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An organized view of the transcripome



Library:1348 (dbEST ID)

UI-R-C1

Library Description

Organism:Rattus norvegicus
Strain:Sprague-Dawley
Developmental stage:Adult
Vector:pT7T3D-PacI
Vector type:Phagemid
Cloning site 1:Not I
Cloning site 2:Eco RI
Lab host:DH10B (Life Technologies)

The UI-R-C1 library is a subtracted library derived from the UI-R-C0 library, which is a subtracted library derived from the UI-R-A1 and UI-R-E1 libraries. The UI-R-A1 library consisted of a mixture of individually tagged normalized libraries constructed from rat placenta, adult lung, brain, liver, kidney, heart, spleen, ovary, and muscle. The UI-R-E1 library consisted of a mixture of individually tagged normalized libraries constructed from 8, 12 and 18-day embryo. The tag is a string of 3-5 nucleotides present between the Not I site and the oligo-dT track which allows identification of the library of origin of a clone within the mixture. The subtracted library (UI-R-C1) was constructed as follows: PCR amplified cDNA inserts from UI-R-C0 clones from which 3' ESTs had been derived was used as a driver in a hybridization with the UI-R-C0 library in the form of single-stranded circles. The remaining single-stranded circles (subtracted library) was purified by hydroxyapatite column chromatography, converted to double-stranded circles and electroporated into DH10B bacteria (Life Technologies) to generate the UI-R-C1 library. This procedure has been previously described (Bonaldo, Lennon and Soares, Genome Research 6: 791-806, 1996)

Source: Soares, MB, Children's Memorial Research Center

Gene Content Analysis

6,210 ESTs from this library were grouped into 3,717 UniGene entries (putative genes) [UniGene build #195, 23-Mar-2013]. EST counts for each entry may be used to calculate an approximate expression level in transcripts per million (TPM).

ESTs TPM   UniGene Entry
23 3704 Rn.16065 Protein phosphatase 4, regulatory subunit 1.
13 2093 Rn.7787 Amnion associated transmembrane protein.
9 1449 Rn.76647 Cytidine and dCMP deaminase domain containing 1.
9 1449 Rn.3807 Endonuclease G.
9 1449 Rn.28195 GTP cyclohydrolase 1.
8 1288 Rn.93819 Uncharacterized LOC100912411.
7 1127 Rn.7632 SET binding factor 1.
7 1127 Rn.7078 Synaptopodin 2.
7 1127 Rn.2305 ATPase, Ca++ transporting, cardiac muscle, slow twitch 2.
7 1127 Rn.22934 Nuclear factor of activated T-cells 5, tonicity-responsive.
7 1127 Rn.203831 Cytochrome b561 family, member A3.
6 966 Rn.9560 Myristoylated alanine rich protein kinase C substrate.
6 966 Rn.6834 ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited).
6 966 Rn.40930 Low density lipoprotein receptor-related protein 11.
6 966 Rn.3337 Transcribed locus, strongly similar to NP_859067.2 centromere protein V [Homo sapiens].
6 966 Rn.16145 Complement component 6.
6 966 Rn.11378 Complement component 3.
5 805 Rn.91221 Defensin, alpha 5, Paneth cell-specific.
5 805 Rn.8070 Family with sequence similarity 117, member B.
5 805 Rn.72824 Neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase.
5 805 Rn.6788 Kelch-like family member 8.
5 805 Rn.6215 Acyl-CoA synthetase long-chain family member 1.
5 805 Rn.47870 Transcribed locus, strongly similar to XP_002727894.1 PREDICTED: BAH domain and coiled-coil containing 1 [Rattus norvegicus].
5 805 Rn.44847 Testis derived transcript.
5 805 Rn.23446 Ubiquilin 2.
5 805 Rn.219309 Transcribed locus.
5 805 Rn.211693 Echinoderm microtubule associated protein like 1.
5 805 Rn.202955 Thymopoietin.
5 805 Rn.199020 RNA binding motif protein 24.
5 805 Rn.19041 NEDD4 binding protein 2-like 2.
5 805 Rn.17383 Hepatoma-derived growth factor, related protein 3.
5 805 Rn.166705 Sushi domain containing 2.
5 805 Rn.16164 Negative elongation factor complex member E.
5 805 Rn.15995 Zinc finger protein 418.
5 805 Rn.14669 Zinc finger protein 180.
5 805 Rn.12732 Fibroblast growth factor receptor 2.
5 805 Rn.126653 Protein tyrosine phosphatase, receptor type, K.
5 805 Rn.106771 Stromal interaction molecule 1.
5 805 Rn.105705 TL0AAA68YC11 mRNA sequence.
5 805 Rn.103732 Phosphatidylserine synthase 1.
4 644 Rn.9975 Very low density lipoprotein receptor.
4 644 Rn.992 Transmembrane protein 50B.
4 644 Rn.96138 Similar to KIAA2026 protein.
4 644 Rn.95083 Coiled-coil domain containing 104.
4 644 Rn.94992 Proline rich 3.
4 644 Rn.9283 Coenzyme Q6 homolog, monooxygenase (S. cerevisiae).
4 644 Rn.91077 Homeo box A2.
4 644 Rn.878 Transcribed locus.
4 644 Rn.86273 Mannosidase, alpha, class 1B, member 1.
4 644 Rn.85539 Ring finger protein, LIM domain interacting.
4 644 Rn.7040 Hydroxysteroid (17-beta) dehydrogenase 7.
4 644 Rn.6646 Cytoskeleton associated protein 5.
4 644 Rn.6259 TL0AEA61YK22 mRNA sequence.
4 644 Rn.6158 PDGFA associated protein 1.
4 644 Rn.61149 GA binding protein transcription factor, beta subunit 1.
4 644 Rn.5909 SH3-domain GRB2-like 3.
4 644 Rn.54498 Coagulation factor II.
4 644 Rn.50051 Ubiquitin specific peptidase 39.
4 644 Rn.42579 M-phase phosphoprotein 8.
4 644 Rn.4187 Galactosidase, beta 1.
4 644 Rn.3622 Integrin alpha FG-GAP repeat containing 1.
4 644 Rn.35776 CREB/ATF bZIP transcription factor.
4 644 Rn.3383 NADH dehydrogenase (ubiquinone) 1 beta subcomplex 8.
4 644 Rn.33443 Orthodenticle homeobox 1.
4 644 Rn.28242 Proteasome maturation protein.
4 644 Rn.234367 Basic leucine zipper and W2 domains 1.
4 644 Rn.22866 Lysine (K)-specific demethylase 5B.
4 644 Rn.224476 StAR-related lipid transfer (START) domain containing 7.
4 644 Rn.222599 Sumo1/sentrin/SMT3 specific peptidase 5.
4 644 Rn.220207 Transcribed locus.
4 644 Rn.219310 Transcribed locus.
4 644 Rn.21000 Transcribed locus, strongly similar to XP_001077695.3 PREDICTED: NFAT activation molecule 1 [Rattus norvegicus].
4 644 Rn.204053 Annexin A6.
4 644 Rn.203141 NADH dehydrogenase (ubiquinone) Fe-S protein 4.
4 644 Rn.202620 CCAAT/enhancer binding protein (C/EBP), delta.
4 644 Rn.202598 Transcribed locus, strongly similar to NP_080962.1 UPF0585 protein C16orf13 homolog [Mus musculus].
4 644 Rn.201831 Transcribed locus, strongly similar to XP_002728445.1 PREDICTED: palladin [Rattus norvegicus].
4 644 Rn.198615 Hypothetical protein LOC691931.
4 644 Rn.198339 CDK5 regulatory subunit associated protein 1-like 1 (CDKAL1).
4 644 Rn.19553 Transcribed locus.
4 644 Rn.19480 V-rel reticuloendotheliosis viral oncogene homolog A (avian).
4 644 Rn.19437 Protein phosphatase 1, regulatory subunit 7.
4 644 Rn.19327 Polymerase (DNA directed), gamma.
4 644 Rn.19170 Exportin 5.
4 644 Rn.19106 Transmembrane and coiled-coil domain family 3.
4 644 Rn.18996 Serine palmitoyltransferase, long chain base subunit 1.
4 644 Rn.18983 CDP-diacylglycerol synthase 1.
4 644 Rn.18973 Transcribed locus, strongly similar to XP_002729048.2 PREDICTED: ras GTPase-activating-like protein IQGAP2-like [Rattus norvegicus].
4 644 Rn.18909 Janus kinase 2.
4 644 Rn.17771 Tumor protein p53 inducible protein 13.
4 644 Rn.16740 Class II, major histocompatibility complex, transactivator.
4 644 Rn.166182 Transcribed locus, strongly similar to NP_001101761.1 luc7-like protein 3 [Rattus norvegicus].
4 644 Rn.166179 Transcribed locus, strongly similar to NP_113950.2 Cdkn1b gene product [Rattus norvegicus].
4 644 Rn.162786 EMG1 nucleolar protein homolog (S. cerevisiae).
4 644 Rn.16272 TRAF type zinc finger domain containing 1.
4 644 Rn.162481 Transcribed locus, strongly similar to NP_001009930.1 Brsk2 gene product [Mus musculus].
4 644 Rn.16232 Transcribed locus.
4 644 Rn.162144 T-box 3.
4 644 Rn.161980 Similar to RIKEN cDNA 1110059G10.
4 644 Rn.16165 Centromere protein A.

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Source: NCBI UniGene

EST Sequences

7,422 EST sequences from this library have been submitted to the public sequence database as of 23-Mar-2013.

Source: NCBI GenBank

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

References

Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al., Genome Res 6, 791-806 (1996).



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