Human Gene LHX6 (uc022bmw.1)
  Description: Homo sapiens LIM homeobox 6 (LHX6), transcript variant 5, mRNA.
RefSeq Summary (NM_001242335): This gene encodes a member of a large protein family that contains the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein has tandem LIM domains as well as a DNA-binding homeodomain. The protein functions as a transcription factor involved in embryogenesis and head development and is highly expressed in neural crest derived mesenchyme cells. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2017].
Transcript (Including UTRs)
   Position: hg19 chr9:124,964,856-124,984,019 Size: 19,164 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr9:124,967,039-124,979,380 Size: 12,342 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:124,964,856-124,984,019)mRNA (may differ from genome)Protein (176 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsH-INV
HGNCLynxMalacardsMGIOMIMPubMed
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: H0YN76_HUMAN
DESCRIPTION: SubName: Full=LIM/homeobox protein Lhx6;
SUBCELLULAR LOCATION: Nucleus (By similarity).
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LHX6
CDC HuGE Published Literature: LHX6

-  MalaCards Disease Associations
  MalaCards Gene Search: LHX6
Diseases sorted by gene-association score: image syndrome (6)

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 6.99 RPKM in Adipose - Subcutaneous
Total median expression: 84.65 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 -390.10879-0.444 Picture PostScript Text
3' UTR -736.122183-0.337 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
IPR017970 - Homeobox_CS
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like

Pfam Domains:
PF00046 - Homeobox domain
PF05920 - Homeobox KN domain

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on H0YN76
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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AL136570 - Homo sapiens mRNA; cDNA DKFZp761G2023 (from clone DKFZp761G2023).
LF205667 - JP 2014500723-A/13170: Polycomb-Associated Non-Coding RNAs.
AK126982 - Homo sapiens cDNA FLJ45036 fis, clone BRAWH3019629, highly similar to LIM/homeobox protein Lhx6.1.
JD250239 - Sequence 231263 from Patent EP1572962.
JD516578 - Sequence 497602 from Patent EP1572962.
JD459225 - Sequence 440249 from Patent EP1572962.
JD195479 - Sequence 176503 from Patent EP1572962.
BC103936 - Homo sapiens LIM homeobox 6, mRNA (cDNA clone MGC:119542 IMAGE:40008208), complete cds.
BC103937 - Homo sapiens LIM homeobox 6, mRNA (cDNA clone MGC:119544 IMAGE:40008210), complete cds.
BC103938 - Homo sapiens LIM homeobox 6, mRNA (cDNA clone MGC:119545 IMAGE:40008211), complete cds.
JD114542 - Sequence 95566 from Patent EP1572962.
JD216473 - Sequence 197497 from Patent EP1572962.
JD514503 - Sequence 495527 from Patent EP1572962.
JD102509 - Sequence 83533 from Patent EP1572962.
JD250800 - Sequence 231824 from Patent EP1572962.
JD306960 - Sequence 287984 from Patent EP1572962.
JD448551 - Sequence 429575 from Patent EP1572962.
JD484256 - Sequence 465280 from Patent EP1572962.
JD163298 - Sequence 144322 from Patent EP1572962.
JD153875 - Sequence 134899 from Patent EP1572962.
JD200580 - Sequence 181604 from Patent EP1572962.
JD390808 - Sequence 371832 from Patent EP1572962.
JD349346 - Sequence 330370 from Patent EP1572962.
JD165468 - Sequence 146492 from Patent EP1572962.
JD215119 - Sequence 196143 from Patent EP1572962.
JD331374 - Sequence 312398 from Patent EP1572962.
JD086691 - Sequence 67715 from Patent EP1572962.
JD308425 - Sequence 289449 from Patent EP1572962.
JD237236 - Sequence 218260 from Patent EP1572962.
JD217726 - Sequence 198750 from Patent EP1572962.
LF347003 - JP 2014500723-A/154506: Polycomb-Associated Non-Coding RNAs.
JD474839 - Sequence 455863 from Patent EP1572962.
JD503957 - Sequence 484981 from Patent EP1572962.
JD169082 - Sequence 150106 from Patent EP1572962.
AK299709 - Homo sapiens cDNA FLJ55589 complete cds, highly similar to LIM/homeobox protein Lhx6.1.
AK297175 - Homo sapiens cDNA FLJ55755 complete cds, highly similar to LIM/homeobox protein Lhx6.1.
LF347004 - JP 2014500723-A/154507: Polycomb-Associated Non-Coding RNAs.
JD222462 - Sequence 203486 from Patent EP1572962.
AK289827 - Homo sapiens cDNA FLJ77966 complete cds, highly similar to Homo sapiens LIM homeobox 6 (LHX6), transcript variant 1, mRNA.
JD254108 - Sequence 235132 from Patent EP1572962.
JD061767 - Sequence 42791 from Patent EP1572962.
JD226833 - Sequence 207857 from Patent EP1572962.
JD054669 - Sequence 35693 from Patent EP1572962.
JD321901 - Sequence 302925 from Patent EP1572962.
JD455268 - Sequence 436292 from Patent EP1572962.
JD098413 - Sequence 79437 from Patent EP1572962.
AB031041 - Homo sapiens hLhx6.1a mRNA for LIM-homeodomain (LHX) protein 6.1a, complete cds.
AB031042 - Homo sapiens hLhx6.1b mRNA for LIM-homeodomain (LHX) protein 6.1b, complete cds.
AK313808 - Homo sapiens cDNA, FLJ94426, Homo sapiens LIM homeobox 6 (LHX6), mRNA.
KJ902431 - Synthetic construct Homo sapiens clone ccsbBroadEn_11825 LHX6 gene, encodes complete protein.
EU446700 - Synthetic construct Homo sapiens clone IMAGE:100070068; IMAGE:100011909; FLH257163.01L LIM homeobox 6 (LHX6) gene, encodes complete protein.
AM392697 - Synthetic construct Homo sapiens clone IMAGE:100001678 for hypothetical protein (LHX6 gene).
AM393362 - Synthetic construct Homo sapiens clone IMAGE:100001731 for hypothetical protein (LHX6 gene).
MA582580 - JP 2018138019-A/154506: Polycomb-Associated Non-Coding RNAs.
MA582581 - JP 2018138019-A/154507: Polycomb-Associated Non-Coding RNAs.
MA441244 - JP 2018138019-A/13170: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: H0YN76, H0YN76_HUMAN, NM_001242335, NP_001229264
UCSC ID: uc022bmw.1
RefSeq Accession: NM_001242335
Protein: H0YN76 CCDS: CCDS59144.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001242335.1
exon count: 7CDS single in 3' UTR: no RNA size: 3603
ORF size: 531CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 954.50frame shift in genome: no % Coverage: 99.72
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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