Difference between revisions of "Phosphatase Subfamily PTPRN Tech Note"
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=== When was RESP18 domain gained? === | === When was RESP18 domain gained? === | ||
| − | We found the origin of CA domain in a narrow-down approach by BLASTing the sequence of | + | 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. | We then BLASTed the region against protein NR dataset, limiting to vertebrates except Euteleostomi. We found no hit. | ||
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Thus, we inferred RESP18 domain was gained in Euteleostomi. | Thus, we inferred RESP18 domain was gained in Euteleostomi. | ||
| − | === | + | === The evolution of IA-2 === |
| − | We found the origin of IA-2 domain in a narrow-down approach by BLASTing the sequence of | + | 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. | We then BLASTed the region against protein NR dataset, limiting to vertebrates except Gnathostomata. We found no hit. | ||
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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. | 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 | + | Thus, we inferred the IA-2 domain of human PTPRN was gained in Gnathostomata. |
Revision as of 20:47, 14 October 2015
Phosphatase Classification: Fold CC1:Superfamily CC1: Family PTP: Subfamily PTPRN: Technical notes
When was RESP18 domain gained?
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.
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.
The evolution of IA-2
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.
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 the IA-2 domain of human PTPRN was gained in Gnathostomata.
