Human Gene LECT2 (uc003lbe.1) Description and Page Index
  Description: Homo sapiens leukocyte cell-derived chemotaxin 2 (LECT2), mRNA.
RefSeq Summary (NM_002302): This gene encodes a secreted, 16 kDa protein that acts as a chemotactic factor to neutrophils and stimulates the growth of chondrocytes and osteoblasts. This protein has high sequence similarity to the chondromodulin repeat regions of the chicken myb-induced myeloid 1 protein. A polymorphism in this gene may be associated with rheumatoid arthritis. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: D63521.1, SRR5189664.25165.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA2155590 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000274507.6/ ENSP00000274507.1 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr5:135,282,600-135,290,723 Size: 8,124 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr5:135,283,020-135,290,522 Size: 7,503 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:135,282,600-135,290,723)mRNA (may differ from genome)Protein (151 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: LECT2_HUMAN
DESCRIPTION: RecName: Full=Leukocyte cell-derived chemotaxin-2; Short=LECT-2; Short=hLECT2; Flags: Precursor;
FUNCTION: Has a neutrophil chemotactic activity. Also a positive regulator of chondrocyte proliferation.
SUBCELLULAR LOCATION: Cytoplasm. Secreted.
TISSUE SPECIFICITY: Highly expressed in adult and fetal liver and weakly in testis. Not expressed in bone marrow.
INDUCTION: By phytohemagglutinin (PHA).
SIMILARITY: Belongs to the LECT2/MIM-1 family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LECT2
CDC HuGE Published Literature: LECT2
Positive Disease Associations: Magnesium
Related Studies:
  1. Magnesium
    , , . [PubMed 0]

-  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: 19.45 RPKM in Liver
Total median expression: 24.15 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 -44.10201-0.219 Picture PostScript Text
3' UTR -78.30420-0.186 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
IPR008663 - LECT2
IPR017381 - LECT2_chordata
IPR016047 - Peptidase_M23

Pfam Domains:
PF01551 - Peptidase family M23

ModBase Predicted Comparative 3D Structure on O14960
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 orthologGenome BrowserNo ortholog
Gene Details   Gene Details 
Gene Sorter   Gene Sorter 
  Ensembl WormBase 
  Protein Sequence Protein Sequence 
  Alignment Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0001501 skeletal system development
GO:0006935 chemotaxis

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  E11436 - cDNA encoding human leukocyte cell-derived chemotaxins 2b,LECT2b.
D63521 - Homo sapiens mRNA for LECT2 precursor, complete cds.
JD092944 - Sequence 73968 from Patent EP1572962.
JD292215 - Sequence 273239 from Patent EP1572962.
BC093670 - Homo sapiens leukocyte cell-derived chemotaxin 2, mRNA (cDNA clone MGC:120705 IMAGE:7939515), complete cds.
BC101579 - Homo sapiens leukocyte cell-derived chemotaxin 2, mRNA (cDNA clone MGC:126628 IMAGE:8069085), complete cds.
AK314092 - Homo sapiens cDNA, FLJ94772, Homo sapiens leukocyte cell-derived chemotaxin 2 (LECT2), mRNA.
KJ897125 - Synthetic construct Homo sapiens clone ccsbBroadEn_06519 LECT2 gene, encodes complete protein.
AB590696 - Synthetic construct DNA, clone: pFN21AE1635, Homo sapiens LECT2 gene for leukocyte cell-derived chemotaxin 2, without stop codon, in Flexi system.
JD305187 - Sequence 286211 from Patent EP1572962.
JD175086 - Sequence 156110 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RA90, LECT2_HUMAN, NM_002302, NP_002293, O14565, O14960, Q52M49
UCSC ID: uc003lbe.1
RefSeq Accession: NM_002302
Protein: O14960 (aka LECT2_HUMAN or LCT2_HUMAN)
CCDS: CCDS4190.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002302.2
exon count: 4CDS single in 3' UTR: no RNA size: 1077
ORF size: 456CDS single in intron: no Alignment % ID: 99.81
txCdsPredict score: 969.00frame 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.