RubberDandelionOmics Rubber Dandelion Multi-omics Website
More
Transcriptome Expression Annotation Rubber Pathway TF Prediction Targets Protein Network Resequencing Tools Downloads
ZH EN

How to use this page

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_019900
Reference: OH-1004 Chr: Chr04 Coordinates: 43779601-43780727 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

816 bp · LXL04_019900|LXL04_019900|OH1004|cDNA

ATGGCAATGGAACAATACACTCAAGAATCCGTCCCTCAAAACAGCTTCATCAAAGACAACGAAACCTCGTCCGACAAATGGAAATCATTAACCGAATCAATAGACGACTTCGAAAACAATCCTTCATCCGGTTTTGACTGCAATATTTGTCTAGATTCGGTCCAAGATCCAGTCGTAACACTCTGCGGCCACCTCTATTGTTGGCCATGCATATACAAGTGGATACAACACCAAAACACTTCACCCGAAACCCCAAAAAA...

CDS

Download CDS FASTA

816 bp · LXL04_019900|LXL04_019900|OH1004|CDS

ATGGCAATGGAACAATACACTCAAGAATCCGTCCCTCAAAACAGCTTCATCAAAGACAACGAAACCTCGTCCGACAAATGGAAATCATTAACCGAATCAATAGACGACTTCGAAAACAATCCTTCATCCGGTTTTGACTGCAATATTTGTCTAGATTCGGTCCAAGATCCAGTCGTAACACTCTGCGGCCACCTCTATTGTTGGCCATGCATATACAAGTGGATACAACACCAAAACACTTCACCCGAAACCCCAAAAAA...

Protein

Download Protein FASTA

271 aa · LXL04_019900|LXL04_019900|OH1004|PROTEIN

MAMEQYTQESVPQNSFIKDNETSSDKWKSLTESIDDFENNPSSGFDCNICLDSVQDPVVTLCGHLYCWPCIYKWIQHQNTSPETPKKHKPQCPVCKQDISQKTLVPLYGRDQTTKPESDDKGLDLGMVIPRRPLSPSCGAVRSATEQVNDRGHQLQTQFVINPTSPTTGMLGEMVYGGVFGNTQTSLYAYPNSYNLVAVSTQRARRHAIQADRSLGRICSKQQRDSKSTLECFEPEKPGCLKRPNNIQSLEVKRFMIEES...

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.

Download Gene (CDS) Download Protein

ID Mapping

Input IDLXL04_019900
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_019900
LocationChr04:43779601-43780727 (-)
DescriptionSimilar to RMA1H1: E3 ubiquitin-protein ligase RMA1H1
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At4g03510 E3 ubiquitin-protein ligase that promotes the ubiquitination and proteasomal degradation of aquaporin PIP2-1.
Rma1, a novel type of RING finger protein conserved from Arabidopsis to human, is a membrane-bound ubiquitin ligase.2001 · DOI: 10.1242/jcs.114.10.1949
Characterization of three Arabidopsis homologs of human RING membrane anchor E3 ubiquitin ligase.2009 · DOI: 10.1007/s00299-009-0680-8
Drought stress-induced Rma1H1, a RING membrane-anchor E3 ubiquitin ligase homolog, regulates aquaporin levels via ubiquitination in transgenic Arabidopsis plants.2009 · DOI: 10.1105/tpc.108.061994
At4g28270 E3 ubiquitin-protein ligase that promotes the ubiquitination and proteasomal degradation of the auxin-binding protein ERABP1.
Characterization of three Arabidopsis homologs of human RING membrane anchor E3 ubiquitin ligase.2009 · DOI: 10.1007/s00299-009-0680-8
In vitro and in vivo interaction of AtRma2 E3 ubiquitin ligase and auxin binding protein 1.2010 · DOI: 10.1016/j.bbrc.2010.02.032
At4g27470 E3 ubiquitin-protein ligase.
Characterization of three Arabidopsis homologs of human RING membrane anchor E3 ubiquitin ligase.2009 · DOI: 10.1007/s00299-009-0680-8

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_019900 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006511 ubiquitin-dependent protein catabolic process Biological Process
GO:0006914 autophagy Biological Process
GO:0006970 response to osmotic stress Biological Process
GO:0009409 response to cold Biological Process
GO:0009414 response to water deprivation Biological Process
GO:0009611 response to wounding Biological Process
GO:0009723 response to ethylene Biological Process
GO:0016567 protein ubiquitination Biological Process
GO:0032527 protein exit from endoplasmic reticulum Biological Process
GO:0036503 ERAD pathway Biological Process
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process Biological Process
GO:0044314 protein K27-linked ubiquitination Biological Process
KEGG gene cross-reference
ath:AT4G03510
ath:AT4G27470
ath:AT4G28270
cann:107855034
mmu:193670
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.

Nucleus0.740
Rank 1 · LXL04_019900 · OH-1004
Cytoplasm0.323
Rank 2 · LXL04_019900 · OH-1004
Cell membrane0.049
Rank 3 · LXL04_019900 · OH-1004
Mitochondrion0.037
Rank 4 · LXL04_019900 · OH-1004
Endoplasmic reticulum0.032
Rank 5 · LXL04_019900 · 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.

PF13639.13zf-RING_246-96 aa
PF13920.13zf-C3HC4_346-101 aa
PF14634.13zf-RING_546-97 aa
PF24921.2RING_XB3-XBAT3147-101 aa
PF00097.32zf-C3HC447-95 aa
PF13923.13zf-C3HC4_247-82 aa
PF13445.13zf-RING_UBOX47-79 aa
PF15227.13zf-C3HC4_447-95 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_019900PF13639.13zf-RING_246961.6e-0835.4
LXL04_019900PF13920.13zf-C3HC4_3461013.5e-0627.4
LXL04_019900PF14634.13zf-RING_546978.2e-0626.4
LXL04_019900PF24921.2RING_XB3-XBAT31471011.2e-1041.9
LXL04_019900PF00097.32zf-C3HC447952.7e-1040.7
LXL04_019900PF13923.13zf-C3HC4_247822.2e-0937.7
LXL04_019900PF13445.13zf-RING_UBOX47796.9e-0936.3
LXL04_019900PF15227.13zf-C3HC4_447955.3e-0730.3

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

ProteinOrganismDescriptionIdentityDatabaseConfidence
O64425Arabidopsis thalianaE3 ubiquitin-protein ligase RMA141.089%Swiss-Protmoderate database homology
P93030Arabidopsis thalianaE3 ubiquitin-protein ligase RMA240.223%Swiss-Protmoderate database homology
Q8GUK7Arabidopsis thalianaE3 ubiquitin-protein ligase RMA335.683%Swiss-Protmoderate database homology

JBrowse

View in Genome Browser