Human Gene LIX1 (uc003kmy.4) Description and Page Index
  Description: Homo sapiens Lix1 homolog (chicken) (LIX1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr5:96,427,574-96,478,520 Size: 50,947 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr5:96,430,452-96,478,280 Size: 47,829 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:96,427,574-96,478,520)mRNA (may differ from genome)Protein (282 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: LIX1_HUMAN
DESCRIPTION: RecName: Full=Protein limb expression 1 homolog;
SIMILARITY: Belongs to the LIX1 family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LIX1
CDC HuGE Published Literature: LIX1

-  MalaCards Disease Associations
  MalaCards Gene Search: LIX1
Diseases sorted by gene-association score: common bile duct disease (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 12.11 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 97.09 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -79.80240-0.333 Picture PostScript Text
3' UTR -674.502878-0.234 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
  Pfam Domains:
PF14954 - Limb expression 1

ModBase Predicted Comparative 3D Structure on Q8N485
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0097352 autophagosome maturation

Cellular Component:
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  BC036467 - Homo sapiens Lix1 homolog (chicken), mRNA (cDNA clone MGC:33866 IMAGE:5264055), complete cds.
AK098400 - Homo sapiens cDNA FLJ25534 fis, clone CBR08513.
AK291034 - Homo sapiens cDNA FLJ78158 complete cds.
AK307885 - Homo sapiens cDNA, FLJ97833.
KJ900373 - Synthetic construct Homo sapiens clone ccsbBroadEn_09767 LIX1 gene, encodes complete protein.
JD237646 - Sequence 218670 from Patent EP1572962.
JD082950 - Sequence 63974 from Patent EP1572962.
JD108519 - Sequence 89543 from Patent EP1572962.
JD168635 - Sequence 149659 from Patent EP1572962.
JD236444 - Sequence 217468 from Patent EP1572962.
JD146813 - Sequence 127837 from Patent EP1572962.
JD102934 - Sequence 83958 from Patent EP1572962.
JD088019 - Sequence 69043 from Patent EP1572962.
JD508065 - Sequence 489089 from Patent EP1572962.
JD241742 - Sequence 222766 from Patent EP1572962.
JD499059 - Sequence 480083 from Patent EP1572962.
JD299220 - Sequence 280244 from Patent EP1572962.
JD357406 - Sequence 338430 from Patent EP1572962.
JD110675 - Sequence 91699 from Patent EP1572962.
JD314571 - Sequence 295595 from Patent EP1572962.
JD374366 - Sequence 355390 from Patent EP1572962.
JD310089 - Sequence 291113 from Patent EP1572962.
JD511781 - Sequence 492805 from Patent EP1572962.
JD184362 - Sequence 165386 from Patent EP1572962.
JD330995 - Sequence 312019 from Patent EP1572962.
JD562286 - Sequence 543310 from Patent EP1572962.
JD046370 - Sequence 27394 from Patent EP1572962.
JD563863 - Sequence 544887 from Patent EP1572962.
JD244131 - Sequence 225155 from Patent EP1572962.
JD349573 - Sequence 330597 from Patent EP1572962.
JD132601 - Sequence 113625 from Patent EP1572962.
JD479147 - Sequence 460171 from Patent EP1572962.
JD357013 - Sequence 338037 from Patent EP1572962.
LF210706 - JP 2014500723-A/18209: Polycomb-Associated Non-Coding RNAs.
JD512237 - Sequence 493261 from Patent EP1572962.
JD446047 - Sequence 427071 from Patent EP1572962.
MA446283 - JP 2018138019-A/18209: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K4R9, C5orf11, LIX1_HUMAN, NM_153234, NP_694966, Q8N485, Q8N7I2
UCSC ID: uc003kmy.4
RefSeq Accession: NM_153234
Protein: Q8N485 (aka LIX1_HUMAN)
CCDS: CCDS4088.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_153234.4
exon count: 6CDS single in 3' UTR: no RNA size: 3979
ORF size: 849CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1795.00frame shift in genome: no % Coverage: 99.70
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.