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Table 3 Top 20 Pfam domains that are often inserted or deleted among protein isoforms*.

From: Splice-mediated Variants of Proteins (SpliVaP) – data and characterization of changes in signatures among protein isoforms due to alternative splicing

Pfam Domain No. of genes$ Pfam Description of the domain Associated GO terms Keywords associated with the domain
zf-C2H2 104 (75%) Zinc finger, C2H2 type Zinc ion binding Nucleic Acid binding
  61 (48%)    
PH 59 (62%) pleckstrin homology   Intracellular signaling/constituent of cytoskeleton
  22 (44%)    
Ank 54 (80%) Ankyrin repeat   Protein-protein interaction
  25 (34%)    
ig 51 (82%) Immunoglobulin family   Domains for cell surface recognition.
  Not seen in asd    
fn3 46 (77%) Fibronectin type III domain   Multi-domain glycoproteins.
  6 (28%)    
SPRY 46 (77%) SPIa and the Ryanodine receptor   
  3 (75%)    
Collagen 45 (88%) Collagen triple helix repeat Phosphate transport Extracellular structural proteins
  8 (66%)    
zf-C3HC4 44 (61%) Zinc finger, C3HC4 type (RING finger) Protein binding, zinc ion binding Key role in ubiquitination pathway.
  7 (50%)    
Pkinase 44 (29%) Protein kinase domain ATP binding, protein kinase activity, protein amino acid phosphorylation  
  1 (2%)    
PDZ 43 (66%) PDZ domain Protein binding Signaling
  18 (42%)    
KRAB 42 (46%) Kruppel-associated box present in proteins containg C2H2 fingers. Nucleic acid binding, intracellular, DNA-dependent regulation of transcription Protein-protein interactions
  34 (49%)    
C1-set 41 (37%) Immunoglobulin C1-set domain   Cell-cell recognition, cell-surface receptors, muscle structure, immune system.
  1 (50%)    
WD40 40 (83)% WD or beta-transducin repeats   Signal transduction, transcription regulation, cell cycle control, apoptosis.
  35 (38%)    
EGF 40 (83%) Epidermal growth factor – like domain   Found in extracellular domain.
  5 (18%)    
SH3_1 40 (51%) Src homology 3   Signal transduction
  4 (8%)    related to cytoskeletal organisation.
Sushi 39 (97%) Complement control protein (CCP) modules, or short consensus repeats (SCR).   Complement and adhesion
  17 (73%)    
Helicase_C 32 (62%) Helicase conserved C-terminal domain Nucleic acid binding Helicase
  12 (44%)    
I-set 32 (66%) Immunoglobulin I-set domain   Cell-cell recognition, cell-surface receptors, muscle structure, immune system
  Not present in ASD    
RRM_1 31 (72%) RNA recognition motif Nucleic Acid binding RNA binding
  21 (46%)    
C2 27 (61%) Ca2+-dependent membrane-targeting module   Signal transduction/membrane trafficking
  16 (53%)    
LIM 19 (82%) LIM domain (Binding protein) Zinc ion binding Interface for protein-protein interaction
  20 (74%)    
Mito_carr 21 (91%) Mitochondrial carrier Transport, binding, membrane  
  19 (86%)    
CH 16 (53%) Calponin homology domain   Cytoskeletal/signal transduction
  12 (66%)    
Hormone_receptor 9 (32%) Ligand-binding domain of nuclear hormone receptor Transcription factor; regulation of transcription Hormone binding
  12 (60%)    
Trypsin 20 (41%) Trypsin Proteolysis Proteolytic enzyme
  11 (30%)    
  1. $, presents the number of genes in which the domain is seen as undergoing domain insertion/deletion event. In brackets, is given in terms of percentage fraction of genes containing the domain – in what percentage fraction of genes (that contain the domain), the domain undergoes insertion/deletion.
  2. *, Line 1 gives values from Vega data set and line 2 gives values from ASD data set.