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Table 1 Proposed systematic names for all Physcomitrella patens MIPs

From: Unexpected complexity of the Aquaporin gene family in the moss Physcomitrella patens

New namea

Borstlapb

PpDBc

ESTd

ProteinIDe

Commentsf

PIP1;1

-

PIP1

Y

62169

 

PIP1;2

PIP1

PIP

Y

166091

 

PIP1;3

PIP1

PIP

Y

171662

 

PIP2;1

-

PIP

Y

202226

 

PIP2;2

PIP2

PIP

Y

209703

 

PIP2;3

PIP2

PIP

Y

196472

 

PIP2;4

-

PIP

?

135286

Identical to 83986g

-

-

PIP

?

83986

Identical to 135286g

PIP3;1

-

PIP2

?

68172

 

PseudoPIP#1

-

-h

?

113412

Pseudogene, PIP-like, based on ProteinID = 113412 but encoding 123 amino acids in two exons

PseudoPIP#2

-

-

?

-

Pseudogene, PIP-like, encoding 83 amino acids in one exon

TIP6;1

-

TIP

Y

73809

 

TIP6;2

TIP

TIP

Y

191107

 

TIP6;3

TIP

-h

Y

214518

 

TIP6;4

TIP

TIP

Y

219971

 

NIP3;1

-

NIP5

?

94322

The PpDB classification refers to ProteinID = 147365 which is a truncated version

NIP5;1

-

NIP4

Y

115513

Misannotated: delete the first amino acid and add exon 1 (68 amino acids)

NIP5;2

NIP

NIP4

Y

186237

Misannotated: delete first eleven amino acids and add exon 1 (68 amino acids)

NIP5;3

 

NIP4

Y

179749

Misannotated: delete first seven amino acids and add exon 1 (66 amino acids)

NIP6;1

-

NIP

?

16763

Misannotated: add exon 1 (65 amino acids) and extend last exon 24 amino acids

PartialNIP#1

-

Possibly an aquaporini

?

103774

Possibly a full length gene (NIP5) but the genomic sequence is only 825 bp long and interrupted by a 34 kb gap. The model which the classification refers to (ProteinID = 103774) is completely wrong, but in the opposite direction is an exon encoding 103 amino acids.

PseudoNIP#1

-

-

?

73549

Pseudogene, NIP-like, delete first 22 amino acids from model

SIP1;1

SIP

SIP

?

112053

 

SIP1;2

SIP

SIP

Y

200882

 

GIP1;1

-

PpGlP1-1

Y

171260

 

HIP1;1

-

-h

?

91611

Misannotated, we removed 141 aa from beginning of exon 1, 22 aa from end of exon 2 and 15 aa from beginning of exon 3

XIP1;1

-

TIP1

Y

71087

The PpDB classification refers to ProteinID = 26452 which is a truncated version

XIP1;2

-

TIP

Y

71489

Misannotated, removed 15 amino acids from exon 2 and replaced exon 1 (now 31 aa) The PpDB classification refers to ProteinID = 47381 which is a truncated version

  1. a Proposed new names for P. patens MIPs. b Classification used in Borstlap (2002). c Classification used to describe gene models by Shizong Ma in PpDB. d Matching ESTs in PpDB: Y = Yes, ? = Not found. e Protein ID number for the protein or related protein in PpDB. f Alternative exon/intron positions proposed and used in this paper and odd features of genes and/or proteins encoded. g both genes are in a region of 3023 bp of identical genomic sequence, the two genes were therefore treated as one in all analyzes. h Classified as belonging to one of the Aquaporin KOG groups (KOG0223 or KOG0224) but without further description in PpDB i the complete comment is "Possibly an aquaporin, similar to NIP1;2, with one signature peptide, "HFNPAVSV"".