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KeywordFamilyClanGene   

Entry: CD20 (PF04103)

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Very fast search for clan entries. The
search can be done either by clan ID
(e.g. CL0192) or by clan name (e.g. GPCR_A).

Pfam summary

Description

CD20/IgE Fc receptor beta subunit family

This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. The alpha subunit of Fc epsilon RI and most Fc receptors are homologous members of the Ig superfamily. By contrast, the beta and gamma subunits from Fc epsilon RI are not homologous to the Ig superfamily. Both molecules have four putative transmembrane segments and a probably topology where both amino- and carboxy termini protrude into the cytoplasm [1]. This family also includes LR8 like proteins from humans, mice and rats. The function of the human LR8 protein is unknown although it is known to be strongly expressed in the lung fibroblasts [2]. This family also includes sarcospan is a transmembrane component of dystrophin-associated glycoprotein. Loss of the sarcoglycan complex and sarcospan alone is sufficient to cause muscular dystrophy. The role of the sarcoglycan complex and sarcospan is thought to be to strengthen the dystrophin axis connecting the basement membrane with the cytoskeleton [3].
 
Literature1. Hupp K, Siwarski D, Mock BA, Kinet JP; J Immunol 1989;143:3787-3791.Gene mapping of the three subunits of the high affinity FcR for IgE to mouse chromosomes 1 and 19. PUBMED:2531187
2. Lurton J, Rose TM, Raghu G, Narayanan AS; Am J Respir Cell Mol Biol 1999;20:327-331.Isolation of a gene product expressed by a subpopulation of human lung fibroblasts by differential display. PUBMED:9922225
3. Araishi K, Sasaoka T, Imamura M, Noguchi S, Hama H, Wakabayashi E, Yoshida M, Hori T, Ozawa E; Hum Mol Genet. 1999;8:1589-1598.Loss of the sarcoglycan complex and sarcospan leads to muscular dystrophy in beta-sarcoglycan-deficient mice. PUBMED:10441321
 
Clan

CL0347 (Tetraspannin)

The clan contains the following members: PF04103(CD20); PF00335(Tetraspannin);
 
InterPro entry IPR007237
 

Alignment

New Hampshire tree

The seed alignment for this family in the PANDIT database contains 16 aligned sequences:

  CD20_HUMAN/58-224   CD20_MOUSE/51-218   FCEB_HUMAN/67-212   FCEB_MOUSE/59-203   M4A12_HUMAN/97-232   M4A4A_HUMAN/72-215   M4A6A_HUMAN/54-216   M4A6C_MOUSE/54-215   M4A6D_MOUSE/54-215   M4A7_HUMAN/54-215   M4A8A_MOUSE/113-252   M4A8B_HUMAN/78-215   MS4A5_HUMAN/56-197   Q9D2W6_MOUSE/54-193   Q9D3F6_MOUSE/50-179   Q9ES61_MOUSE/50-179  

The full alignment for this family in the Pfam database contains 299 aligned sequences

Species in the seed alignment

List of species covered in the seed alignment. The number in brackets denotes the number of sequences taken from each organism.

  Homo sapiens (8);   Mus musculus (8);  

The full alignment covers 51 species.

Pre-computed estimates from Markov codon substitution models (explanation)

Following are maximum-likelihood estimates and log-likelihood scores from codon models M0, M1, M2, M7 and M8, implemented in PAML v.4.1

Model name  

Model M0

Model M1

Model M2

Model M7

Model M8

Log-likelihood score  

-4497.28-4451.104988-4449.957899-4451.326436-4446.150267

Tree Length  

20.2720.2700520.2700520.2700520.27005

κ  

2.212.1910512.2451722.156942.228706

ω-ratio  

ω=0.53663p0=0.588782 ~ ω0=0.318804
p1=0.411218 ~ ω1=1
p0=0.578588 ~ ω0=0.333443
p1=0.379784 ~ ω1=1
p2=0.041628 ~ ω2=1.932044
ω~Β(1.33088,1.080844)p0=0.873672 ~ ω~Β(1.980283,2.123699)
p1=0.126328 ~ ω=1.486047

P-value for testing  
positive selection  

M1 vs M2: P-value=0.31756
family classification: conserved
M7 vs M8: P-value=0.00565
family classification: positively selected

Positively selected sites - the underlined numbers denote the position in the AA sequence, while the number in brackets denote the estimated probability for having positive selection at that position. Only positions where the estimated probability for positive selection is ≥0.95 are shown.

   Model M8:
      Naive Empirical Bayes (NEB) analysis: 16 (0.974); 61 (0.978);
      Bayes Empirical Bayes (BEB) analysis: 16 (0.955); 61 (0.957);

Maximum-likelihood estimates and log-likelihood scores from codon models Nonsynonymous and Dual implemented in HYPHY

Model name  

Model Nonsynonymous

Model Dual

Log-likelihood score  

-6895.32051-6889.60637

Mean ω-ratio  

ω = 0.62111ω = 0.70522

Coeff. of variation  
of ω-ratio  

CVω = 0.70435CVω = 1.02308
 

Annotations

InteractionsThis family has 0 known interactions:

StructuresThis family has 3 structures:
Notation: PDB_ID (PDB chain, PDB residues)

Gene Ontologies
Cellular component
 integral to membrane[GO:0016021]
Biological Process
 signal transduction[GO:0007165]
Molecular Function
 receptor activity[GO:0004872]

KEGG Pathways - for genes coding for sequences from full alignment
Metabolism
Carbohydrate Metabolism
Ascorbate and aldarate metabolism [KEGG]
Energy Metabolism
Oxidative phosphorylation [KEGG]
Nitrogen metabolism [KEGG]
Lipid Metabolism
Glycerophospholipid metabolism [KEGG]
Glycan Biosynthesis and Metabolism
Peptidoglycan biosynthesis [KEGG]
Metabolism of Cofactors and Vitamins
Ubiquinone and menaquinone biosynthesis [KEGG]
Nicotinate and nicotinamide metabolism [KEGG]
Folate biosynthesis [KEGG]
Porphyrin and chlorophyll metabolism [KEGG]
Genetic Information Processing
Folding, Sorting and Degradation
Protein export [KEGG]
Type II secretion system [KEGG]
Environmental Information Processing
Membrane Transport
ABC transporters [KEGG]
Phosphotransferase system (PTS) [KEGG]
Signal Transduction
Two-component system [KEGG]
Signaling Molecules and Interaction
Cytokine-cytokine receptor interaction [KEGG]
Neuroactive ligand-receptor interaction [KEGG]
Cell adhesion molecules (CAMs) [KEGG]
Cellular Processes
Cell Communication
Tight junction [KEGG]
Immune System
Hematopoietic cell lineage [KEGG]
Fc epsilon RI signaling pathway [KEGG]
Leukocyte transendothelial migration [KEGG]
Sensory System
Olfactory transduction [KEGG]
Human Diseases
Immune Disorders
Asthma [KEGG]
 

Expression data (explanation)

 
Bgee expression data - for genes coding for sequences from seed alignment     Click here for overview of Bgee data

The numbers in brackets correspond to the number of genes that are associated with the selected family and are expressed in the corresponding tissue. Click on the tissue to see all the families that possibly have function in that tissue and click on the genes to see the corresponding genes.

Homo sapiens
Mus musculus

HumanProteinpedia expression data - for human genes coding for sequences from full alignment     Click here for overview of Human Proteinpedia data

The numbers in brackets correspond to the number of human genes that are associated with the selected family and are expressed in the corresponding tissue. Click on the tissue to see all the families that possibly have function in that tissue and click on the genes to see the corresponding genes.

Healthy tissues
Disease tissues

Human disease association

 
Genetic Association Database - data for human genes coding for sequences from full alignment

The numbers in brackets correspond to the number of genes that are associated with the selected family and are associated with the corresponding disease. Click on the disease name to see all the families possibly associated with that disease and click on the genes to see the corresponding genes.

Associated diseases and disorders

Links to OMIM - for human genes coding for sequences from full alignment
 
605908 (1) 112210 (1) 606499 (1) 610334 (1) 602983 (1) 608403 (1) 608402 (1) 606498 (1) 601267 (1) 606549 (1) 606502 (1) 606547 (1) 602982 (1) 606921 (1) 147138 (1) 603733 (1) 606548 (1) 606550 (1) 605879 (1) 610385 (1)