Phosphatase Subfamily PTPRN Tech Note - Revision history

Gerard: /* When was RESP18 domain gained? */

2016-01-04T02:16:43Z

‎When was RESP18 domain gained?

Mark at 20:47, 14 October 2015

2015-10-14T20:47:30Z

Mark at 19:00, 14 October 2015

2015-10-14T19:00:13Z

Mark: Created page with "Phosphatase Classification: Fold CC1:Superfamily CC1: Phosphatase_Family_PTP|Family P..."

2015-10-14T18:23:11Z

Created page with "Phosphatase Classification: Fold CC1:Superfamily CC1: Phosphatase_Family_PTP|Family P..."

New page

[[Phosphatase classification|Phosphatase Classification]]: [[Phosphatase_Fold_CC1|Fold CC1]]:[[Phosphatase_Superfamily_CC1|Superfamily CC1]]: [[Phosphatase_Family_PTP|Family PTP]]: [[Phosphatase_Subfamily_PTPRN|Subfamily PTPRN]]: [[Phosphatase_Subfamily_PTPRN_Tech_Note|Technical notes]]

=== When was RESP18 domain gained? ===
We found the origin of CA domain in a narrow-down approach by BLASTing the sequence of CA domain against different clades. We BLASTed the RESP18 region defined by CDD (60-160 of human PTPRN) against protein NR dataset, limiting the search of vertebrate genomes. We found the RESP18 domain-containing PTPRNs across Euteleostomi.

We then BLASTed the region against protein NR dataset, limiting to vertebrates except Euteleostomi. We found no hit.

We then BLASTed the region against protein NR dataset, limiting to all organisms except vertebrates. We found no hit.

Thus, we inferred RESP18 domain was gained in Euteleostomi.

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 [[Phosphatase classification|Phosphatase Classification]]: [[Phosphatase_Fold_CC1|Fold CC1]]:[[Phosphatase_Superfamily_CC1|Superfamily CC1]]: [[Phosphatase_Family_PTP|Family PTP]]: [[Phosphatase_Subfamily_PTPRN|Subfamily PTPRN]]: [[Phosphatase_Subfamily_PTPRN_Tech_Note|Technical notes]]
-=== When was RESP18 domain gained? ===
+=== Evolutionary origin of the RESP18 domain in PTPRN ===
 We found the origin of CA domain in a narrow-down approach by BLASTing the sequence of RESP18 domain against different clades. We BLASTed the RESP18 region defined by CDD (60-160 of human PTPRN) against protein NR dataset, limiting the search of vertebrate genomes. We found the RESP18 domain-containing PTPRNs across Euteleostomi.

@@ Line 2: / Line 2: @@
 === When was RESP18 domain gained? ===
-We found the origin of CA domain in a narrow-down approach by BLASTing the sequence of CA domain against different clades. We BLASTed the RESP18 region defined by CDD (60-160 of human PTPRN) against protein NR dataset, limiting the search of vertebrate genomes. We found the RESP18 domain-containing PTPRNs across Euteleostomi.
+We found the origin of CA domain in a narrow-down approach by BLASTing the sequence of RESP18 domain against different clades. We BLASTed the RESP18 region defined by CDD (60-160 of human PTPRN) against protein NR dataset, limiting the search of vertebrate genomes. We found the RESP18 domain-containing PTPRNs across Euteleostomi.
 We then BLASTed the region against protein NR dataset, limiting to vertebrates except Euteleostomi. We found no hit.
@@ Line 10: / Line 10: @@
 Thus, we inferred RESP18 domain was gained in Euteleostomi.
-=== When was IA-2 domain gained? ===
+=== The evolution of IA-2 ===
-We found the origin of IA-2 domain in a narrow-down approach by BLASTing the sequence of CA domain against different clades. We BLASTed the IA-2 domain defined by CDD (468-558 of human PTPRN) against protein NR dataset, limiting the search of vertebrate genomes. We found the IA-2 domain-containing PTPRNs across Gnathostomata.
+We found the origin of IA-2 domain in a narrow-down approach by BLASTing the sequence of IA-2 domain against different clades. We BLASTed the IA-2 domain defined by CDD (468-558 of human PTPRN) against protein NR dataset, limiting the search of vertebrate genomes. We found the IA-2 domain-containing PTPRNs across Gnathostomata.
 We then BLASTed the region against protein NR dataset, limiting to vertebrates except Gnathostomata. We found no hit.
@@ Line 17: / Line 17: @@
 We then BLASTed the region against protein NR dataset, limiting to all organisms except vertebrates. We found some hit, but they were apparently not phosphatases.
-Thus, we inferred RESP18 domain was gained in Gnathostomata.
+Thus, we inferred the IA-2 domain of human PTPRN was gained in Gnathostomata.

← Older revision		Revision as of 19:00, 14 October 2015
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	Thus, we inferred RESP18 domain was gained in Euteleostomi.		Thus, we inferred RESP18 domain was gained in Euteleostomi.
		+
		+	=== When was IA-2 domain gained? ===
		+	We found the origin of IA-2 domain in a narrow-down approach by BLASTing the sequence of CA domain against different clades. We BLASTed the IA-2 domain defined by CDD (468-558 of human PTPRN) against protein NR dataset, limiting the search of vertebrate genomes. We found the IA-2 domain-containing PTPRNs across Gnathostomata.
		+
		+	We then BLASTed the region against protein NR dataset, limiting to vertebrates except Gnathostomata. We found no hit.
		+
		+	We then BLASTed the region against protein NR dataset, limiting to all organisms except vertebrates. We found some hit, but they were apparently not phosphatases.
		+
		+	Thus, we inferred RESP18 domain was gained in Gnathostomata.