Human Gene ITM2C (uc002vqz.3) Description and Page Index
  Description: Homo sapiens integral membrane protein 2C (ITM2C), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr2:231,729,621-231,743,963 Size: 14,343 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr2:231,729,741-231,742,814 Size: 13,074 Coding Exon Count: 6 

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 (chr2:231,729,621-231,743,963)mRNA (may differ from genome)Protein (267 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: ITM2C_HUMAN
DESCRIPTION: RecName: Full=Integral membrane protein 2C; AltName: Full=Cerebral protein 14; AltName: Full=Transmembrane protein BRI3; Contains: RecName: Full=CT-BRI3;
FUNCTION: Negative regulator of beta amyloid peptide production. May inhibit the processing of APP by blocking its access to alpha- and beta-secretase. Binding to the beta-secretase-cleaved APP C- terminal fragment is negligible, suggesting that ITM2C is a poor gamma-secretase cleavage inhibitor. May play a role in TNF-induced cell death and neuronal differentiation (By similarity).
SUBUNIT: Interacts with BACE1. Interacts with APP. Interacts with STMN2.
SUBCELLULAR LOCATION: Lysosome membrane; Single-pass type II membrane protein (By similarity). Cell membrane; Single-pass type II membrane protein.
TISSUE SPECIFICITY: High levels in the brain, specifically in the cerebral cortex, medulla, amygdala, hippocampus, thalamus, caudate nucleus, cerebellum, olfactory lobe and spinal cord. Very low levels in other organs.
PTM: Type I membrane-bound, as well as soluble, furin has a pre- eminent role in ITM2C proteolytic processing. PCSK7 and PCSK5 may also be involved although to a lesser extent. The soluble form of PCSK7 is incapable of processing ITM2C. Fails to undergo shedding by ADAM10 and intramembanaire cleavage by SPPL2B.
SIMILARITY: Belongs to the ITM2 family.
SIMILARITY: Contains 1 BRICHOS domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ITM2C
CDC HuGE Published Literature: ITM2C

-  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: 469.60 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 5790.88 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 -52.60120-0.438 Picture PostScript Text
3' UTR -455.361149-0.396 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
IPR007084 - BRICHOS_dom

Pfam Domains:
PF04089 - BRICHOS domain

ModBase Predicted Comparative 3D Structure on Q9NQX7
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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001540 beta-amyloid binding
GO:0005515 protein binding
GO:0005524 ATP binding

Biological Process:
GO:0010977 negative regulation of neuron projection development
GO:0030182 neuron differentiation
GO:0042985 negative regulation of amyloid precursor protein biosynthetic process
GO:2001238 positive regulation of extrinsic apoptotic signaling pathway

Cellular Component:
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AF272043 - Homo sapiens BRI3 mRNA, complete cds.
AF271781 - Homo sapiens NPD018 mRNA, complete cds.
AK303199 - Homo sapiens cDNA FLJ54212 complete cds, highly similar to Integral membrane protein 2C.
AK075361 - Homo sapiens cDNA PSEC0047 fis, clone NT2RP1001042, highly similar to Integral membrane protein 2C.
AK090975 - Homo sapiens cDNA FLJ33656 fis, clone BRAMY2025175, highly similar to Homo sapiens BRI3 mRNA.
AX746713 - Sequence 238 from Patent EP1308459.
AK222697 - Homo sapiens mRNA for integral membrane protein 3 variant, clone: CBR05009.
AK056321 - Homo sapiens cDNA FLJ31759 fis, clone NT2RI2007723, highly similar to Homo sapiens integral membrane protein 2C (ITM2C), transcript variant 3, mRNA.
AK307702 - Homo sapiens cDNA, FLJ97650.
AL136603 - Homo sapiens mRNA; cDNA DKFZp564L1216 (from clone DKFZp564L1216).
BC050668 - Homo sapiens integral membrane protein 2C, mRNA (cDNA clone MGC:60191 IMAGE:5759920), complete cds.
BC002424 - Homo sapiens integral membrane protein 2C, mRNA (cDNA clone MGC:3011 IMAGE:3162430), complete cds.
AL713651 - Homo sapiens mRNA; cDNA DKFZp586H032 (from clone DKFZp586H032).
BC025742 - Homo sapiens integral membrane protein 2C, mRNA (cDNA clone MGC:34128 IMAGE:5224043), complete cds.
AK295503 - Homo sapiens cDNA FLJ55065 complete cds, highly similar to Integral membrane protein 2C.
BC098563 - Homo sapiens integral membrane protein 2C, mRNA (cDNA clone MGC:111364 IMAGE:30558635), complete cds.
AY049777 - Homo sapiens BRI3 mRNA, complete cds.
EU831696 - Synthetic construct Homo sapiens clone HAIB:100066725; DKFZo003C0620 integral membrane protein 2C protein (ITM2C) gene, encodes complete protein.
EU831609 - Synthetic construct Homo sapiens clone HAIB:100066638; DKFZo007C0619 integral membrane protein 2C protein (ITM2C) gene, encodes complete protein.
EU831632 - Synthetic construct Homo sapiens clone HAIB:100066661; DKFZo007E0519 integral membrane protein 2C protein (ITM2C) gene, encodes complete protein.
EU832568 - Synthetic construct Homo sapiens clone HAIB:100067597; DKFZo004E0630 integral membrane protein 2C protein (ITM2C) gene, encodes complete protein.
EU832488 - Synthetic construct Homo sapiens clone HAIB:100067517; DKFZo008E0629 integral membrane protein 2C protein (ITM2C) gene, encodes complete protein.
HQ448579 - Synthetic construct Homo sapiens clone IMAGE:100072017; CCSB011732_03 integral membrane protein 2C (ITM2C) gene, encodes complete protein.
KJ894853 - Synthetic construct Homo sapiens clone ccsbBroadEn_04247 ITM2C gene, encodes complete protein.
KJ899684 - Synthetic construct Homo sapiens clone ccsbBroadEn_09078 ITM2C gene, encodes complete protein.
CR457208 - Homo sapiens full open reading frame cDNA clone RZPDo834H0212D for gene ITM2C, integral membrane protein 2C; complete cds, incl. stopcodon.
AB003629 - Homo sapiens hucep-14 mRNA for cerebral protein-14, complete cds.
JD462914 - Sequence 443938 from Patent EP1572962.
JD535152 - Sequence 516176 from Patent EP1572962.
JD186234 - Sequence 167258 from Patent EP1572962.
JD128032 - Sequence 109056 from Patent EP1572962.
AK126739 - Homo sapiens cDNA FLJ44785 fis, clone BRACE3038012.
CR749389 - Homo sapiens mRNA; cDNA DKFZp686L07102 (from clone DKFZp686L07102).
JD396945 - Sequence 377969 from Patent EP1572962.
JD263112 - Sequence 244136 from Patent EP1572962.
D87062 - Homo sapiens hucep-3 mRNA for cerebral protein-3, complete cds.
JD548218 - Sequence 529242 from Patent EP1572962.
JD457787 - Sequence 438811 from Patent EP1572962.
JD261259 - Sequence 242283 from Patent EP1572962.
JD233195 - Sequence 214219 from Patent EP1572962.
JD115061 - Sequence 96085 from Patent EP1572962.
JD395642 - Sequence 376666 from Patent EP1572962.
JD393325 - Sequence 374349 from Patent EP1572962.
JD484280 - Sequence 465304 from Patent EP1572962.
JD421365 - Sequence 402389 from Patent EP1572962.
JD223543 - Sequence 204567 from Patent EP1572962.
JD181173 - Sequence 162197 from Patent EP1572962.
JD307548 - Sequence 288572 from Patent EP1572962.
JD098099 - Sequence 79123 from Patent EP1572962.
JD368919 - Sequence 349943 from Patent EP1572962.
JD039106 - Sequence 20130 from Patent EP1572962.
JD426881 - Sequence 407905 from Patent EP1572962.
JD486412 - Sequence 467436 from Patent EP1572962.
JD224829 - Sequence 205853 from Patent EP1572962.
JD516416 - Sequence 497440 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B3KPG4, BRI3, hucep-14, ITM2C_HUMAN, NM_030926, NPD018, NP_112188, PSEC0047, Q4G0A8, Q53H84, Q6IAE7, Q86VK5, Q8N288, Q8TAW0, Q9BUP8, Q9NQX7
UCSC ID: uc002vqz.3
RefSeq Accession: NM_030926
Protein: Q9NQX7 (aka ITM2C_HUMAN)
CCDS: CCDS2479.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_030926.4
exon count: 6CDS single in 3' UTR: no RNA size: 2123
ORF size: 804CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1808.00frame shift in genome: no % Coverage: 97.64
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.