Amphioxus Branchiostoma floridae unpublished cDNA library CAXF, gastrula whole animal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

13,931 ESTs from this library were grouped into 3,675 UniGene entries (putative genes) [UniGene build #11, 16-Oct-2008]. EST counts for each entry may be used to calculate an approximate expression level in transcripts per million (TPM).

ESTs	TPM	UniGene Entry
2832	203288	Bfl.19	Transcribed locus, weakly similar to XP_001204176.1 PREDICTED: similar to HrEpiB [Strongylocentrotus purpuratus].
111	7968	Bfl.560	Transcribed locus, moderately similar to NP_033130.1 ribonucleotide reductase M2 [Mus musculus].
92	6604	Bfl.12889	Intermediate filament protein D1.
87	6245	Bfl.12867	Transcribed locus, strongly similar to NP_990627.1 H3 histone, family 3B (H3.3B) [Gallus gallus].
69	4953	Bfl.1274	Transcribed locus, weakly similar to NP_031656.2 cyclin B2 [Mus musculus].
64	4594	Bfl.17620	Transcribed locus, strongly similar to NP_001026545.1 H2A histone family, member V [Gallus gallus].
63	4522	Bfl.12925	Transcribed locus, moderately similar to NP_001032328.1 tissue specific transplantation antigen P35B [Xenopus (Silurana) tropicalis].
62	4451	Bfl.19629	Transcribed locus, strongly similar to NP_035794.1 ubiquitin B [Mus musculus].
58	4163	Bfl.13090	Transcribed locus, strongly similar to NP_062667.1 HLA-B-associated transcript 1A [Mus musculus].
58	4163	Bfl.12968	Transcribed locus, strongly similar to NP_524352.1 Histone H4 replacement CG3379-PC, isoform C [Drosophila melanogaster].
51	3661	Bfl.13438	Keratin type I (IF1).
47	3374	Bfl.373	Transcribed locus, moderately similar to XP_001951958.1 PREDICTED: similar to serine/arginine rich splicing factor [Acyrthosiphon pisum].
47	3374	Bfl.12873	Homeodomain protein (Nk2-2).
46	3302	Bfl.13109	Transcribed locus, strongly similar to NP_001026545.1 H2A histone family, member V [Gallus gallus].
41	2943	Bfl.403	Transcribed locus, strongly similar to NP_001012474.1 Sec61 gamma subunit [Homo sapiens].
39	2800	Bfl.17568	Transcribed locus, moderately similar to NP_001006443.1 solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4 [Gallus gallus].
38	2728	Bfl.13366	Transcribed locus, weakly similar to NP_003304.1 tissue specific transplantation antigen P35B [Homo sapiens].
37	2656	Bfl.15	Cytoplasmic actin.
35	2512	Bfl.12898	Transcribed locus, moderately similar to XP_427116.1 PREDICTED: similar to histone H2B [Gallus gallus].
34	2441	Bfl.13000	Transcribed locus, weakly similar to NP_009294.1 catechol-O-methyltransferase isoform S-COMT [Homo sapiens].
31	2225	Bfl.17783	Transcribed locus, weakly similar to NP_035084.1 neural cell adhesion molecule 2 isoform b [Mus musculus].
31	2225	Bfl.17516	Transcribed locus, strongly similar to NP_724345.1 His3:CG31613 CG31613-PA [Drosophila melanogaster].
29	2082	Bfl.13579	Transcribed locus, weakly similar to NP_001091381.1 hypothetical protein LOC100037235 [Xenopus laevis].
29	2082	Bfl.12893	Transcribed locus, weakly similar to NP_054757.1 basic leucine zipper and W2 domains 2 [Homo sapiens].
27	1938	Bfl.12921	Transcribed locus, weakly similar to NP_990729.1 tumor protein, translationally-controlled 1 [Gallus gallus].
26	1866	Bfl.3686	Transcribed locus.
26	1866	Bfl.19523	Transcribed locus, weakly similar to NP_001004022.1 keratin 15 [Rattus norvegicus].
26	1866	Bfl.10741	Transcribed locus, moderately similar to XP_992688.1 PREDICTED: similar to chromosome 13 open reading frame 21 [Mus musculus].
25	1795	Bfl.19257	Transcribed locus, moderately similar to NP_001035074.1 hypothetical protein LOC664756 [Danio rerio].
25	1795	Bfl.17552	Transcribed locus, strongly similar to NP_035794.1 ubiquitin B [Mus musculus].
25	1795	Bfl.12976	Transcribed locus, moderately similar to NP_001958.2 eukaryotic translation initiation factor 4A2 [Homo sapiens].
25	1795	Bfl.12926	Transcribed locus, moderately similar to NP_001006443.1 solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4 [Gallus gallus].
24	1723	Bfl.13200	Transcribed locus, weakly similar to NP_062804.1 protein arginine N-methyltransferase 1 [Mus musculus].
23	1651	Bfl.123	Transcribed locus, moderately similar to NP_001076672.1 hypothetical protein F01G4.6 [Caenorhabditis elegans].
22	1579	Bfl.841	Transcribed locus.
22	1579	Bfl.5279	Transcribed locus, moderately similar to NP_006799.1 Sec61 beta subunit [Homo sapiens].
22	1579	Bfl.2817	Transcribed locus, weakly similar to XP_001195570.1 PREDICTED: similar to Myc-induced nuclear antigen with a molecular mass of 53 kDa-like 1, partial [Strongylocentrotus purpuratus].
22	1579	Bfl.19472	Transcribed locus, strongly similar to NP_524352.1 Histone H4 replacement CG3379-PC, isoform C [Drosophila melanogaster].
22	1579	Bfl.17664	Transcribed locus, strongly similar to XP_688383.1 PREDICTED: wu:fb37a10 isoform 1 [Danio rerio].
22	1579	Bfl.12923	Transcribed locus, weakly similar to NP_035934.1 cellular repressor of E1A-stimulated genes 1 [Mus musculus].
22	1579	Bfl.12860	Type I keratin k1 (gene k1).
21	1507	Bfl.9785	Transcribed locus, weakly similar to XP_423669.1 PREDICTED: similar to HMT1 hnRNP methyltransferase-like 3 protein, partial [Gallus gallus].
21	1507	Bfl.19630	Transcribed locus, moderately similar to XP_001518802.1 PREDICTED: similar to eIF-5A2, partial [Ornithorhynchus anatinus].
21	1507	Bfl.18654	Transcribed locus, weakly similar to XP_788796.2 PREDICTED: similar to NG,NG-dimethylarginine dimethylaminohydrolase [Strongylocentrotus purpuratus].
20	1436	Bfl.5727	Transcribed locus.
20	1436	Bfl.19594	Transcribed locus, weakly similar to NP_999861.1 synaptotagmin binding, cytoplasmic RNA interacting protein [Danio rerio].
20	1436	Bfl.18525	Transcribed locus, weakly similar to NP_036269.1 dimethylarginine dimethylaminohydrolase 1 isoform 1 [Homo sapiens].
20	1436	Bfl.17656	Transcribed locus, weakly similar to XP_001694459.1 glycine-rich RNA-binding protein [Chlamydomonas reinhardtii].
20	1436	Bfl.17551	Transcribed locus, moderately similar to XP_418815.1 PREDICTED: similar to protein translation factor sui1 homolog [Gallus gallus].
20	1436	Bfl.13049	Transcribed locus, moderately similar to XP_331213.1 hypothetical protein [Neurospora crassa OR74A].
19	1364	Bfl.17869	Transcribed locus, weakly similar to XP_786612.2 PREDICTED: similar to calcyphosine, partial [Strongylocentrotus purpuratus].
19	1364	Bfl.17814	Transcribed locus, weakly similar to NP_003478.1 TBP-associated factor 15 isoform 2 [Homo sapiens].
19	1364	Bfl.13111	Transcribed locus, moderately similar to NP_996408.1 Glutamine synthetase 2 CG1743-PA, isoform A [Drosophila melanogaster].
19	1364	Bfl.11045	Transcribed locus, weakly similar to XP_970338.1 PREDICTED: similar to cabeza CG3606-PB [Tribolium castaneum].
18	1292	Bfl.8976	Transcribed locus, weakly similar to XP_001633247.1 predicted protein [Nematostella vectensis].
18	1292	Bfl.8915	Transcribed locus, moderately similar to XP_001180940.1 PREDICTED: similar to ENSANGP00000021579 [Strongylocentrotus purpuratus].
18	1292	Bfl.617	Transcribed locus, strongly similar to NP_055555.1 eukaryotic translation initiation factor 4A, isoform 3 [Homo sapiens].
18	1292	Bfl.4874	Transcribed locus.
18	1292	Bfl.2609	Transcribed locus.
18	1292	Bfl.19356	Transcribed locus, strongly similar to NP_001026545.1 H2A histone family, member V [Gallus gallus].
17	1220	Bfl.9935	Transcribed locus.
17	1220	Bfl.19583	Transcribed locus, moderately similar to NP_989488.2 eukaryotic translation elongation factor 1 alpha 1 [Gallus gallus].
17	1220	Bfl.17781	Transcribed locus, strongly similar to NP_034890.1 mago-nashi homolog, proliferation-associated [Mus musculus].
17	1220	Bfl.17586	Transcribed locus, weakly similar to XP_002131325.1 PREDICTED: similar to cold-inducible RNA-binding protein [Ciona intestinalis].
17	1220	Bfl.17514	Transcribed locus, moderately similar to NP_001007839.1 small nuclear ribonucleoprotein D3 polypeptide 18kDa [Gallus gallus].
17	1220	Bfl.13371	Transcribed locus, moderately similar to NP_034610.1 heat shock protein 1, alpha [Mus musculus].
16	1149	Bfl.17599	Transcribed locus, moderately similar to NP_032324.1 DnaJ (Hsp40) homolog, subfamily A, member 1 [Mus musculus].
16	1149	Bfl.15971	Transcribed locus, weakly similar to NP_001026599.1 DAZ associated protein 1 [Gallus gallus].
16	1149	Bfl.13099	Transcribed locus, moderately similar to NP_058941.1 eukaryotic translation elongation factor 2 [Rattus norvegicus].
16	1149	Bfl.11351	Transcribed locus.
15	1077	Bfl.8431	Transcribed locus, moderately similar to NP_652189.1 CG11985 CG11985-PA [Drosophila melanogaster].
15	1077	Bfl.5111	Transcribed locus.
15	1077	Bfl.451	Transcribed locus.
15	1077	Bfl.19593	Transcribed locus, weakly similar to NP_783193.2 heterogeneous nuclear ribonucleoprotein R [Rattus norvegicus].
15	1077	Bfl.17674	Transcribed locus, strongly similar to NP_035794.1 ubiquitin B [Mus musculus].
15	1077	Bfl.176	Transcribed locus, weakly similar to XP_522347.2 PREDICTED: similar to p27kip1 [Pan troglodytes].
15	1077	Bfl.13264	Transcribed locus.
15	1077	Bfl.13163	Transcribed locus, moderately similar to NP_991230.1 small nuclear ribonucleoprotein polypeptides B and B1 [Danio rerio].
15	1077	Bfl.13112	Transcribed locus, moderately similar to NP_058797.1 peptidylprolyl isomerase A (cyclophilin A) [Rattus norvegicus].
15	1077	Bfl.13079	Transcribed locus, weakly similar to NP_001032501.1 hypothetical protein LOC641484 [Danio rerio].
15	1077	Bfl.12971	Transcribed locus, strongly similar to NP_031615.1 calmodulin 2 [Mus musculus].
15	1077	Bfl.10804	Transcribed locus, moderately similar to NP_036379.2 selenophosphate synthetase 1 [Homo sapiens].
14	1005	Bfl.558	Transcribed locus, weakly similar to NP_002887.2 RNA binding motif protein 4 [Homo sapiens].
14	1005	Bfl.5109	Transcribed locus, weakly similar to XP_001636026.1 predicted protein [Nematostella vectensis].
14	1005	Bfl.4755	Transcribed locus, weakly similar to XP_001181019.1 PREDICTED: hypothetical protein [Strongylocentrotus purpuratus].
14	1005	Bfl.17885	Transcribed locus, weakly similar to NP_001035003.1 akirin 2 [Rattus norvegicus].
14	1005	Bfl.17882	Transcribed locus, weakly similar to NP_001006358.1 basic leucine zipper and W2 domains 2 [Gallus gallus].
14	1005	Bfl.17796	Transcribed locus, weakly similar to XP_001633483.1 predicted protein [Nematostella vectensis].
14	1005	Bfl.13668	Transcribed locus.
14	1005	Bfl.13107	Transcribed locus.
14	1005	Bfl.12142	Clone bfne016p05 winged helix/forkhead transcription factor FoxQ2a.
13	933	Bfl.9772	Transcribed locus.
13	933	Bfl.878	Transcribed locus.
13	933	Bfl.8663	Beta-catenin (AmphiBetaCat).
13	933	Bfl.8452	Transcribed locus.
13	933	Bfl.824	Transcribed locus, weakly similar to XP_786419.2 PREDICTED: similar to nuclear matrix protein 1, partial [Strongylocentrotus purpuratus].
13	933	Bfl.4886	Transcribed locus, moderately similar to XP_001945146.1 PREDICTED: similar to Sp-like zinc finger transcription factor [Acyrthosiphon pisum].
13	933	Bfl.39	Transcribed locus.
13	933	Bfl.3768	Transcribed locus, strongly similar to NP_006588.1 heat shock 70kDa protein 8 isoform 1 [Homo sapiens].
13	933	Bfl.18629	Transcribed locus.