Table I.
Proposed new names for all Arabidopsis MIPs
| New Namea | Johanson et al.b | Weig et al.c | AGI Gened | BAC Genee | Accession No.f | Expressed Sequence Tag (EST)g | Commentsh |
|---|---|---|---|---|---|---|---|
| PIP1;1 | PIP1a | PIP1a | At3g61430 | F2A19.30 | CAB71073 | Yes | |
| PIP1;2 | PIP1b | PIP1b | At2g45960 | F4I18.6 | AAC28529 | Yes | AthH2, TMP-A |
| PIP1;3 | PIP1c | PIP1c | At1g01620 | F22L4.16 | AAF81320 | Yes | TMP-B |
| PIP1;4 | PIP1e | TMP-C | At4g00430 | F5I10.2 | AAF02782 | Yes | Exon 2 ends at 86,121, not 86,097; compare with TMP-C. |
| PIP1;5 | PIP1d | pCR55 | At4g23400 | F16G20.100 | CAA20461 | Yes | |
| PIP2;1 | PIP2a | PIP2a | At3g53420 | F4P12_120 | CAB67649 | Yes | |
| PIP2;2 | PIP2b | PIP2b | At2g37170 | T2N18.7 | AAD18142 | Yes | |
| PIP2;3 | PIP2c | RD28 | At2g37180 | T2N18.6 | AAD18141 | Yes | |
| PIP2;4 | PIP2f | T04164 | At5g60660 | MUP24.8 | BAB09839 | Yes | |
| PIP2;5 | PIP2d | – | At3g54820 | F28P10.200 | CAB41102 | Yes | |
| PIP2;6 | PIP2e | T22419 | At2g39010 | T7F6.18 | AAC79629 | Yes | |
| PIP2;7 | PIP3a | PIP3 | At4g35100 | M4E13.150 | CAA17774 | Yes | Salt-stress-inducible MIP |
| PIP2;8 | PIP3b | – | At2g16850 | F12A24.3 | AAC64216 | Yes | |
| – | Pseudo PIP3 | – | At2g16830 | F12A24.1 | AAC64228 | ? | Pseudogene encoding 26 amino acids with second NPA. Similar to F12A24.3. |
| – | – | – | – | T8O11i | 77,410–77,455 | ? | Partial F5I10.2-like sequence encoding helix 4. |
| – | – | – | – | F5I10i | 77,564–77,656 | ? | Partial F5I10.2-like sequence encoding loop B and helix 3. |
| TIP1;1 | γTIP1 | γTIP | At2g36830 | T1J8.1 | AAD31569 | Yes | |
| TIP1;2 | γTIP2 | Z30833, T21060, T22237 | At3g26520 | MFE16.3 | BAB01832 | Yes | Salt-stress-inducible TIP, γTIP2 |
| TIP1;3 | γTIP3 | – | At4g01470 | F11O4.1 | AAC62778 | ? | No introns |
| TIP2;1 | δTIP1 | δTIP | At3g16240 | MYA6.5 | BAB01264 | Yes | |
| TIP2;2 | δTIP2 | Z18142 | At4g17340 | d14705w | CAB10515 | Yes | |
| TIP2;3 | δTIP3 | T20432, T76151 | At5g47450 | MNJ7.4 | BAB09071 | Yes | |
| TIP3;1 | αTIP | αTIP | At1g73190 | T18K17.14 | AAG52132 | Yes | |
| TIP3;2 | βTIP | βTIP | At1g17810 | F2H15.4 | AAF97261 | Yes | |
| TIP4;1 | ɛTIP | T21742 | At2g25810 | F17H15.16 | AAC42249 | Yes | Similar to NtTIPa |
| TIP5;1 | ζTIP | – | At3g47440 | T21L8.190 | CAB51216 | ? | |
| – | Pseudo-γTIP2 | – | – | F7P1i | 79,395–79,728 | ? | Pseudogene similar to MFE16.3, truncated, NPV instead of NPA, no exon 2. |
| – | Pseudo-δTIP | – | At1g52180 | F9I5.3 | AAF29403 | ? | Pseudogene, only exon 2, 124 amino acids. |
| NIP1;1 | NLM1 | NLM1 | At4g19030 | F13C5.200 | CAA16760 | Yes | Misannotated: delete amino acids 205 through 216; exon 4 starts at 86,879, not 86,915. |
| NIP1;2 | NLM2 | NLM2 | At4g18910 | F13C5.80 | CAA16748 | Yes | |
| NIP2;1 | NLM3 | NLM4 | At2g34390 | T31E10.27 | AAC26712 | Yesj | |
| NIP3;1 | NLM9 | – | At1g31880k | F5M6.28 | AAG50717 | ? | F5M6.28 is missing exon 1; exon 1, 38,681 through 38,550; exon 2 starts at 38,310, long C terminus. |
| NIP4;1 | NLM4 | – | At5g37810 | K22F20.9 | BAB10360 | ? | |
| NIP4;2 | NLM5 | NLM5 | At5g37820 | K22F20.10 | BAB10361 | Yesj | |
| NIP5;1 | NLM6 | NLM8 | At4g10380 | F24G24.180 | CAB39791 | Yes | Long N terminus. |
| NIP6;1 | NLM7 | NLM7 | At1g80760 | F23A5.11 | AAF14664 | Yes | Long N terminus. |
| NIP7;1 | NLM8 | NLM6 | At3g06100 | F28L1.3 | AAF30303 | Yes | Intron 3, 8,151 through 7,945, avoids TT acceptor splice site, restores conserved length of exon 4. |
| – | Pseudo-NLM3 | NLM3 | At2g29870 | T27A16.3 | AAC35214 | ? | Pseudogene encoding 139 amino acids, missing first NPA. |
| – | Pseudo-NLM9 | – | At2g21020 | F26H11.22 | AAD29814 | ? | Pseudogene, version 3 missing second NPA. Alternate annotation results in two NPAs, but missing helix 3 and 4, long C terminus. |
| SIP1;1 | SIP1a | – | At3g04090 | T6K12.29 | AAF26804 | Yes | |
| SIP1;2 | SIP1b | – | At5g18290 | MRG7.25 | BAB09487 | Yes | |
| SIP2;1 | SIP2 | – | At3g56950 | F24I3.30 | CAB72165 | Yes |
Proposed new names for Arabidopsis MIPs. When referring to the corresponding gene, the name is written in italics. Genes encoding partial MIP-like sequences without all transmembrane regions are regarded as nonfunctional pseudogenes. Pseudogenes are not included in the proposed nomenclature as indicated by “–”.
Nomenclature used in Johansson et al. (2000) and in U. Johanson and S. Gustavsson (unpublished data).
Nomenclature used in Weig et al. (1997) and Weig and Jakob (2000a, 2000b).
Arabidopsis Genome Initiative (AGI) gene nomenclature; At3g56950 indicates gene no. 5,695 (counting from top) on chromosome 3.
Gene name used in annotation of bacterial artificial chromosome (BAC) or P1 sequences.
Protein accession no. for a translation of the corresponding gene. When a gene annotation is missing, the location in the BAC is given in base pairs.
Matching EST found in databases. ?, Not found.
Alternative exon/introns positions proposed and used in this paper and odd features of the gene or the encoded protein. Some older names found in the literature (Kaldenhoff et al., 1993; Shagan and Bar-Zvi, 1993; Shagan et al., 1993; Pih et al., 1999) and in Genbank accession no. AF057137.
Not annotated.
cDNA cloned by reverse transcriptase-PCR (Weig and Jakob, 2000b).
At1g31880 has 285 amino acids added at the N terminus, previously annotated as a separate gene (F5M6.11). At1g31880 is missing 29 amino acids close to the C terminus.