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An organized view of the transcripome



Library:22808 (dbEST ID)

Amphioxus Branchiostoma floridae unpublished cDNA library CAXF, gastrula whole animal

Library Description

Organism:Branchiostoma floridae
Developmental stage:gastrula
Tissue:whole animal
Vector:pDONR222
Cloning site 1:attB1
Cloning site 2:attB2

The library was made from oligo(dT)-primed cDNA and cloned into Invitrogen vector pDONR222 (Invitrogen Corp., Carlsbad, CA). PolyA RNA was primed with a biotin-attB2-Oligo(dT) primer (5'-GGCGGCCGCACAACTTTGTACAAGAAAGTTGGGT(T)19-3') and the first strand synthesized using Superscript II (Invitrogen Corp., Carlsbad, CA). The second strand was synthesized and an attB1 adaptor ligated to the 5' end (5'-TCGTCGGGGACAACTTTGTACAAAAAAGTTGG-3' and 5'-CCAACTTTTTTGTACAAAGTTGTCCCC-3'). cDNA was size selected using column chromatography and then inserted into the vector using site specific recombination (flanking attB sites on cDNA). RNA prepared at University of California, San Diego, library constructed at Kyoto University (Kyoto, Japan), and sequencing was done at DOE Joint Genome Institute (Walnut Creek, CA).

Source: Lindquist,E.A., Richardson,P., DOE Joint Genome Institute

Gene Content Analysis

13,870 ESTs from this library were grouped into 3,828 UniGene entries (putative genes) [UniGene build #13, 03-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
260 18745 Bfl.24859 Hypothetical protein.
130 9373 Bfl.24629 Hypothetical protein.
115 8291 Bfl.4655 Hypothetical protein.
114 8219 Bfl.560 Transcribed locus, moderately similar to NP_033130.1 ribonucleoside-diphosphate reductase subunit M2 [Mus musculus].
114 8219 Bfl.23458 Hypothetical protein.
99 7138 Bfl.12889 Hypothetical protein.
98 7066 Bfl.17783 Hypothetical protein.
88 6345 Bfl.23492 Hypothetical protein.
87 6273 Bfl.12867 Hypothetical protein.
81 5840 Bfl.23544 Hypothetical protein.
78 5624 Bfl.18643 Transcribed locus, weakly similar to XP_002595870.1 hypothetical protein BRAFLDRAFT_123774 [Branchiostoma floridae].
73 5263 Bfl.12860 Hypothetical protein.
69 4975 Bfl.1274 Transcribed locus, moderately similar to NP_001158480.1 cyclin B [Saccoglossus kowalevskii].
64 4614 Bfl.12925 Hypothetical protein.
63 4542 Bfl.12926 Hypothetical protein.
62 4470 Bfl.23928 Transcribed locus, strongly similar to NP_001026545.1 histone H2A.Z [Gallus gallus].
56 4037 Bfl.23469 Hypothetical protein.
52 3749 Bfl.12968 Transcribed locus, strongly similar to NP_524352.1 histone H4 replacement, isoform C [Drosophila melanogaster].
52 3749 Bfl.12873 Nk homeobox 2-2.
50 3605 Bfl.23542 Hypothetical protein.
50 3605 Bfl.19323 Hypothetical protein.
47 3389 Bfl.373 Transcribed locus, moderately similar to NP_001155685.1 serine/arginine rich splicing factor-like [Acyrthosiphon pisum].
47 3389 Bfl.23497 Hypothetical protein.
45 3244 Bfl.23450 Transcribed locus.
44 3172 Bfl.26147 Transcribed locus, weakly similar to XP_002598793.1 hypothetical protein BRAFLDRAFT_74528 [Branchiostoma floridae].
44 3172 Bfl.24965 Hypothetical protein.
43 3100 Bfl.403 Hypothetical protein.
43 3100 Bfl.24829 Hypothetical protein.
40 2884 Bfl.19257 Hypothetical protein.
39 2812 Bfl.23456 Hypothetical protein.
39 2812 Bfl.13366 Hypothetical protein.
39 2812 Bfl.13109 Transcribed locus, strongly similar to NP_001026545.1 histone H2A.Z [Gallus gallus].
37 2668 Bfl.23506 Hypothetical protein.
37 2668 Bfl.13200 Hypothetical protein.
36 2596 Bfl.841 Hypothetical protein.
35 2523 Bfl.15 Hypothetical protein.
35 2523 Bfl.13000 Hypothetical protein.
35 2523 Bfl.12898 Hypothetical protein.
33 2379 Bfl.23602 Hypothetical protein.
32 2307 Bfl.17534 Hypothetical protein.
31 2235 Bfl.24855 Hypothetical protein.
31 2235 Bfl.17960 Hypothetical protein.
31 2235 Bfl.176 Hypothetical protein.
31 2235 Bfl.17516 Transcribed locus, strongly similar to NP_724345.1 histone H3 [Drosophila melanogaster].
30 2163 Bfl.5089 Hypothetical protein.
30 2163 Bfl.23674 Hypothetical protein.
30 2163 Bfl.13090 Hypothetical protein.
29 2091 Bfl.23875 Hypothetical protein.
29 2091 Bfl.19523 Transcribed locus, strongly similar to XP_002586318.1 hypothetical protein BRAFLDRAFT_132259 [Branchiostoma floridae].
29 2091 Bfl.13579 Hypothetical protein.
29 2091 Bfl.12893 Hypothetical protein.
28 2019 Bfl.26148 Transcribed locus, strongly similar to XP_002607616.1 hypothetical protein BRAFLDRAFT_71494 [Branchiostoma floridae].
28 2019 Bfl.18654 Dimethylarginine dimethylaminohydrolase protein.
27 1947 Bfl.19356 Hypothetical protein.
27 1947 Bfl.17548 Hypothetical protein.
26 1875 Bfl.10741 Transcribed locus, strongly similar to XP_002593768.1 hypothetical protein BRAFLDRAFT_130743 [Branchiostoma floridae].
24 1730 Bfl.752 Transcribed locus, weakly similar to XP_002402708.1 secreted protein, putative [Ixodes scapularis].
24 1730 Bfl.335 Hypothetical protein.
24 1730 Bfl.10678 Transcribed locus, strongly similar to XP_002590787.1 hypothetical protein BRAFLDRAFT_218629 [Branchiostoma floridae].
24 1730 Bfl.10236 Transcribed locus, moderately similar to XP_001518802.1 PREDICTED: similar to eIF-5A2, partial [Ornithorhynchus anatinus].
23 1658 Bfl.23482 Hypothetical protein.
23 1658 Bfl.13091 Hypothetical protein.
23 1658 Bfl.12976 Hypothetical protein.
23 1658 Bfl.12923 Hypothetical protein.
23 1658 Bfl.123 Hypothetical protein.
23 1658 Bfl.11045 Hypothetical protein.
22 1586 Bfl.8915 Hypothetical protein.
22 1586 Bfl.5279 Hypothetical protein.
22 1586 Bfl.18530 Hypothetical protein.
21 1514 Bfl.18526 Hypothetical protein.
21 1514 Bfl.17656 Transcribed locus, strongly similar to XP_002596380.1 hypothetical protein BRAFLDRAFT_215468 [Branchiostoma floridae].
21 1514 Bfl.13111 Hypothetical protein.
21 1514 Bfl.13049 Transcribed locus, strongly similar to XP_002595082.1 hypothetical protein BRAFLDRAFT_115227 [Branchiostoma floridae].
21 1514 Bfl.1001 Transcribed locus, strongly similar to XP_002602697.1 hypothetical protein BRAFLDRAFT_172245 [Branchiostoma floridae].
20 1442 Bfl.24940 Hypothetical protein.
20 1442 Bfl.23654 Hypothetical protein.
20 1442 Bfl.23584 Hypothetical protein.
20 1442 Bfl.19629 Transcribed locus, strongly similar to NP_035794.1 polyubiquitin-B [Mus musculus].
20 1442 Bfl.18525 Hypothetical protein.
20 1442 Bfl.17551 Hypothetical protein.
19 1370 Bfl.838 Hypothetical protein.
19 1370 Bfl.19240 Transcribed locus, weakly similar to XP_002163616.1 PREDICTED: hypothetical protein [Hydra magnipapillata].
18 1298 Bfl.8207 Hypothetical protein.
18 1298 Bfl.6501 Hypothetical protein.
18 1298 Bfl.617 Hypothetical protein.
18 1298 Bfl.4874 Hypothetical protein.
18 1298 Bfl.2609 Hypothetical protein.
18 1298 Bfl.24479 Hypothetical protein.
18 1298 Bfl.24209 Hypothetical protein.
18 1298 Bfl.21223 Hypothetical protein.
18 1298 Bfl.18655 Hypothetical protein.
18 1298 Bfl.18099 Hypothetical protein.
17 1226 Bfl.9935 Hypothetical protein.
17 1226 Bfl.9924 Hypothetical protein.
17 1226 Bfl.6369 Hypothetical protein.
17 1226 Bfl.366 Hypothetical protein.
17 1226 Bfl.23681 Hypothetical protein.
17 1226 Bfl.23645 Hypothetical protein.
17 1226 Bfl.23601 Hypothetical protein.
17 1226 Bfl.18432 Hypothetical protein.

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Source: NCBI UniGene

EST Sequences

15,230 EST sequences from this library have been submitted to the public sequence database as of 03-Apr-2011.

Source: NCBI GenBank

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

Keywords

  • embryo
  • oligo-dT primed

Source: NCBI Clone Registry



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