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An organized view of the transcripome



Library:12046 (dbEST ID)

RT1

Library Description

Organism:Saccharum hybrid cultivar SP80-3280
Cultivar:SP80-3280
Organ:Root tips (0.3cm-long) from adult plants
Vector:pSport1
Cloning site 1:SalI
Cloning site 2:NotI
Lab host:DH10B

An unidirectional cDNA library generated from [Root tips (0.3cm-long) from adult plants]. cDNA was prepared from polyA+ mRNA using SuperScript Plasmid System Kit (Invitrogen). The double-strand cDNAs were fractionated in a sepharose CL-2B 40cm-columns and fragments sizing between 0.8 and 1.5 Kb were directionally cloned into the vector. Details of each source of RNA and library construction can be obtained at http://sucest.lad.ic.unicamp.br/public

Source: Arruda P, Universidade Estadual de Campinas

Gene Content Analysis

5,822 ESTs from this library were grouped into 2,773 UniGene entries (putative genes) [UniGene build #15, 04-Apr-2011]. EST counts for each entry may be used to calculate an approximate expression level in transcripts per million (TPM).

ESTs TPM   UniGene Entry
45 7729 Sof.17825 Phenylalanine ammonia-lyase.
32 5496 Sof.18007 Transcribed locus, strongly similar to XP_002450268.1 hypothetical protein SORBIDRAFT_05g002860 [Sorghum bicolor].
28 4809 Sof.17827 Transcribed locus, strongly similar to XP_001691876.1 alpha tubulin 1 [Chlamydomonas reinhardtii].
27 4638 Sof.2646 Transcribed locus, strongly similar to NP_001105385.1 glyceraldehyde-3-phosphate dehydrogenase, cytosolic 3 [Zea mays].
25 4294 Sof.20507 Transcribed locus, strongly similar to NP_001064504.1 Os10g0390500 [Oryza sativa Japonica Group].
24 4122 Sof.17947 Transcribed locus, strongly similar to NP_001056727.1 Os06g0136600 [Oryza sativa Japonica Group].
23 3951 Sof.17841 Transcribed locus, strongly similar to NP_001050319.1 Os03g0401300 [Oryza sativa Japonica Group].
23 3951 Sof.17828 Transcribed locus, strongly similar to NP_001055494.1 Os05g0402700 [Oryza sativa Japonica Group].
22 3779 Sof.18087 Caffeic acid 3-O-methyltransferase.
21 3607 Sof.17848 Transcribed locus, strongly similar to NP_187864.1 heat shock protein 70-4 [Arabidopsis thaliana].
20 3435 Sof.513 Transcribed locus, strongly similar to XP_002450328.1 hypothetical protein SORBIDRAFT_05g003860 [Sorghum bicolor].
20 3435 Sof.20387 Transcribed locus, strongly similar to NP_001151562.1 glycine-rich RNA-binding protein 2 [Zea mays].
20 3435 Sof.17923 Transcribed locus, strongly similar to NP_001061602.1 Os08g0345700 [Oryza sativa Japonica Group].
20 3435 Sof.1580 Transcribed locus, strongly similar to NP_001044317.1 Os01g0760600 [Oryza sativa Japonica Group].
19 3263 Sof.3810 Sucrose synthase-2.
19 3263 Sof.18092 Transcribed locus, strongly similar to NP_001048668.1 Os03g0103300 [Oryza sativa Japonica Group].
18 3092 Sof.4072 Transcribed locus, strongly similar to NP_001140424.1 triosephosphate isomerase, cytosolic [Zea mays].
18 3092 Sof.20399 Transcribed locus, strongly similar to NP_001064223.1 Os10g0167300 [Oryza sativa Japonica Group].
18 3092 Sof.17865 Transcribed locus, strongly similar to XP_002439934.1 hypothetical protein SORBIDRAFT_09g022970 [Sorghum bicolor].
17 2920 Sof.676 Transcribed locus, weakly similar to NP_001174671.1 Os06g0226050 [Oryza sativa Japonica Group].
17 2920 Sof.4932 Transcribed locus, strongly similar to XP_002450060.1 hypothetical protein SORBIDRAFT_05g027670 [Sorghum bicolor].
17 2920 Sof.20384 Transcribed locus, strongly similar to XP_002442600.1 hypothetical protein SORBIDRAFT_08g022740 [Sorghum bicolor].
16 2748 Sof.3204 Transcribed locus, moderately similar to NP_001049857.1 Os03g0300400 [Oryza sativa Japonica Group].
16 2748 Sof.2899 Transcribed locus, strongly similar to NP_001057556.1 Os06g0336200 [Oryza sativa (japonica cultivar-group)].
16 2748 Sof.18212 Transcribed locus, strongly similar to XP_002449852.1 hypothetical protein SORBIDRAFT_05g024390 [Sorghum bicolor].
15 2576 Sof.3156 Transcribed locus, strongly similar to NP_001148521.1 LOC100282137 [Zea mays].
15 2576 Sof.12942 Transcribed locus, strongly similar to XP_002448783.1 hypothetical protein SORBIDRAFT_06g033080 [Sorghum bicolor].
14 2405 Sof.18077 Glutamine synthetase (GS1.a).
14 2405 Sof.17829 Saccharum hybrid cultivar CP72-2086 elongation factor 1 alpha (SEF1a).
13 2233 Sof.790 Transcribed locus, strongly similar to XP_002436448.1 hypothetical protein SORBIDRAFT_10g002890 [Sorghum bicolor].
13 2233 Sof.20437 Transcribed locus, strongly similar to NP_001048523.1 Os02g0817700 [Oryza sativa Japonica Group].
13 2233 Sof.20419 Transcribed locus, strongly similar to NP_724345.1 histone H3 [Drosophila melanogaster].
13 2233 Sof.18030 Transcribed locus, strongly similar to NP_001060897.1 Os08g0126300 [Oryza sativa Japonica Group].
13 2233 Sof.18029 Aquaporin.
13 2233 Sof.15412 Alcohol dehydrogenase 2 (adh-2 gene).
12 2061 Sof.8341 Transcribed locus, moderately similar to NP_001054087.1 Os04g0650000 [Oryza sativa (japonica cultivar-group)].
12 2061 Sof.3475 Transcribed locus, strongly similar to NP_001130296.1 exoglucanase1 [Zea mays].
12 2061 Sof.17855 Transcribed locus, strongly similar to NP_001067313.1 Os12g0623900 [Oryza sativa Japonica Group].
11 1889 Sof.726 Transcribed locus, strongly similar to XP_002454527.1 hypothetical protein SORBIDRAFT_04g032680 [Sorghum bicolor].
11 1889 Sof.526 Transcribed locus, strongly similar to XP_002450658.1 hypothetical protein SORBIDRAFT_05g008830 [Sorghum bicolor].
11 1889 Sof.3771 Transcribed locus, strongly similar to NP_171751.1 S-adenosylmethionine synthetase 1 [Arabidopsis thaliana].
11 1889 Sof.19028 Transcribed locus, moderately similar to XP_002968099.1 hypothetical protein SELMODRAFT_73177 [Selaginella moellendorffii].
11 1889 Sof.18088 Pyruvate decarboxylase (pdc gene).
11 1889 Sof.17942 Transcribed locus, strongly similar to XP_002458541.1 hypothetical protein SORBIDRAFT_03g035420 [Sorghum bicolor].
11 1889 Sof.17899 Transcribed locus, strongly similar to XP_002441512.1 hypothetical protein SORBIDRAFT_09g028400 [Sorghum bicolor].
11 1889 Sof.17881 Transcribed locus, strongly similar to NP_001105024.1 aquaporin PIP2-1 [Zea mays].
11 1889 Sof.17835 Transcribed locus, strongly similar to NP_567286.1 ubiquitin 11 [Arabidopsis thaliana].
11 1889 Sof.10422 Transcribed locus, strongly similar to NP_001054118.1 Os04g0656100 [Oryza sativa Japonica Group].
10 1718 Sof.630 Transcribed locus, strongly similar to XP_002455837.1 hypothetical protein SORBIDRAFT_03g026000 [Sorghum bicolor].
10 1718 Sof.602 Transcribed locus, strongly similar to NP_001148461.1 lichenase-2 [Zea mays].
10 1718 Sof.4237 Transcribed locus, strongly similar to NP_001105366.1 glutathione S-transferase 4 [Zea mays].
10 1718 Sof.3860 Transcribed locus, strongly similar to NP_001065749.1 Os11g0148500 [Oryza sativa Japonica Group].
10 1718 Sof.3021 Alcohol dehydrogenase (adh-1 gene).
10 1718 Sof.23671 Transcribed locus, weakly similar to NP_001182868.1 hypothetical protein LOC100501131 [Zea mays].
10 1718 Sof.18253 Transcribed locus, strongly similar to NP_001174338.1 Os05g0310500 [Oryza sativa Japonica Group].
10 1718 Sof.18015 Transcribed locus, strongly similar to XP_002463862.1 hypothetical protein SORBIDRAFT_01g007760 [Sorghum bicolor].
10 1718 Sof.17973 Transcribed locus, strongly similar to XP_002466730.1 hypothetical protein SORBIDRAFT_01g013000 [Sorghum bicolor].
10 1718 Sof.17935 Transcribed locus, strongly similar to NP_001058640.1 Os06g0728000 [Oryza sativa Japonica Group].
10 1718 Sof.17885 Transcribed locus, moderately similar to XP_002451666.1 hypothetical protein SORBIDRAFT_04g005520 [Sorghum bicolor].
9 1546 Sof.826 Transcribed locus, strongly similar to XP_002457709.1 hypothetical protein SORBIDRAFT_03g011980 [Sorghum bicolor].
9 1546 Sof.603 Transcribed locus, strongly similar to XP_002445757.1 hypothetical protein SORBIDRAFT_07g025220 [Sorghum bicolor].
9 1546 Sof.5435 Transcribed locus, moderately similar to NP_001142712.1 hypothetical protein LOC100275040 [Zea mays].
9 1546 Sof.4245 Transcribed locus, strongly similar to NP_001031627.1 adenosylhomocysteinase 1 [Arabidopsis thaliana].
9 1546 Sof.4199 Transcribed locus, strongly similar to XP_002446740.1 hypothetical protein SORBIDRAFT_06g021540 [Sorghum bicolor].
9 1546 Sof.3576 Transcribed locus, strongly similar to NP_001131013.1 asparagine synthetase2 [Zea mays].
9 1546 Sof.20413 Transcribed locus, strongly similar to XP_958803.1 polyubiquitin [Neurospora crassa OR74A].
9 1546 Sof.18441 Transcribed locus, strongly similar to NP_001047482.1 Os02g0626400 [Oryza sativa Japonica Group].
9 1546 Sof.17979 Transcribed locus, moderately similar to NP_001049113.1 Os03g0171600 [Oryza sativa Japonica Group].
8 1374 Sof.9137 Transcribed locus, strongly similar to XP_002450037.1 hypothetical protein SORBIDRAFT_05g027340 [Sorghum bicolor].
8 1374 Sof.4490 Transcribed locus, strongly similar to NP_001149538.1 LOC100283164 [Zea mays].
8 1374 Sof.3550 Transcribed locus, strongly similar to XP_002459074.1 hypothetical protein SORBIDRAFT_03g045460 [Sorghum bicolor].
8 1374 Sof.2450 Transcribed locus, strongly similar to XP_002445848.1 hypothetical protein SORBIDRAFT_07g026860 [Sorghum bicolor].
8 1374 Sof.18109 Transcribed locus, weakly similar to NP_001140208.1 hypothetical protein LOC100272240 [Zea mays].
8 1374 Sof.17959 Transcribed locus, strongly similar to XP_002442150.1 hypothetical protein SORBIDRAFT_08g015010 [Sorghum bicolor].
8 1374 Sof.17872 Transcribed locus, strongly similar to NP_001105358.1 histone H2B.5 [Zea mays].
8 1374 Sof.17871 Transcribed locus, strongly similar to XP_002453177.1 hypothetical protein SORBIDRAFT_04g001130 [Sorghum bicolor].
8 1374 Sof.152 Transcribed locus.
8 1374 Sof.10909 Transcribed locus, strongly similar to XP_002445523.1 hypothetical protein SORBIDRAFT_07g020930 [Sorghum bicolor].
7 1202 Sof.572 Transcribed locus, moderately similar to XP_002447154.1 hypothetical protein SORBIDRAFT_06g029550 [Sorghum bicolor].
7 1202 Sof.553 Transcribed locus, strongly similar to XP_002464945.1 hypothetical protein SORBIDRAFT_01g029270 [Sorghum bicolor].
7 1202 Sof.5029 Transcribed locus, strongly similar to NP_001050779.1 Os03g0648400 [Oryza sativa Japonica Group].
7 1202 Sof.411 Transcribed locus, strongly similar to XP_002459313.1 hypothetical protein SORBIDRAFT_02g002260 [Sorghum bicolor].
7 1202 Sof.3996 Transcribed locus, moderately similar to XP_002450127.1 hypothetical protein SORBIDRAFT_05g000940 [Sorghum bicolor].
7 1202 Sof.3660 Transcribed locus, strongly similar to NP_001140324.1 isocitrate dehydrogenase2 [Zea mays].
7 1202 Sof.3631 Transcribed locus, strongly similar to NP_001048364.1 Os02g0792900 [Oryza sativa Japonica Group].
7 1202 Sof.3107 Transcribed locus, strongly similar to XP_002454259.1 hypothetical protein SORBIDRAFT_04g027660 [Sorghum bicolor].
7 1202 Sof.2469 Transcribed locus, strongly similar to NP_001055755.1 Os05g0460200 [Oryza sativa Japonica Group].
7 1202 Sof.2354 Transcribed locus, strongly similar to XP_002455781.1 hypothetical protein SORBIDRAFT_03g025160 [Sorghum bicolor].
7 1202 Sof.20595 Transcribed locus, strongly similar to XP_002463451.1 hypothetical protein SORBIDRAFT_02g044060 [Sorghum bicolor].
7 1202 Sof.20393 Transcribed locus, strongly similar to XP_002439223.1 hypothetical protein SORBIDRAFT_09g002510 [Sorghum bicolor].
7 1202 Sof.18298 Transcribed locus, strongly similar to XP_002456550.1 hypothetical protein SORBIDRAFT_03g038290 [Sorghum bicolor].
7 1202 Sof.18260 Transcribed locus, strongly similar to XP_002466284.1 hypothetical protein SORBIDRAFT_01g005010 [Sorghum bicolor].
7 1202 Sof.17937 Transcribed locus, strongly similar to NP_001054575.1 Os05g0135700 [Oryza sativa Japonica Group].
7 1202 Sof.17914 Transcribed locus, strongly similar to XP_002459438.1 hypothetical protein SORBIDRAFT_02g004660 [Sorghum bicolor].
7 1202 Sof.17903 Transcribed locus, strongly similar to NP_001152232.1 LOC100285870 [Zea mays].
7 1202 Sof.1472 Transcribed locus, strongly similar to NP_001066706.1 Os12g0443600 [Oryza sativa Japonica Group].
7 1202 Sof.1348 Transcribed locus, strongly similar to NP_001058597.1 Os06g0717800 [Oryza sativa Japonica Group].
7 1202 Sof.11381 Transcribed locus, strongly similar to XP_002446562.1 hypothetical protein SORBIDRAFT_06g018130 [Sorghum bicolor].
7 1202 Sof.10180 Transcribed locus, strongly similar to NP_001130834.1 hypothetical protein LOC100191938 [Zea mays].
6 1031 Sof.6401 Transcribed locus, strongly similar to XP_002460242.1 hypothetical protein SORBIDRAFT_02g025180 [Sorghum bicolor].

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Source: NCBI UniGene

EST Sequences

7,211 EST sequences from this library have been submitted to the public sequence database as of 04-Apr-2011.

Source: NCBI GenBank

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

Keywords

  • root
  • ripening

Source: NCBI Clone Registry



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