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The Human Proteome > Small intestine

The small intestine-specific proteome

The duodenum is succeeded by jejunum and ileum, the remaining two sections of the small intestine. Here, the jejunum/ileum region is referred to as small intestine. The major function of this part of the digestive system is the absorption of nutrients derived from the digestion of food in more distal regions, water and electrolytes. The transcriptome analysis shows that 66% of all human proteins (n=19692) are expressed in the small intestine and 339 of these genes show an elevated expression in small intestine compared to other tissue types. An analysis of the genes with elevated expression in the small intestine with regards to subcellular localization reveals that the corresponding proteins are most often located in the brush boarder, secreted mucus, cellular membrane, or cytoplasm.

  • 6 small intestine enriched genes
  • 339 genes defined as elevated in the small intestine
  • Large number of genes show shared expression in small intestine and duodenum

Figure 1. The distribution of all genes across the five categories based on transcript abundance in small intestine as well as in all other tissues.

339 genes show some level of elevated expression in the small intestine compared to other tissues. The four categories of genes with elevated expression in small intestine compared to other organs are shown in Table 1.

Table 1. The genes with elevated expression in small intestine


Number of genes


Tissue enriched 6 At least five-fold higher mRNA levels in a particular tissue as compared to all other tissues
Group enriched 180 At least five-fold higher mRNA levels in a group of 2-7 tissues
Tissue enhanced 153 At least five-fold higher mRNA levels in a particular tissue as compared to average levels in all tissues
Total 339 Total number of elevated genes in small intestine

Table 2. The 6 genes with the highest level of enriched expression in small intestine. "Predicted localization" shows the classification of each gene into three main classes: Secreted, Membrane, and Intracellular, where the latter consists of genes without any predicted membrane and secreted features. "mRNA (tissue)" shows the transcript level asáFPKM values,áTS-score (Tissue Specificity score) corresponds to the score calculated as the fold change to the second highest tissue.



Predicted localization

mRNA (tissue)


CPO carboxypeptidase O Secreted 83.1 142
FABP6 fatty acid binding protein 6, ileal Intracellular,Secreted 2540.8 52
KCNJ13 potassium inwardly-rectifying channel, subfamily J, member 13 Membrane 82.9 12
PLB1 phospholipase B1 Intracellular,Membrane 29.1 7
SLC17A8 solute carrier family 17 (vesicular glutamate transporter), member 8 Membrane 4.3 7
NAALADL1 N-acetylated alpha-linked acidic dipeptidase-like 1 Intracellular 67.9 5

Some of the proteins predicted to be membrane-spanning are intracellular, e.g., in the Golgi or mitochondrial membranes, and some of the proteins predicted to be secreted can potentially be retained in a compartment belonging to the secretory pathway, such as the ER, or remain attached to the outer face of the cell membrane by a GPI anchor.

The small intestine transcriptome

An analysis of the expression levels of each gene makes it possible to calculate the relative mRNA pool for each of the categories. The analysis shows that 76% of the mRNA molecules derived from small intestine correspond to housekeeping genes and that 16% of the mRNA pool corresponds to genes categorized as small intestine enriched, group enriched or, small intestine enhanced. Thus, most of the transcriptional activity in the small intestine relates to proteins with presumed housekeeping functions as they are found in all tissues and cells analyzed.

Protein expression of genes elevated in small intestine

In-depth analysis of the elevated genes in small intestine using antibody-based protein profiling allowed us to visualize the protein expression patterns in the small intestine with respect to cellular compartments. The expression profile of small intestine is very similar to duodenum, FABP6 is one of the genes that are present in small intestine but not in duodenum and is involved in ileal fatty acid binding. ALPI, DEFA6, and FABP2 are examples of genes shared by duodenum and small intestine and with less expression in the other parts of gastrointestinal tract.

Genes shared between small intestine and other tissues

There are 180 group-enriched genes expressed in the small intestine. Group enriched genes are defined as genes showing a 5-fold higher average level of mRNA expression in a group of 2-7 tissues, including small intestine, compared to all other tissues.

In order to illustrate the relation of small intestine tissue to other tissue types, a network plot was generated, displaying the number of commonly expressed genes between different tissue types.

Figure 2. An interactive network plot of theásmall intestineáenriched and group enriched genes connected to their respective enriched tissues (grey circles).áRedánodes represent the number ofásmall intestine enriched genes andáorangeánodes represent the number of genes that are group enriched. The sizes of the red and orange nodes are related to the number of genes displayed within the node. Each node is clickable and results in a list of all enriched genes connected to the highlighted edges. The network is limited to group enriched genes in combinations of up toá4átissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.

Small intestine histology

The small intestine (jejunum and ileum) measures about 6 meters and absorbs nutrition, water and electrolytes. It is similar to the duodenum in histology and composition. The permanent transverse submucosal fold extending into the lumen of the intestine are termed plica circularis. The plica circularis consist of mucosa as well as submucosa. The core is the submucosa composed of loose connective tissue, blood vessels, nerves and dispersed lymphoid tissue. A distinctive feature of the jejunum and ileum is the lack of glands in the submucosa.

The mucosa is characterized by numerous finger-like villi that protrude into the lumen of the intestine. Enterocytes, which are columnar epithelial cells with basally located oval nuclei and an apical brush border line the villi. The enterocytes located to the villi have mainly absorptive function. Interspersed between the enterocytes are goblet cells, which are recognized by their content of a large mucous globule, resembling a small "empty bubble" within the epithelial lining. The goblet cells are connected to the basement membrane by a thin, cytoplasmic strand that is difficult to distinguish in haematoxylin and eosin staining. Underlying the intestinal villi are the intestinal glands. They are straight tubular glands that are slightly dilated at their bottom. Intestinal stem cells line the proximal part of the glands. The stem cells give rise to all the cells in the epithelium, which are the paneth cells, the enterocytes, the goblet cells and the enteroendocrine cells. The paneth cells secrete antibacterial enzymes and are located in the lower portion of the intestinal glands. Paneth cells are recognized by eosinophilic granules in the cytoplasm.

The histology of human small intestine including detailed images and information about the different cell types can be viewed in the Protein Atlas Histology Dictionary.


Here, the protein-coding genes expressed in the small intestine are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize protein expression patterns of proteins that correspond to genes with elevated expression in the small intestine.

Transcript profiling and RNA-data analyses based on normal human tissues have been described previously (Fagerberg et al., 2013). Analyses of mRNA expression including over 99% of all human protein-coding genes was performed using deep RNA sequencing of 124 individual samples corresponding to 32 different human normal tissue types. RNA sequencing results of 4 fresh frozen tissues representing normal small intestine was compared to 120 other tissue samples corresponding to 31 tissue types, in order to determine genes with elevated expression in small intestine. A tissue-specific score, defined as the ratio between mRNA levels in small intestine compared to the mRNA levels in all other tissues, was used to divide the genes into different categories of expression. These categories include: genes with elevated expression in small intestine, genes expressed in all tissues, genes with a mixed expression pattern, genes not expressed in small intestine, and genes not expressed in any tissue. Genes with elevated expression in small intestine were further sub-categorized as i) genes with enriched expression in small intestine, ii) genes with group enriched expression including small intestine and iii) genes with enhanced expression in small intestine.

Human tissue samples used for protein and mRNA expression analyses were collected and handled in accordance with Swedish laws and regulation and obtained from the Department of Pathology, Uppsala University Hospital, Uppsala, Sweden as part of the sample collection governed by the Uppsala Biobank. All human tissue samples used in the present study were anonymized in accordance with approval and advisory report from the Uppsala Ethical Review Board.

UhlÚn et al (2015). Tissue-based map of the human proteome. Science
PubMed: 25613900 DOI: 10.1126/science.1260419

Yu et al (2015). Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium. Nucleic Acids Res.
PubMed: 26117540 DOI: 10.1093/nar/gkv608

Fagerberg et al (2014). Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Mol Cell Proteomics.
PubMed: 24309898 DOI: 10.1074/mcp.M113.035600

Gremel et al (2014). The human gastrointestinal tract-specific transcriptome and proteome as defined by RNA sequencing and antibody-based profiling. J Gastroenterol.
PubMed: 24789573 DOI: 10.1007/s00535-014-0958-7

Histology dictionary - the small intestine

The small intestine-specific proteome
The small intestine transcriptome
Protein expression of genes elevated in small intestine
Genes shared between small intestine and other tissues
Small intestine histology
Relevant links and publications

Gastrointestinal tract
Salivary gland
Small intestine