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Gene Card

Enter a TK1151 or OH-1004 gene ID to view sequences, annotations and analyses in the corresponding reference genome.
Flanking length, max 10000 bp
Examples TkA01G624900 LXL04_000258

Gene overview

LXL04_039072
Reference: OH-1004 Chr: Chr09 Coordinates: 58506741-58510505 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

3765 bp · LXL04_039072|LXL04_039072|OH1004|cDNA

ATGGAGGCAGCCCTAGCCCCCAACTCGATCACATTTGACACGGAACTTTATGATGGCAGCAACCGATTTGAGGATTACAACAGGGAGATCCCGGCTAACGATGAGGAGGAAAACGCGGATGCCATGGACAATGAAGTTGCACGGAAGTTGGCTTCTTACACTGCCCCGAGGTCTCTGTTGAACGAGATGCCGAGGGGGGGAGACGATGATGAATCTACGGGGTTTCCGAAATCACAGAAGATTATCGACAGGGAGGACGA...

CDS

Download CDS FASTA

3765 bp · LXL04_039072|LXL04_039072|OH1004|CDS

ATGGAGGCAGCCCTAGCCCCCAACTCGATCACATTTGACACGGAACTTTATGATGGCAGCAACCGATTTGAGGATTACAACAGGGAGATCCCGGCTAACGATGAGGAGGAAAACGCGGATGCCATGGACAATGAAGTTGCACGGAAGTTGGCTTCTTACACTGCCCCGAGGTCTCTGTTGAACGAGATGCCGAGGGGGGGAGACGATGATGAATCTACGGGGTTTCCGAAATCACAGAAGATTATCGACAGGGAGGACGA...

Protein

Download Protein FASTA

1254 aa · LXL04_039072|LXL04_039072|OH1004|PROTEIN

MEAALAPNSITFDTELYDGSNRFEDYNREIPANDEEENADAMDNEVARKLASYTAPRSLLNEMPRGGDDDESTGFPKSQKIIDREDEYRRRRLNQVISPERHDAFANGDKTPKPETRSYADIMREAALKREKEETLKVIARRKKEEEENKAAGKEKEREREQQPQAQPSQKRRNRWDQNQEKSDGKKAKTGLDWDMPEDGMSTPGRWDATPTPGRMGDALSRKNRWDETPTPGRTGADSDSTPAGGGATPAGMAWDATPK...

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.

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ID Mapping

Input IDLXL04_039072
Source versionOH-1004 / GCA_047496595.1_OSU_TarKok_2.0
Open Full ID Mapping
SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene IDLXL04_039072
LocationChr09:58506741-58510505 (+)
DescriptionSimilar to sf3b1: Splicing factor 3B subunit 1
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

No hit for this species in the current source table.

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_039072 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0000245 spliceosomal complex assembly Biological Process
GO:0000375 RNA splicing, via transesterification reactions Biological Process
GO:0000387 spliceosomal snRNP assembly Biological Process
GO:0000388 spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) Biological Process
GO:0000398 mRNA splicing, via spliceosome Biological Process
GO:0006338 chromatin remodeling Biological Process
GO:0008380 RNA splicing Biological Process
GO:0009952 anterior/posterior pattern specification Biological Process
GO:0045292 mRNA cis splicing, via spliceosome Biological Process
GO:0045943 positive regulation of transcription by RNA polymerase I Biological Process
GO:0045944 positive regulation of transcription by RNA polymerase II Biological Process
GO:0045945 positive regulation of transcription by RNA polymerase III Biological Process
KEGG gene cross-reference
hsa:23451
spo:2541619
xla:399336
These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.
Open Annotation Module

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.

Cytoplasm0.541
Rank 1 · LXL04_039072 · OH-1004
Nucleus0.459
Rank 2 · LXL04_039072 · OH-1004
Cell membrane0.139
Rank 3 · LXL04_039072 · OH-1004
Endoplasmic reticulum0.048
Rank 4 · LXL04_039072 · OH-1004
Lysosome / Vacuole0.041
Rank 5 · LXL04_039072 · 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.

PF08920.16SF3b1267-397 aa
PF24714.2TOR1L1_N587-752 aa
PF25757.2TPR_DNAAF5588-702 aa
PF23227.2HEAT_MROH2B_C799-922 aa
PF24714.2TOR1L1_N866-1035 aa
PF20926.4Htt_N-HEAT_1890-1029 aa
PF13513.13HEAT_EZ943-991 aa
PF22646.3PPP2R1A-like_HEAT1035-1107 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_039072PF08920.16SF3b12673974.2e-50170.3
LXL04_039072PF24714.2TOR1L1_N5877523.8e-1763.3
LXL04_039072PF25757.2TPR_DNAAF55887023e-1040.5
LXL04_039072PF23227.2HEAT_MROH2B_C7999225.1e-1453.0
LXL04_039072PF24714.2TOR1L1_N86610353.8e-1763.3
LXL04_039072PF20926.4Htt_N-HEAT_189010291.9e-0732.3
LXL04_039072PF13513.13HEAT_EZ9439911.5e-1351.6
LXL04_039072PF22646.3PPP2R1A-like_HEAT103511072.3e-2279.9

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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