Human Gene LRRC58 (uc003edr.2) Description and Page Index
  Description: Homo sapiens leucine rich repeat containing 58 (LRRC58), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr3:120,043,576-120,068,186 Size: 24,611 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr3:120,050,047-120,068,090 Size: 18,044 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:120,043,576-120,068,186)mRNA (may differ from genome)Protein (371 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
HGNCHPRDLynxMGIneXtProtPubMed
Stanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: LRC58_HUMAN
DESCRIPTION: RecName: Full=Leucine-rich repeat-containing protein 58;
SIMILARITY: Contains 9 LRR (leucine-rich) repeats.
SEQUENCE CAUTION: Sequence=AAH13757.1; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LRRC58
CDC HuGE Published Literature: LRRC58
Positive Disease Associations: Bone Density
Related Studies:
  1. Bone Density
    Douglas P Kiel et al. BMC medical genetics 2007, Genome-wide association with bone mass and geometry in the Framingham Heart Study., BMC medical genetics. [PubMed 17903296]
    The FHS 100K SNP project offers an unbiased genome-wide strategy to identify new candidate loci and to replicate previously suggested candidate genes for osteoporosis.

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 10.56 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 256.64 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 -52.4096-0.546 Picture PostScript Text
3' UTR -1674.126471-0.259 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
IPR001611 - Leu-rich_rpt
IPR025875 - Leu-rich_rpt_2_copies
IPR003591 - Leu-rich_rpt_typical-subtyp

Pfam Domains:
PF00560 - Leucine Rich Repeat
PF12799 - Leucine Rich repeats (2 copies)
PF13516 - Leucine Rich repeat
PF13855 - Leucine rich repeat

SCOP Domains:
52047 - RNI-like
52058 - L domain-like
52075 - Outer arm dynein light chain 1

ModBase Predicted Comparative 3D Structure on Q96CX6
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 BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  EnsemblFlyBaseWormBase 
  Protein SequenceProtein SequenceProtein Sequence 
  AlignmentAlignmentAlignment 

-  Descriptions from all associated GenBank mRNAs
  BC013757 - Homo sapiens leucine rich repeat containing 58, mRNA (cDNA clone IMAGE:4525041), partial cds.
AB528173 - Synthetic construct DNA, clone: pF1KE0208, Homo sapiens LRRC58 gene for leucine rich repeat containing 58, without stop codon, in Flexi system.
AM393236 - Synthetic construct Homo sapiens clone IMAGE:100002541 for hypothetical protein (LRRC58 gene).
AK056809 - Homo sapiens cDNA FLJ32247 fis, clone PROST1000120.
JD497720 - Sequence 478744 from Patent EP1572962.
DQ572144 - Homo sapiens piRNA piR-40256, complete sequence.
JD337282 - Sequence 318306 from Patent EP1572962.
JD249009 - Sequence 230033 from Patent EP1572962.
JD110899 - Sequence 91923 from Patent EP1572962.
JD504792 - Sequence 485816 from Patent EP1572962.
JD285335 - Sequence 266359 from Patent EP1572962.
JD564981 - Sequence 546005 from Patent EP1572962.
JD490308 - Sequence 471332 from Patent EP1572962.
JD571862 - Sequence 9 from Patent WO2015030616.
JD209467 - Sequence 190491 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: LRC58_HUMAN, NM_001099678, NP_001093148, Q96CX6
UCSC ID: uc003edr.2
RefSeq Accession: NM_001099678
Protein: Q96CX6 (aka LRC58_HUMAN)
CCDS: CCDS46892.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001099678.1
exon count: 4CDS single in 3' UTR: no RNA size: 7683
ORF size: 1116CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2432.00frame shift in genome: no % Coverage: 100.00
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.