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Table 1 MIP genes in Populus genome identified from the NCBI whole genome shotgun contigs.

From: Genome-wide analysis of major intrinsic proteins in the tree plant Populus trichocarpa: Characterization of XIP subfamily of aquaporins from evolutionary perspective

Name NCBI WGS contig accession number JGI accession number EST accession NPA motif (LB)a NPA motif (LE)a Chromosome locatione
PtPIP1;1 AARH01004386 724520 DT472648 - - X
PtPIP1;2 AARH01003541 656216 BU868142 - - VIII
PtPIP1;3 AARH01001832 711735 DT474111 - - III
PtPIP1;4 AARH01003029 831918   - - VI
PtPIP1;5 AARH01006875 835561   - - XVI
PtPIP2;1 AARH01003794 821084 DT478685 - - IX
PtPIP2;2 AARH01002541 648808 DT473513 - - IV
PtPIP2;3 AARH01004412 567607 DT474367 - - X
PtPIP2;4 AARH01003539 563742 DT472264 - - VIII
PtPIP2;5 AARH01008299 826419 BU868919 - - *
PtPIP2;6b AARH01008299 N/A CV227359 - - *
PtPIP2;7 AARH01006751 735495 DT498815 - - XVI
PtPIP2;8 AARH01003912 821627   - - IX
PtPIP2;9c   836572   - - *
PtPIP2;10 AARH01008738 796664   - - *
PtTIP1;1 AARH01000429 549212   - - I
PtTIP1;2 AARH01003864 833283 DT499779 - - IX
PtTIP1;3 AARH01004405 822504 DT476627 - - X
PtTIP1;4 AARH01003540 656044 BU875073 - - VIII
PtTIP1;5 AARH01006799 667870 DT497619 - - XVI
PtTIP1;6 AARH01008323 589502 DT497300 - - *
PtTIP1;7 AARH01003929 558321   - - IX
PtTIP1;8 AARH01010693 828458   - - *
PtTIP2;1 AARH01000349 548890 DT496472 - - I
PtTIP2;2 AARH01001731 645978 DT488368 - - III
PtTIP2;3 AARH01001777 817166   - - III
PtTIP2;4 AARH01008349 676397   - - *
PtTIP3;1 AARH01010701 584517   - - *
PtTIP3;2 AARH01011328 811826   - - *
PtTIP4;1 AARH01003145 561759 CV233830 - - VI
PtTIP5;1d AARH01001826 414059   - - III
PtTIP5;2d AARH01008384 423803   - - *
PtNIP1;1d AARH01002108 197507   - - IV
PtNIP1;2d AARH01004854 235172   - - XI
PtNIP1;3 AARH01004327 566501   - - X
PtNIP1;4c   756079   - - II
PtNIP1;5c   754717   - - II
PtNIP2;1 AARH01007172 577637   - - XVII
PtNIP3;1 AARH01001861 757987   NPS NPV III
PtNIP3;2 AARH01000110 797136   NPS NPV I
PtNIP3;3 AARH01000968 708017 DT488082 - - I
PtNIP3;4 AARH01005007 823094   - - XI
PtNIP3;5 AARH01003691 803915   - - VIII
PtSIP1;1 AARH01005657 729942   NPT - XIII
PtSIP1;2 AARH01007966 665418 DT487219 NPT - XIX
PtSIP1;3 AARH01001280 755885   - - II
PtSIP1;4c   572968   - - XIX
PtSIP2;1 AARH01006621 734665 DN491635 NPL - XVI
PtSIP2;2 AARH01002935 652505   NPL - VI
PtXIP1;1 AARH01022440 829126   NPI - *
PtXIP1;2 AARH01003797 557139   NPI - IX
PtXIP1;3 AARH01002537 759781   NPI - IV
PtXIP1;4 AARH01003797 767334   NPL - IX
PtXIP1;5 AARH01003797 821124   - - IX
PtXIP2;1 AARH01003797 557138   SPV - IX
  1. aDeviation of NPA signature motif in loops B and E is reported. '-' indicates that NPA motif is conserved.
  2. bThis gene is not listed in JGI. The coding regions in the NCBI WGS contig are 173376-173676, 173811-174106, 174224-174364, 174465-174584.
  3. cFour PtMIP genes are not found in our TBLASTN search of NCBI database. Their JGI accession codes are given.
  4. dThe sequences for these genes predicted by GeneMark are longer than those found in JGI. GeneMark-predicted sequences have extensions in N- or C-terminus. In this study, we have used GeneMark predicted sequences due to their similarity with Arabidopsis sequences
  5. eThe symbol '*' indicates that these genes are located on a scaffold not yet assigned to a chromosome.