmic reticulum0.065

Rank 4 · LXL04_009622 · OH-1004

Cell membrane0.061

Rank 5 · LXL04_009622 · 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-CCHC147-163 aa

PF00098.29zf-CCHC196-212 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009622	`PF00313.29`	CSD	9	73	4e-26	91.4
LXL04_009622	`PF00098.29`	zf-CCHC	147	163	3.9e-16	59.0
LXL04_009622	`PF00098.29`	zf-CCHC	196	212	3.9e-16	59.0

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	58.333%	Swiss-Prot	strong database homology
`O65639`	Arabidopsis thaliana	Cold shock protein 1	41.704%	Swiss-Prot	moderate database homology
`Q94C69`	Arabidopsis thaliana	Cold shock domain-containing protein 3	44.550%	Swiss-Prot	moderate database homology
`Q41188`	Arabidopsis thaliana	Cold shock protein 2	57.346%	Swiss-Prot	strong database homology

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