LXL04_023708 | RubberDandelionOmics

Gene overview

LXL04_023708

Reference: OH-1004 Chr: Chr05 Coordinates: 64143192-64145984 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1629 bp · LXL04_023708|LXL04_023708|OH1004|cDNA

ATGATACCCGAAGGTGATGTTTGGATGGAAGGAGGAGGAAACCAAGATGAAATTGAAACATCTTCATGGAcgccgaccaccaccaccacccacCACCATGTTCTTGGAATTGAAGCTGCTGACACATCATGCAATGACACCACCGCCGCCAATACCTACGCTTCTCTCACCACCTTGAAATCAATGCTTGAAACCGAGTGGTATCACCACAACAATCTCAACCTGTCTTCCAATCCCTCCGATAATAATTCCATCTTCTT...

CDS

Download CDS FASTA

1629 bp · LXL04_023708|LXL04_023708|OH1004|CDS

ATGATACCCGAAGGTGATGTTTGGATGGAAGGAGGAGGAAACCAAGATGAAATTGAAACATCTTCATGGACGCCGACCACCACCACCACCCACCACCATGTTCTTGGAATTGAAGCTGCTGACACATCATGCAATGACACCACCGCCGCCAATACCTACGCTTCTCTCACCACCTTGAAATCAATGCTTGAAACCGAGTGGTATCACCACAACAATCTCAACCTGTCTTCCAATCCCTCCGATAATAATTCCATCTTCTT...

Protein

Download Protein FASTA

542 aa · LXL04_023708|LXL04_023708|OH1004|PROTEIN

MIPEGDVWMEGGGNQDEIETSSWTPTTTTTHHHVLGIEAADTSCNDTTAANTYASLTTLKSMLETEWYHHNNLNLSSNPSDNNSIFLPMDSSSSCSPSHSHHPFTLPDPSPSHSYPFFPPKFNNSYDLGFDFGCDPAFLPNHTSNLMNFNGMCSQTHLAIPELSSSSDFPATNNSNDTSDIGGPGFNPPLTAFDGFHGSAPMNPLFAARSKVLRPLEISPPVGAQPTLFQKRAALRQSSLKLGELGAANWGKRAESNIGA...

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_023708`
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_023708

Location Chr05:64143192-64145984 (-)

Description Similar to SCRM: Transcription factor ICE1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g26744`	Transcriptional activator that regulates the cold-induced transcription of CBF/DREB1 genes.	SIZ1-mediated sumoylation of ICE1 controls CBF3/DREB1A expression and freezing tolerance in Arabidopsis.2007 · DOI: 10.1105/tpc.106.048397 SCREAM/ICE1 and SCREAM2 specify three cell-state transitional steps leading to arabidopsis stomatal differentiation.2008 · DOI: 10.1105/tpc.108.060848
`At1g12860`	Mediates stomatal differentiation in the epidermis probably by controlling successive roles of SPCH, MUTE, and FAMA.	SCREAM/ICE1 and SCREAM2 specify three cell-state transitional steps leading to arabidopsis stomatal differentiation.2008 · DOI: 10.1105/tpc.108.060848
`At5g65640`	Transcription factor.	No verified direct reference in this release
`At5g10570`	Transcription factor bHLH61.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0135700`	Transcription factor involved in defense responses that functions downstream of RAC1 and upstream of PAL1 and WRKY19 genes.	The bHLH Rac Immunity1 (RAI1) Is Activated by OsRac1 via OsMAPK3 and OsMAPK6 in Rice Immunity.2012 · DOI: 10.1093/pcp/pcs033

Functional annotation source

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Functional annotation source: OH1004 · LXL04_023708 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006952 defense response Biological Process

GO:0009409 response to cold Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009960 endosperm development Biological Process

GO:0010115 regulation of abscisic acid biosynthetic process Biological Process

GO:0010162 seed dormancy process Biological Process

GO:0010371 regulation of gibberellin biosynthetic process Biological Process

GO:0010440 stomatal lineage progression Biological Process

GO:0010444 guard mother cell differentiation Biological Process

GO:0031347 regulation of defense response Biological Process

KEGG gene cross-reference

ath:AT1G12860

ath:AT3G26744

ath:AT5G10570

ath:AT5G65640

dosa:Os03g0135700

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.

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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.

Nucleus0.967

Rank 1 · LXL04_023708 · OH-1004

Cytoplasm0.096

Rank 2 · LXL04_023708 · OH-1004

Cell membrane0.031

Rank 3 · LXL04_023708 · OH-1004

Endoplasmic reticulum0.024

Rank 4 · LXL04_023708 · OH-1004

Plastid0.014

Rank 5 · LXL04_023708 · 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.

PF00010.32HLH335-400 aa

PF22754.5bHLH-TF_ACT-like_plant459-531 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_023708	`PF00010.32`	HLH	335	400	2e-07	31.4
LXL04_023708	`PF22754.5`	bHLH-TF_ACT-like_plant	459	531	5.7e-11	43.1

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
`Q9LSE2`	Arabidopsis thaliana	Transcription factor ICE1	53.811%	Swiss-Prot	strong database homology
`Q9LPW3`	Arabidopsis thaliana	Transcription factor SCREAM2	51.049%	Swiss-Prot	strong database homology
`Q9LSL1`	Arabidopsis thaliana	Transcription factor bHLH93	40.000%	Swiss-Prot	weak database homology
`Q9LXA9`	Arabidopsis thaliana	Transcription factor bHLH61	37.339%	Swiss-Prot	weak database homology
`Q10S44`	Oryza sativa subsp. japonica	Transcription factor BHLH3	35.366%	Swiss-Prot	weak database homology

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