PTPRA-details - Revision history

Gerard at 06:42, 11 December 2014

2014-12-11T06:42:14Z

Gerard at 06:37, 11 December 2014

2014-12-11T06:37:14Z

Gerard: Created page with "This page is for some very rough notes on the PTPRA subfamily of phosphatases ===PTPRA evolution==== While clear PTPRA homologs are found ac..."

2014-12-11T06:35:12Z

Created page with "This page is for some very rough notes on the PTPRA subfamily of phosphatases ===PTPRA evolution==== While clear PTPRA homologs are found ac..."

New page

This page is for some very rough notes on the [[Phosphatase_Subfamily_PTPRA|PTPRA subfamily of phosphatases]]

===PTPRA evolution====
While clear PTPRA homologs are found across vertebrates, several invertebrate deuterostome genes are most similar to PTPRA and PTPRE by Blast. These include the sea urchin gene XP_790608.3, which lacks a signal peptide (maybe a fragment) but has a predicted 194 AA extracellular region, and good similarity to PTPRA in the PTP domains, but not in the juxtamembrane region. The extracellular region has no sequence similarity to any other protein.

Saccoglossus also has a fragment like PTPRA (XP_006819820.1). It has no signal peptide or transmembrane region and has just 49 AA upstream of the first PTP domain.

Ciona intestinalis has the most similar invertebrate sequence to PTPRA (XP_002120721.1). It has a full signal peptide, a long extracellular region of ~1180 AA with many Sushi domain repeats, a carbohydrate-binding ricin domain and a mucin_2 domain (reminiscent of the weak mucin-like domain in PTPRA). It is also the only invertebrate protein with significant psi-blast similarity to the juxtamembrane region of PTPRA/PTPRE.

Branchiostoma floridae has several related genes that are also most similar to PTPRA. Homology based gene prediction has expanded one of these to be a credible PTPRA homolog:

>Bflo_extended
MERLEKEFNRRHANDDQLFREEYDALPQEPSASYEAFLLPENSKKNRFVNIIMYDHSRVHLTSIPGVACSDYINANYVDGYKHSKKFIAAQGPKEETLSDFWRMVWEQNTATIVMVTNVKEKNKVKCSQYWPDTGSQQYGDITVRSEETSTLVDYVIRTLTLWKVHGEESRTLLHFHFTTWPDFGVPKSPLGMMKFVRRVKAANPADSGPIVVHCSAGVGRTGTFIVIDAMFDMIAAEQRVDVFGFVGQIRQSRCMMVQTEGQYVFIYQALLEHFLYGDTEIEVTNLRRHLQQLAARLPNSQDTGMEAEFKKLTQIPIEKHNMRSGNLPDNIKKNRVLQILPYDTSRVYITPTVGMKNSDYINAAFVDGYREKDAYIATQGPLPNTVTDFWKMVWEWKSCSIIMLTELEERGHEKCHKYWPGEVEMYGDICVEAKGDKTFQDYTVRTFHITNTKTHKFQKHAEGETEGLLEKKASCRTIQQFHFHGWPEIGIPANAAGMLDLIGQVERQQQQSGNGPITVHCSSGAGRTGAFITLSTVIERVKAEGICDVFQTVKSMRYQRPHMVQT

@@ Line 12: / Line 12: @@
-[[code]]
+>Bflo_extended<br/>
->Bflo_extended
+MERLEKEFNRRHANDDQLFREEYDALPQEPSASYEAFLLPENSKKNRFVNIIMYDHSRVHLTSIPGVACSDYINANYVDG
-MERLEKEFNRRHANDDQLFREEYDALPQEPSASYEAFLLPENSKKNRFVNIIMYDHSRVHLTSIPGVACSDYINANYVDGYKHSKKFIAAQGPKEETLSDFWRMVWEQNTATIVMVTNVKEKNKVKCSQYWPDTGSQQYGDITVRSEETSTLVDYVIRTLTLWKVHGEESRTLLHFHFTTWPDFGVPKSPLGMMKFVRRVKAANPADSGPIVVHCSAGVGRTGTFIVIDAMFDMIAAEQRVDVFGFVGQIRQSRCMMVQTEGQYVFIYQALLEHFLYGDTEIEVTNLRRHLQQLAARLPNSQDTGMEAEFKKLTQIPIEKHNMRSGNLPDNIKKNRVLQILPYDTSRVYITPTVGMKNSDYINAAFVDGYREKDAYIATQGPLPNTVTDFWKMVWEWKSCSIIMLTELEERGHEKCHKYWPGEVEMYGDICVEAKGDKTFQDYTVRTFHITNTKTHKFQKHAEGETEGLLEKKASCRTIQQFHFHGWPEIGIPANAAGMLDLIGQVERQQQQSGNGPITVHCSSGAGRTGAFITLSTVIERVKAEGICDVFQTVKSMRYQRPHMVQT
+YKHSKKFIAAQGPKEETLSDFWRMVWEQNTATIVMVTNVKEKNKVKCSQYWPDTGSQQYGDITVRSEETSTLVDYVIRTL
-[[code]]
+TLWKVHGEESRTLLHFHFTTWPDFGVPKSPLGMMKFVRRVKAANPADSGPIVVHCSAGVGRTGTFIVIDAMFDMIAAEQR

@@ Line 2: / Line 2: @@
-===PTPRA evolution====
+===PTPRA evolution===
-While clear PTPRA homologs are found across vertebrates, several invertebrate deuterostome genes are most similar to PTPRA and PTPRE by Blast. These include the sea urchin gene XP_790608.3,  which lacks a signal peptide (maybe a fragment) but has a predicted 194 AA extracellular region, and good similarity to PTPRA in the PTP domains, but not in the juxtamembrane region. The extracellular region has no sequence similarity to any other protein.
+While clear PTPRA homologs are found across vertebrates, several invertebrate deuterostome genes are most similar to PTPRA and PTPRE by Blast. These include the sea urchin gene XP_790608.3,  which lacks a signal peptide (maybe a fragment) but has a predicted 194 AA extracellular region, and good similarity to PTPRA in the PTP domains, but not in the juxtamembrane region. The extracellular region has no sequence similarity to any other protein. Three invertebrate chordate species also have possible PTPRA homologs:
 Saccoglossus also has a fragment like PTPRA (XP_006819820.1). It has no signal peptide or transmembrane region and has just 49 AA upstream of the first PTP domain.
@@ Line 11: / Line 11: @@
 Branchiostoma floridae has several related genes that are also most similar to PTPRA. Homology based gene prediction has expanded one of these to be a credible PTPRA homolog:
 >Bflo_extended
 MERLEKEFNRRHANDDQLFREEYDALPQEPSASYEAFLLPENSKKNRFVNIIMYDHSRVHLTSIPGVACSDYINANYVDGYKHSKKFIAAQGPKEETLSDFWRMVWEQNTATIVMVTNVKEKNKVKCSQYWPDTGSQQYGDITVRSEETSTLVDYVIRTLTLWKVHGEESRTLLHFHFTTWPDFGVPKSPLGMMKFVRRVKAANPADSGPIVVHCSAGVGRTGTFIVIDAMFDMIAAEQRVDVFGFVGQIRQSRCMMVQTEGQYVFIYQALLEHFLYGDTEIEVTNLRRHLQQLAARLPNSQDTGMEAEFKKLTQIPIEKHNMRSGNLPDNIKKNRVLQILPYDTSRVYITPTVGMKNSDYINAAFVDGYREKDAYIATQGPLPNTVTDFWKMVWEWKSCSIIMLTELEERGHEKCHKYWPGEVEMYGDICVEAKGDKTFQDYTVRTFHITNTKTHKFQKHAEGETEGLLEKKASCRTIQQFHFHGWPEIGIPANAAGMLDLIGQVERQQQQSGNGPITVHCSSGAGRTGAFITLSTVIERVKAEGICDVFQTVKSMRYQRPHMVQT