Human Gene LGMN (ENST00000334869.9_7) from GENCODE V47lift37
  Description: legumain, transcript variant 1 (from RefSeq NM_005606.7)
Gencode Transcript: ENST00000334869.9_7
Gencode Gene: ENSG00000100600.15_15
Transcript (Including UTRs)
   Position: hg19 chr14:93,170,154-93,214,972 Size: 44,819 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr14:93,170,664-93,199,131 Size: 28,468 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:93,170,154-93,214,972)mRNA (may differ from genome)Protein (433 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LGMN_HUMAN
DESCRIPTION: RecName: Full=Legumain; EC=3.4.22.34; AltName: Full=Asparaginyl endopeptidase; AltName: Full=Protease, cysteine 1; Flags: Precursor;
FUNCTION: Has a strict specificity for hydrolysis of asparaginyl bonds. Can also cleave aspartyl bonds slowly, especially under acidic conditions. May be involved in the processing of proteins for MHC class II antigen presentation in the lysosomal/endosomal system.
CATALYTIC ACTIVITY: Hydrolysis of proteins and small molecule substrates at -Asn-|-Xaa- bonds.
SUBCELLULAR LOCATION: Lysosome (By similarity).
TISSUE SPECIFICITY: Ubiquitous. Particularly abundant in kidney, heart and placenta.
PTM: Glycosylated.
SIMILARITY: Belongs to the peptidase C13 family.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: LGMN
Diseases sorted by gene-association score: schistosomiasis (4)

-  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: 106.59 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1285.21 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 -62.40168-0.371 Picture PostScript Text
3' UTR -171.60510-0.336 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
IPR001096 - Peptidase_C13

Pfam Domains:
PF01650 - Peptidase C13 family

ModBase Predicted Comparative 3D Structure on Q99538
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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 DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004197 cysteine-type endopeptidase activity
GO:0008233 peptidase activity
GO:0008234 cysteine-type peptidase activity
GO:0016787 hydrolase activity

Biological Process:
GO:0003014 renal system process
GO:0006508 proteolysis
GO:0006624 vacuolar protein processing
GO:0007613 memory
GO:0008284 positive regulation of cell proliferation
GO:0008306 associative learning
GO:0010447 response to acidic pH
GO:0010629 negative regulation of gene expression
GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:0032801 receptor catabolic process
GO:0035729 cellular response to hepatocyte growth factor stimulus
GO:0040015 negative regulation of multicellular organism growth
GO:0042359 vitamin D metabolic process
GO:0043524 negative regulation of neuron apoptotic process
GO:0045931 positive regulation of mitotic cell cycle
GO:0051603 proteolysis involved in cellular protein catabolic process
GO:0071277 cellular response to calcium ion
GO:0090026 positive regulation of monocyte chemotaxis
GO:0097061 dendritic spine organization
GO:0097202 activation of cysteine-type endopeptidase activity
GO:0097264 self proteolysis
GO:1900273 positive regulation of long-term synaptic potentiation
GO:1901185 negative regulation of ERBB signaling pathway
GO:1904646 cellular response to beta-amyloid
GO:2001028 positive regulation of endothelial cell chemotaxis

Cellular Component:
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005770 late endosome
GO:0036021 endolysosome lumen
GO:0043202 lysosomal lumen
GO:0045177 apical part of cell
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF384880 - JP 2014500723-A/192383: Polycomb-Associated Non-Coding RNAs.
BC008004 - Homo sapiens legumain, mRNA (cDNA clone IMAGE:3507728), **** WARNING: chimeric clone ****.
BC003061 - Homo sapiens legumain, mRNA (cDNA clone MGC:1395 IMAGE:3504506), complete cds.
AK291534 - Homo sapiens cDNA FLJ78452 complete cds, highly similar to Homo sapiens legumain (LGMN), transcript variant 2, mRNA.
AK291560 - Homo sapiens cDNA FLJ78453 complete cds, highly similar to Homo sapiens legumain (LGMN), transcript variant 2, mRNA.
D55696 - Homo sapiens mRNA for cysteine protease, complete cds.
BX161422 - human full-length cDNA clone CS0DI002YH20 of Placenta of Homo sapiens (human).
BX161380 - human full-length cDNA clone CS0DB001YK19 of Neuroblastoma of Homo sapiens (human).
BX161434 - human full-length cDNA clone CS0DI011YN22 of Placenta of Homo sapiens (human).
AK225822 - Homo sapiens mRNA for legumain preproprotein variant, clone: FCC128G03.
AK297780 - Homo sapiens cDNA FLJ53066 complete cds, highly similar to Legumain precursor (EC 3.4.22.34).
AK297074 - Homo sapiens cDNA FLJ53058 complete cds, highly similar to Legumain precursor (EC 3.4.22.34).
Y09862 - H.sapiens mRNA for legumain.
KJ897389 - Synthetic construct Homo sapiens clone ccsbBroadEn_06783 LGMN gene, encodes complete protein.
DQ891884 - Synthetic construct clone IMAGE:100004514; FLH180923.01X; RZPDo839H06134D legumain (LGMN) gene, encodes complete protein.
DQ895070 - Synthetic construct Homo sapiens clone IMAGE:100009530; FLH180919.01L; RZPDo839H06133D legumain (LGMN) gene, encodes complete protein.
DQ895071 - Synthetic construct Homo sapiens clone IMAGE:100009531; FLH263641.01L; RZPDo839H08133D legumain (LGMN) gene, encodes complete protein.
EU176651 - Synthetic construct Homo sapiens clone IMAGE:100011589; FLH263642.01L; RZPDo839H10254D legumain (LGMN) gene, encodes complete protein.
CR457406 - Homo sapiens full open reading frame cDNA clone RZPDo834B0714D for gene LGMN, legumain; complete cds, incl. stopcodon.
CU678352 - Synthetic construct Homo sapiens gateway clone IMAGE:100018279 5' read LGMN mRNA.
MA620457 - JP 2018138019-A/192383: Polycomb-Associated Non-Coding RNAs.
LF209628 - JP 2014500723-A/17131: Polycomb-Associated Non-Coding RNAs.
LF330228 - JP 2014500723-A/137731: Polycomb-Associated Non-Coding RNAs.
BC013678 - Homo sapiens, clone IMAGE:3856715, mRNA, partial cds.
JD292174 - Sequence 273198 from Patent EP1572962.
JD216820 - Sequence 197844 from Patent EP1572962.
JD508321 - Sequence 489345 from Patent EP1572962.
LF330229 - JP 2014500723-A/137732: Polycomb-Associated Non-Coding RNAs.
JD340495 - Sequence 321519 from Patent EP1572962.
JD037247 - Sequence 18271 from Patent EP1572962.
JD272394 - Sequence 253418 from Patent EP1572962.
LF330230 - JP 2014500723-A/137733: Polycomb-Associated Non-Coding RNAs.
JD487050 - Sequence 468074 from Patent EP1572962.
JD144896 - Sequence 125920 from Patent EP1572962.
LF330231 - JP 2014500723-A/137734: Polycomb-Associated Non-Coding RNAs.
LF330232 - JP 2014500723-A/137735: Polycomb-Associated Non-Coding RNAs.
LF330233 - JP 2014500723-A/137736: Polycomb-Associated Non-Coding RNAs.
LF330234 - JP 2014500723-A/137737: Polycomb-Associated Non-Coding RNAs.
LF330235 - JP 2014500723-A/137738: Polycomb-Associated Non-Coding RNAs.
LF330236 - JP 2014500723-A/137739: Polycomb-Associated Non-Coding RNAs.
LF330238 - JP 2014500723-A/137741: Polycomb-Associated Non-Coding RNAs.
LF330239 - JP 2014500723-A/137742: Polycomb-Associated Non-Coding RNAs.
MA565805 - JP 2018138019-A/137731: Polycomb-Associated Non-Coding RNAs.
MA565806 - JP 2018138019-A/137732: Polycomb-Associated Non-Coding RNAs.
MA565807 - JP 2018138019-A/137733: Polycomb-Associated Non-Coding RNAs.
MA565808 - JP 2018138019-A/137734: Polycomb-Associated Non-Coding RNAs.
MA565809 - JP 2018138019-A/137735: Polycomb-Associated Non-Coding RNAs.
MA565810 - JP 2018138019-A/137736: Polycomb-Associated Non-Coding RNAs.
MA565811 - JP 2018138019-A/137737: Polycomb-Associated Non-Coding RNAs.
MA565812 - JP 2018138019-A/137738: Polycomb-Associated Non-Coding RNAs.
MA565813 - JP 2018138019-A/137739: Polycomb-Associated Non-Coding RNAs.
MA565815 - JP 2018138019-A/137741: Polycomb-Associated Non-Coding RNAs.
MA565816 - JP 2018138019-A/137742: Polycomb-Associated Non-Coding RNAs.
MA445205 - JP 2018138019-A/17131: Polycomb-Associated Non-Coding RNAs.
JD381149 - Sequence 362173 from Patent EP1572962.
JD405083 - Sequence 386107 from Patent EP1572962.
JD406053 - Sequence 387077 from Patent EP1572962.
JD056227 - Sequence 37251 from Patent EP1572962.
JD239459 - Sequence 220483 from Patent EP1572962.
JD518933 - Sequence 499957 from Patent EP1572962.
JD057984 - Sequence 39008 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q99538 (Reactome details) participates in the following event(s):

R-HSA-2130336 Initial proteolyis of Ii by aspartic proteases to lip22
R-HSA-1678920 TLR processing at low pH
R-HSA-196791 Vitamin D (calciferol) metabolism
R-HSA-2132295 MHC class II antigen presentation
R-HSA-209943 Steroid hormones
R-HSA-8957322 Metabolism of steroids
R-HSA-1280218 Adaptive Immune System
R-HSA-1679131 Trafficking and processing of endosomal TLR
R-HSA-556833 Metabolism of lipids
R-HSA-168256 Immune System
R-HSA-168898 Toll-Like Receptors Cascades
R-HSA-1430728 Metabolism
R-HSA-168249 Innate Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000334869.1, ENST00000334869.2, ENST00000334869.3, ENST00000334869.4, ENST00000334869.5, ENST00000334869.6, ENST00000334869.7, ENST00000334869.8, LGMN , LGMN_HUMAN, NM_005606, O00123, PRSC1 , Q86TV2, Q86TV3, Q99538, Q9BTY1, uc317ucl.1, uc317ucl.2
UCSC ID: ENST00000334869.9_7
RefSeq Accession: NM_005606.7
Protein: Q99538 (aka LGMN_HUMAN)

-  Gene Model Information
  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.