LXL04_024563 | RubberDandelionOmics

Gene overview

LXL04_024563

Reference: OH-1004 Chr: Chr05 Coordinates: 93838335-93840348 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1770 bp · LXL04_024563|LXL04_024563|OH1004|cDNA

ATGGCATATATGTGCACCGACAGCGGCAATTTAATGGCCATAGCTCAACAAGTTATCcaacaaaaacaacaacaagAACAACAGCTTCATCAACAACAGCAACACCAGCAGCCATTAGTCACTGTGAACGTAAATCCATTCTggaccaccaccggccaccaaTCTCCGACTCTTGCATACGGATTTTCCGATCCGTTTGAAGGAAGTGCGGCGGATATGGCTGGAGCCGAAGAGACAGCTGGATTTCAGTTCCCGAACCT...

CDS

Download CDS FASTA

1770 bp · LXL04_024563|LXL04_024563|OH1004|CDS

ATGGCATATATGTGCACCGACAGCGGCAATTTAATGGCCATAGCTCAACAAGTTATCCAACAAAAACAACAACAAGAACAACAGCTTCATCAACAACAGCAACACCAGCAGCCATTAGTCACTGTGAACGTAAATCCATTCTGGACCACCACCGGCCACCAATCTCCGACTCTTGCATACGGATTTTCCGATCCGTTTGAAGGAAGTGCGGCGGATATGGCTGGAGCCGAAGAGACAGCTGGATTTCAGTTCCCGAACCT...

Protein

Download Protein FASTA

589 aa · LXL04_024563|LXL04_024563|OH1004|PROTEIN

MAYMCTDSGNLMAIAQQVIQQKQQQEQQLHQQQQHQQPLVTVNVNPFWTTTGHQSPTLAYGFSDPFEGSAADMAGAEETAGFQFPNLDHHHHQQPGFRFADFVAASGSVGEFDTDEWMESLIDSTTESSTWQPSSDFTLYAADPFSDCPSRLTCSTDLKNANSTWSPSPPVLASDHLLPPEKELNPPKPDKSPPSKEDIASTSSPESILTKPLLKTLTDCARLADSDPGNAITPLIRIRDSVSADQGDPTERVAFYFAEA...

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_024563`
TK1151 ID	TkA06G131330
OH-1004 ID	LXL04_024563
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.300
Protein coverage (%)	TK1151 98.110 / OH-1004 96.944 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_024563

Location Chr05:93838335-93840348 (+)

Description Similar to SCL7: SCARECROW-LIKE protein 7

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g66770`	Probable transcription factor involved in plant development.	No verified direct reference in this release
`At3g50650`	Probable transcription factor involved in plant development (Probable).	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0723000`	Probable transcription factor involved in plant development (By similarity).	Crystal Structure of the GRAS Domain of SCARECROW-LIKE7 in Oryza sativa.2016 · DOI: 10.1105/tpc.16.00018
`Os07g0583600`	May play a regulatory role in the early step of oligosaccharide elicitor response, downstream of the membrane- associated high-affinity chitin-binding protein.	Identification and characterization of two new members of the GRAS gene family in rice responsive to N-acetylchitooligosaccharide elicitor.2003 · DOI: 10.1016/s0167-4781(02)00626-7

Functional annotation source

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Functional annotation source: OH1004 · LXL04_024563 · 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:0005634 nucleus Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0003677 DNA binding Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

GO:0043565 sequence-specific DNA binding Molecular Function

KEGG gene cross-reference

ath:AT3G50650

ath:AT5G66770

dosa:Os03g0723000

dosa:Os07g0583600

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.

Nucleus0.850

Rank 1 · LXL04_024563 · OH-1004

Cytoplasm0.203

Rank 2 · LXL04_024563 · OH-1004

Cell membrane0.044

Rank 3 · LXL04_024563 · OH-1004

Endoplasmic reticulum0.039

Rank 4 · LXL04_024563 · OH-1004

Plastid0.027

Rank 5 · LXL04_024563 · 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.

PF03514.21GRAS214-570 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_024563	`PF03514.21`	GRAS	214	570	7.3e-106	355.0

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
`Q9FL03`	Arabidopsis thaliana	Scarecrow-like protein 4	57.751%	Swiss-Prot	strong database homology
`Q9SCR0`	Arabidopsis thaliana	Scarecrow-like protein 7	52.696%	Swiss-Prot	strong database homology
`Q53K16`	Oryza sativa subsp. japonica	SCARECROW-LIKE protein 7	56.868%	Swiss-Prot	moderate database homology
`Q8GVE1`	Oryza sativa subsp. japonica	Chitin-inducible gibberellin-responsive protein 2	34.501%	Swiss-Prot	moderate database homology

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