Human Gene CLGN (ENST00000325617.10_7) from GENCODE V47lift37
  Description: calmegin, transcript variant 1 (from RefSeq NM_004362.3)
Gencode Transcript: ENST00000325617.10_7
Gencode Gene: ENSG00000153132.13_15
Transcript (Including UTRs)
   Position: hg19 chr4:141,309,607-141,348,802 Size: 39,196 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr4:141,310,378-141,334,232 Size: 23,855 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:141,309,607-141,348,802)mRNA (may differ from genome)Protein (610 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CLGN_HUMAN
DESCRIPTION: RecName: Full=Calmegin; Flags: Precursor;
FUNCTION: Probably plays an important role in spermatogenesis. Binds calcium ions.
SUBUNIT: Interacts with PDILT.
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Single-pass type I membrane protein.
TISSUE SPECIFICITY: Testis.
SIMILARITY: Belongs to the calreticulin 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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D014212 Tretinoin
  • C006780 bisphenol A
  • C479799 (E)-4-((2-N-(4-methoxybenzenesulfonyl)amino)stilbazole)1-oxide
  • C063002 2,3-dimethoxy-1,4-naphthoquinone
  • D015122 6-Mercaptopurine
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D015124 8-Bromo Cyclic Adenosine Monophosphate
  • D000667 Ampicillin
  • D000965 Antimony
  • D000966 Antimony Potassium Tartrate
          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: 47.55 RPKM in Testis
Total median expression: 122.74 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 -44.20121-0.365 Picture PostScript Text
3' UTR -156.50771-0.203 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
IPR001580 - Calret/calnex
IPR018124 - Calret/calnex_CS
IPR009033 - Calreticulin/calnexin_P
IPR008985 - ConA-like_lec_gl_sf
IPR013320 - ConA-like_subgrp

Pfam Domains:
PF00262 - Calreticulin family

SCOP Domains:
63887 - P-domain of calnexin/calreticulin
49899 - Concanavalin A-like lectins/glucanases

ModBase Predicted Comparative 3D Structure on O14967
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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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding
GO:0044183 protein binding involved in protein folding
GO:0051082 unfolded protein binding

Biological Process:
GO:0006457 protein folding
GO:0007338 single fertilization
GO:0007339 binding of sperm to zona pellucida
GO:0065003 macromolecular complex assembly

Cellular Component:
GO:0005635 nuclear envelope
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  D86322 - Homo sapiens mRNA for calmegin, complete cds.
HM005702 - Homo sapiens clone HTL-T-79P testis tissue sperm-binding protein Li 79P mRNA, complete cds.
JD190134 - Sequence 171158 from Patent EP1572962.
JD350443 - Sequence 331467 from Patent EP1572962.
JD236247 - Sequence 217271 from Patent EP1572962.
AK093096 - Homo sapiens cDNA FLJ35777 fis, clone TESTI2005363, highly similar to CALMEGIN PRECURSOR.
BC028357 - Homo sapiens calmegin, mRNA (cDNA clone MGC:26321 IMAGE:4830135), complete cds.
AK302149 - Homo sapiens cDNA FLJ54199 complete cds, highly similar to Calmegin precursor.
JD350240 - Sequence 331264 from Patent EP1572962.
AK290819 - Homo sapiens cDNA FLJ78187 complete cds, highly similar to Homo sapiens calmegin, mRNA.
JD052154 - Sequence 33178 from Patent EP1572962.
JD284968 - Sequence 265992 from Patent EP1572962.
AK299243 - Homo sapiens cDNA FLJ55357 complete cds, highly similar to Calmegin precursor.
DQ892100 - Synthetic construct clone IMAGE:100004730; FLH183030.01X; RZPDo839F01140D calmegin (CLGN) gene, encodes complete protein.
KJ890894 - Synthetic construct Homo sapiens clone ccsbBroadEn_00288 CLGN gene, encodes complete protein.
DQ895295 - Synthetic construct Homo sapiens clone IMAGE:100009755; FLH263718.01L; RZPDo839F03139D calmegin (CLGN) gene, encodes complete protein.
CU688458 - Synthetic construct Homo sapiens gateway clone IMAGE:100020370 5' read CLGN mRNA.

-  Other Names for This Gene
  Alternate Gene Symbols: B3KS90, B4DXV8, CLGN_HUMAN, D3DNY8, ENST00000325617.1, ENST00000325617.2, ENST00000325617.3, ENST00000325617.4, ENST00000325617.5, ENST00000325617.6, ENST00000325617.7, ENST00000325617.8, ENST00000325617.9, NM_004362, O14967, uc317rxd.1, uc317rxd.2
UCSC ID: ENST00000325617.10_7
RefSeq Accession: NM_004362.3
Protein: O14967 (aka CLGN_HUMAN or CALG_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.