Human Gene LMO4 (ENST00000370544.10) from GENCODE V44
  Description: Homo sapiens LIM domain only 4 (LMO4), transcript variant 1, mRNA. (from RefSeq NM_006769)
RefSeq Summary (NM_006769): This gene encodes a cysteine-rich protein that contains two LIM domains but lacks a DNA-binding homeodomain. The encoded protein may play a role as a transcriptional regulator or as an oncogene. [provided by RefSeq, Aug 2008]. Sequence Note: The RefSeq transcript and protein were derived from transcript and genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments.
Gencode Transcript: ENST00000370544.10
Gencode Gene: ENSG00000143013.13
Transcript (Including UTRs)
   Position: hg38 chr1:87,328,880-87,348,923 Size: 20,044 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg38 chr1:87,332,016-87,344,796 Size: 12,781 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:87,328,880-87,348,923)mRNA (may differ from genome)Protein (165 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGencode
GeneCardsHGNCHPRDLynxMalacardsMGI
neXtProtOMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LMO4_HUMAN
DESCRIPTION: RecName: Full=LIM domain transcription factor LMO4; AltName: Full=Breast tumor autoantigen; AltName: Full=LIM domain only protein 4; Short=LMO-4;
FUNCTION: Probable transcriptional factor (By similarity).
SUBUNIT: Interacts strongly with LDBS. Interacts with DEAF1, CLIM1 and CLIM2. Interacts (via the LIM zinc-binding domain 1) with RBBP8. Interacts with BRCA1 (via the BRCT domains); the interaction represses BRCA1 transcriptional activity (By similarity).
SIMILARITY: Contains 2 LIM zinc-binding domains.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 66.83 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 672.18 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -132.70368-0.361 Picture PostScript Text
3' UTR -1030.704127-0.250 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001781 - Znf_LIM

Pfam Domains:
PF00412 - LIM domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2L4Z - NMR MuPIT


ModBase Predicted Comparative 3D Structure on P61968
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001158 enhancer sequence-specific DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0008134 transcription factor binding
GO:0046872 metal ion binding

Biological Process:
GO:0001843 neural tube closure
GO:0003281 ventricular septum development
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0021514 ventral spinal cord interneuron differentiation
GO:0021522 spinal cord motor neuron differentiation
GO:0021527 spinal cord association neuron differentiation
GO:0030334 regulation of cell migration
GO:0031333 negative regulation of protein complex assembly
GO:0033674 positive regulation of kinase activity
GO:0042659 regulation of cell fate specification
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048538 thymus development
GO:0050865 regulation of cell activation

Cellular Component:
GO:0005667 transcription factor complex
GO:0031252 cell leading edge


-  Descriptions from all associated GenBank mRNAs
  U24576 - Homo sapiens breast tumor autoantigen (LMO4) mRNA, complete cds.
AK292578 - Homo sapiens cDNA FLJ77516 complete cds, highly similar to Homo sapiens LIM domain only 4 (LMO4), mRNA.
JD407117 - Sequence 388141 from Patent EP1572962.
BC017673 - Homo sapiens LIM domain only 4, mRNA (cDNA clone MGC:17816 IMAGE:3893112), complete cds.
JD339220 - Sequence 320244 from Patent EP1572962.
JD059307 - Sequence 40331 from Patent EP1572962.
JD368585 - Sequence 349609 from Patent EP1572962.
BC003600 - Homo sapiens LIM domain only 4, mRNA (cDNA clone MGC:872 IMAGE:3355972), complete cds.
JD166932 - Sequence 147956 from Patent EP1572962.
JD190284 - Sequence 171308 from Patent EP1572962.
AY321514 - Homo sapiens LIM-only 4 protein mRNA, 5' UTR and partial cds.
BC065818 - Homo sapiens LIM domain only 4, mRNA (cDNA clone MGC:75040 IMAGE:6196307), complete cds.
DQ891447 - Synthetic construct clone IMAGE:100004077; FLH177033.01X; RZPDo839C04124D LIM domain only 4 (LMO4) gene, encodes complete protein.
DQ894626 - Synthetic construct Homo sapiens clone IMAGE:100009086; FLH177030.01L; RZPDo839C04123D LIM domain only 4 (LMO4) gene, encodes complete protein.
AB384751 - Synthetic construct DNA, clone: pF1KB3107, Homo sapiens LMO4 gene for LIM domain transcription factor LMO4, complete cds, without stop codon, in Flexi system.
KJ897865 - Synthetic construct Homo sapiens clone ccsbBroadEn_07259 LMO4 gene, encodes complete protein.
JD238789 - Sequence 219813 from Patent EP1572962.
JD283829 - Sequence 264853 from Patent EP1572962.
JD371466 - Sequence 352490 from Patent EP1572962.
JD251572 - Sequence 232596 from Patent EP1572962.
JD177886 - Sequence 158910 from Patent EP1572962.
JD181720 - Sequence 162744 from Patent EP1572962.
JD502777 - Sequence 483801 from Patent EP1572962.
JD554775 - Sequence 535799 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: D3DT23, ENST00000370544.1, ENST00000370544.2, ENST00000370544.3, ENST00000370544.4, ENST00000370544.5, ENST00000370544.6, ENST00000370544.7, ENST00000370544.8, ENST00000370544.9, LMO4_HUMAN, NM_006769, O00158, O88894, P61968, uc001dmi.1, uc001dmi.2, uc001dmi.3, uc001dmi.4, uc001dmi.5
UCSC ID: ENST00000370544.10
RefSeq Accession: NM_006769
Protein: P61968 (aka LMO4_HUMAN)
CCDS: CCDS713.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.