LXL04_000038 | RubberDandelionOmics

Gene overview

LXL04_000038

Reference: OH-1004 Chr: Chr01 Coordinates: 743788-746844 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2613 bp · LXL04_000038|LXL04_000038|OH1004|cDNA

ATGGAGCAAAATCTTCTGTCGACTTTCgaagaaaatttcaaaaaccCAACAAAAATATCTCTAAAACCCTTGTCTATTGCTAGAACTCTCATTGTAAACCCCTCAACCTCCGATGAGACAATCTCTTCCATTCTCCAAAATCTCATGGTAAACCCACCCGAGTTGTACCATCTCCATGTCATCACCCTCCTGTGTGAAATCTCCATCCTCCGCAGCCATTTCTCCCCGCGCATCACCACCATACTCCACTCTCACTCTCa...

CDS

Download CDS FASTA

2613 bp · LXL04_000038|LXL04_000038|OH1004|CDS

ATGGAGCAAAATCTTCTGTCGACTTTCGAAGAAAATTTCAAAAACCCAACAAAAATATCTCTAAAACCCTTGTCTATTGCTAGAACTCTCATTGTAAACCCCTCAACCTCCGATGAGACAATCTCTTCCATTCTCCAAAATCTCATGGTAAACCCACCCGAGTTGTACCATCTCCATGTCATCACCCTCCTGTGTGAAATCTCCATCCTCCGCAGCCATTTCTCCCCGCGCATCACCACCATACTCCACTCTCACTCTCA...

Protein

Download Protein FASTA

870 aa · LXL04_000038|LXL04_000038|OH1004|PROTEIN

MEQNLLSTFEENFKNPTKISLKPLSIARTLIVNPSTSDETISSILQNLMVNPPELYHLHVITLLCEISILRSHFSPRITTILHSHSHSHSLSPNIIALCTCVSEMTEGLFLSLCFGSCVSVRQKLLSDVEMFDVRPSLLLTVLTGFAKDPYPYVRKAALDGLIGLCKYIVVEDPGMIQGCYLRAVELLFDTEESVRCSAVQMVMYLQFPFIELREEGSQINFGWQVSEWGKLLVANSDGKSKRDCSDALYVQLCSMVRDM...

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_000038`
TK1151 ID	TkA01G640400
OH-1004 ID	LXL04_000038
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	92.900
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_000038

Location Chr01:743788-746844 (-)

Description Similar to SIEL: Protein SIEL

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g08800`	Intracellular shuttle that promotes movement of SHR from the stele into the endodermis.	An essential protein that interacts with endosomes and promotes movement of the SHORT-ROOT transcription factor.2011 · DOI: 10.1016/j.cub.2011.08.013

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_000038 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0010496 intercellular transport Biological Process

GO:0016180 snRNA processing Biological Process

GO:0034243 regulation of transcription elongation by RNA polymerase II Biological Process

GO:0034472 snRNA 3'-end processing Biological Process

GO:0090057 root radial pattern formation Biological Process

GO:0160240 RNA polymerase II transcription initiation surveillance Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005768 endosome Cellular Component

GO:0005938 cell cortex Cellular Component

KEGG gene cross-reference

ath:AT3G08800

dme:Dmel_CG12113

hsa:92105

mmu:101861

xla:447293

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.

Nucleus0.753

Rank 1 · LXL04_000038 · OH-1004

Cytoplasm0.235

Rank 2 · LXL04_000038 · OH-1004

Cell membrane0.044

Rank 3 · LXL04_000038 · OH-1004

Endoplasmic reticulum0.043

Rank 4 · LXL04_000038 · OH-1004

Golgi apparatus0.033

Rank 5 · LXL04_000038 · 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.

PF25458.2INTS4_C757-863 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000038	`PF25458.2`	INTS4_C	757	863	6.9e-08	33.1

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
`Q8VZA0`	Arabidopsis thaliana	Protein SIEL	35.233%	Swiss-Prot	moderate database homology

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