Homological Analysis

These are the results for the 3 domain-pairs, with the following legend: - The numbers on each species represent the number of genes with the ceratin domain in the organism. - The numbers on each node represent the minimal/average/maximal number of genes with the domain.

• RRM (Superfam-ID: 54929):
  Tree: assets/RRM(54929).tree
  Postscript: assets/RRM(54929).ps
  
  

  Table 1: Distribution of RRM domain in all taxa

  Taxon	#Gene: min/avg/max number of genes possessing the domain	known/all organisms from superfam database
  Bacteria	1/2.1/8	(159/669)
  Archaea	1/2.5/4	(2/52)
  Eukaryota	14/130.9/562	(190/207)
  - Stramenopiles	62/70.3/78	(6/6)
  - Streptophyta	122/265.7/496	(10/14)
  - Chlorophyta	60/78.4/94	(7/8)
  - Euglenozoa	76/91/144	(5/6)
  - Amoebozoa	88/90.7/94	(3/3)
  - Alveolata	42/79.3/213	(13/13)
  - Fungi	20/64.8/121	(75/81)
  - Metazoa	101/219.7/562	(64/69)
  - - Protostomia	110/151.2/335	(22/24)
  - - Deuterostomia	125/269.7/562	(37/39)

  
  The RRM domain is common in all eukaryota as well as in some Bacteria which is not suprising given the fact that RNA-binding is essential in RNA processing (but RRM is not the only RNA-binding domain).

• RS (Superfam-ID: 52065):
  Tree: assets/RS(52065).tree
  Postscript: assets/RS(52065).ps
  
  

  Table 2: Distribution of RS domain in all taxa

  Taxon	#Gene: min/avg/max number of genes possessing the domain	known/all organisms from superfam database
  Bacteria	1/1.0/1	(1/669)
  Archaea	0/0/0	(0/52)
  Eukaryota	1/3.1/22	(167/207)
  - Stramenopiles	1/1.7/3	(3/6)
  - Streptophyta	1/7.2/15	(10/14)
  - Chlorophyta	1/1.0/1	(4/8)
  - Euglenozoa	3/3.2/4	(5/6)
  - Amoebozoa	2/8.7/13	(3/3)
  - Alveolata	1/1.0/3	(5/13)
  - Fungi	1/1.3/7	(71/81)
  - Metazoa	1/4.7/22	(57/69)
  - - Protostomia	2/4.0/10	(22/24)
  - - Deuterostomia	1/5.1/22	(35/39)

  
  The RS domain is only common in eukaryota, mostly in fungi and metazoa.

• RRM(Family-ID: 54928) - RS (Family-ID: 52065):
  Tree: assets/RRM(54928)-RS(52065).tree
  Postscript: assets/RRM(54928)-RS(52065).ps
  
  

  Table 3: Distribution of combined RRM and RS domain in all taxa

  Taxon	#Gene: min/avg/max number of genes possessing the domain	known/all organisms from superfam database
  Bacteria	0/0/0	(0/669)
  Archaea	0/0/0	(0/52)
  Eukaryota	1/2.5/14	(55/207)
  - Stramenopiles	0/0/0	(0/6)
  - Streptophyta	0/0/0	(0/14)
  - Chlorophyta	0/0/0	(0/8)
  - Euglenozoa	0/0/0	(0/6)
  - Amoebozoa	0/0/0	(0/3)
  - Alveolata	0/0/0	(0/13)
  - Fungi	0/0/0	(0/81)
  - Metazoa	1/2.5/14	(55/69)
  - - Protostomia	1/1.2/2	(21/24)
  - - Deuterostomia	1/3.3/14	(34/39)

  
  The occurrence of both RRM and RS domains is restricted to metazoa which indicates that both domains were speratly existent before and connected to each other later in the evolution, infering that the development of SR-related proteins may took place before (as SR proteins are defined to have at least one RRM and an RS domain in this context).