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An organized view of the transcripome



Library:21507 (dbEST ID)

JCVI-SOY3

Library Description

Organism:Glycine max
Cultivar:Williams 82
Tissue:nodules, root tip, strip root, whole root, inoculated root, drought stressed root, salt stressed root, waterlogged root
Vector:pDNR-LIB (Clontech)
Cloning site 1:SfiIA
Cloning site 2:SfiIB

Total RNA isolated using TRIzol reagent. No DNaseI digestion was performed. Total RNAs were pooled together. Double strand cDNA were synthesized from pooled RNA using SMART technology (Clontech). The prepared cDNA was normalized by cDNA denaturation/reassociation, treatment by duplex-specific nuclease(DSN) and amplification of normalized fraction by PCR. The normalized cDNA was then digested with SfiI, size-fractioned, directionally ligated into pDNR-LIB (Clontech) and electroprated into GC10 competent cells (Gene Choice). Clones were sequenced from the 5' end only. RNAs provided by Marc Libault and Babu Valliyodan. This library is also called GLNA.

Source: Town, Christopher, The J. Craig Venter Institute

Gene Content Analysis

16,605 ESTs from this library were grouped into 7,699 UniGene entries (putative genes) [UniGene build #42, 26-Feb-2012]. EST counts for each entry may be used to calculate an approximate expression level in transcripts per million (TPM).

ESTs TPM   UniGene Entry
23 1385 Gma.266 Nodulin (C51) (aa 1-224).
22 1325 Gma.18168 Uncharacterized LOC100499863.
17 1024 Gma.7697 31 kDa protein.
17 1024 Gma.5632 Uncharacterized LOC100306609.
17 1024 Gma.26448 Uncharacterized LOC100527454.
17 1024 Gma.10939 40S ribosomal protein S21-like.
16 964 Gma.4330 Uncharacterized LOC100305879.
15 903 Gma.6161 Uncharacterized LOC100306058.
15 903 Gma.54762 Uncharacterized LOC100527501.
14 843 Gma.8570 Proteasome subunit alpha type-3-like.
14 843 Gma.54796 Universal stress protein A-like protein-like.
14 843 Gma.54729 Uncharacterized LOC100499834.
14 843 Gma.54629 Uncharacterized LOC100306184.
14 843 Gma.3678 Uncharacterized LOC100306445.
14 843 Gma.30952 60S ribosomal protein L27a.
14 843 Gma.30849 NEDD8-conjugating enzyme Ubc12-like.
14 843 Gma.265 Nodulin (E27) (aa 1-360).
14 843 Gma.26340 Uncharacterized LOC100527287.
13 783 Gma.54685 Uncharacterized LOC100305493.
13 783 Gma.51609 Uncharacterized LOC100527032.
13 783 Gma.3541 Probable prefoldin subunit 2-like.
13 783 Gma.31210 Ribosomal protein S6.
13 783 Gma.30912 Uncharacterized LOC100306153.
13 783 Gma.27547 Leghemoglobin.
13 783 Gma.19 Nodulin-22.
12 723 Gma.58666 Uncharacterized LOC100499804.
12 723 Gma.55907 Uncharacterized LOC100527391.
12 723 Gma.5421 Signal peptidase complex catalytic subunit SEC11C-like.
12 723 Gma.4307 Thioredoxin-like protein Clot-like.
12 723 Gma.414 Uncharacterized LOC100306077.
12 723 Gma.4095 Uncharacterized LOC100305686.
12 723 Gma.30703 28 kDa protein.
12 723 Gma.30061 Uncharacterized LOC100777981.
12 723 Gma.29722 Glutathione S-transferase GST 22.
12 723 Gma.28771 Uncharacterized LOC100305973.
12 723 Gma.17600 Uncharacterized LOC100499783.
12 723 Gma.15766 40S ribosomal protein S19-1-like.
12 723 Gma.1449 Nucleoside diphosphate kinase.
12 723 Gma.12947 Chlorophyll a/b-binding protein.
12 723 Gma.11033 Uncharacterized LOC100305473.
12 723 Gma.10722 Triosephosphate isomerase.
12 723 Gma.10689 Uncharacterized LOC100527742.
11 662 Gma.7542 Uncharacterized LOC100499801.
11 662 Gma.6404 40S ribosomal protein S12-like.
11 662 Gma.54722 Histone H3.3-like.
11 662 Gma.54649 Uncharacterized LOC100527338.
11 662 Gma.54632 Uncharacterized LOC100306566.
11 662 Gma.45300 Uncharacterized LOC100305587.
11 662 Gma.30835 Hypersensitive-induced response protein 1-like.
11 662 Gma.30797 Uncharacterized LOC100306186.
11 662 Gma.30794 Uncharacterized LOC100305583.
11 662 Gma.270 Nodulin-20.
11 662 Gma.24412 Uncharacterized LOC100527392.
11 662 Gma.19255 Uncharacterized LOC100527648.
11 662 Gma.11206 Ribosomal protein S13.
10 602 Gma.7029 Uncharacterized LOC100808780.
10 602 Gma.6738 Uncharacterized LOC100800221.
10 602 Gma.5947 Uncharacterized LOC100305867.
10 602 Gma.5833 Uncharacterized LOC100500169.
10 602 Gma.5723 Uncharacterized LOC100305663.
10 602 Gma.56413 Uncharacterized LOC100500094.
10 602 Gma.55960 Uncharacterized LOC100527337.
10 602 Gma.54845 60S ribosomal protein L13-2-like.
10 602 Gma.4624 Organ-specific protein S2-like.
10 602 Gma.36879 Uncharacterized LOC100306516.
10 602 Gma.32627 Uncharacterized LOC100306247.
10 602 Gma.31789 Uncharacterized LOC100305517.
10 602 Gma.30922 40S ribosomal protein S26-1-like.
10 602 Gma.30787 Uncharacterized LOC100527259.
10 602 Gma.30742 Putative ribosomal protein S15.
10 602 Gma.30081 Polyubiquitin-like.
10 602 Gma.3008 Uncharacterized LOC100305592.
10 602 Gma.30050 Uncharacterized LOC100306129.
10 602 Gma.29999 2-on-2 hemoglobin.
10 602 Gma.21337 Glycine cleavage system H protein, mitochondrial-like.
10 602 Gma.1997 Uncharacterized LOC100794840.
10 602 Gma.17933 Uncharacterized LOC100305929.
10 602 Gma.16051 Uncharacterized LOC100305857.
10 602 Gma.14500 Uncharacterized LOC100305838.
10 602 Gma.14 Early nodulin.
10 602 Gma.1246 Ascorbate peroxidase 1, cytosolic.
10 602 Gma.11024 Uncharacterized LOC100527333.
9 542 Gma.8517 Glutathione S-transferase GST 9.
9 542 Gma.8065 NADP-dependent alkenal double bond reductase P2-like.
9 542 Gma.7569 Uncharacterized LOC100500024.
9 542 Gma.58746 Uncharacterized LOC100306699.
9 542 Gma.5834 ATP synthase subunit O, mitochondrial-like.
9 542 Gma.57171 Uncharacterized LOC100500182.
9 542 Gma.54984 SKP1-like protein 1A-like.
9 542 Gma.54783 Uncharacterized LOC100499848.
9 542 Gma.52641 Uncharacterized LOC100306382.
9 542 Gma.4176 Homeobox-leucine zipper protein REVOLUTA-like.
9 542 Gma.4110 Uncharacterized LOC100500398.
9 542 Gma.3735 Uncharacterized LOC100499698.
9 542 Gma.3441 Uncharacterized LOC100526960.
9 542 Gma.31730 Transcribed locus, strongly similar to NP_001242215.1 uncharacterized protein LOC100795218 precursor [Glycine max].
9 542 Gma.31332 Uncharacterized LOC100305568.
9 542 Gma.30981 Uncharacterized LOC100305671.
9 542 Gma.29183 Uncharacterized LOC100305763.
9 542 Gma.2854 Nodulin 35.

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Source: NCBI UniGene

EST Sequences

17,777 EST sequences from this library have been submitted to the public sequence database as of 26-Feb-2012.

Source: NCBI GenBank

Click the button to save sequences to a file (FASTA format)

Keywords

  • root
  • unknown developmental stage
  • normalized

Source: NCBI Clone Registry



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