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An organized view of the transcripome



Library:24182 (dbEST ID)

CCUF Peromyscus maniculatus bairdii BW:Nb

Library Description

Organism:Peromyscus maniculatus bairdii
Strain:BW
Developmental stage:newborn
Sex:pooled male and female
Tissue:3 pooled whole animals
Vector:pDNR-LIB
Cloning site 1:SfiIA
Cloning site 2:SfiIB
Lab host:DH10B T1-resistant

The library was made from oligo(dT)-primed cDNA and cloned into vector pDNR-LIB (Clontech Laboratories, Inc., Mountain View, CA) using the SMART system (BD Biosciences, San Jose, CA). To generate the first strand, polyA RNA was primed with an oligo(dT) primer (5'-ATTCTAGAGGCCGAGGCGGCCGACATG(T)30 VN-3', where V = A, G, or C). The second strand was synthesized by PCR using primer 5'-AAGCAGTGGTATCAACGCAGAGTGGCCATTACGGCCGGG-3' followed by digestion of the SfiI sites. cDNA was size selected using 1.1% agarose gel electrophoresis, then ligated into pDNR-LIB. Library is normalized. Library was created and sequencing performed by the DOE Joint Genome Institute (Walnut Creek, CA).

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

Gene Content Analysis

14,228 ESTs from this library were grouped into 3,893 UniGene entries (putative genes) [UniGene build #2, 09-Mar-2010]. EST counts for each entry may be used to calculate an approximate expression level in transcripts per million (TPM).

ESTs TPM   UniGene Entry
106 7450 Pmn.16339 Transcribed locus, moderately similar to XP_003084764.1 PREDICTED: hemoglobin subunit beta-1-like isoform 4 [Mus musculus].
32 2249 Pmn.4354 Transcribed locus, strongly similar to NP_001077424.1 hemoglobin alpha, adult chain 2 [Mus musculus].
26 1827 Pmn.7068 Transcribed locus, strongly similar to NP_033138.1 protein S100-A10 [Mus musculus].
26 1827 Pmn.3268 Transcribed locus, strongly similar to XP_001076104.2 PREDICTED: microsomal glutathione S-transferase 3 [Rattus norvegicus].
24 1687 Pmn.9959 Transcribed locus, moderately similar to NP_001120641.1 transcription elongation factor A protein-like 7 [Mus musculus].
24 1687 Pmn.7069 Transcribed locus, moderately similar to NP_064420.2 calmodulin-4 [Mus musculus].
24 1687 Pmn.6141 Transcribed locus, strongly similar to NP_001003405.1 trypsin 5 [Mus musculus].
24 1687 Pmn.3583 Transcribed locus, strongly similar to NP_001007968.1 60S ribosomal protein L30 [Gallus gallus].
24 1687 Pmn.3079 Transcribed locus, strongly similar to XP_423225.1 PREDICTED: similar to rat ribosomal protein L9 homologue [Gallus gallus].
24 1687 Pmn.3006 Transcribed locus, strongly similar to NP_001014297.1 transcription elongation factor A protein-like 8 [Rattus norvegicus].
24 1687 Pmn.2228 Transcribed locus, strongly similar to NP_058898.1 cytochrome c oxidase subunit 4 isoform 1, mitochondrial precursor [Rattus norvegicus].
23 1617 Pmn.555 Transcribed locus, strongly similar to NP_058849.1 40S ribosomal protein S3a [Rattus norvegicus].
23 1617 Pmn.3894 Transcribed locus, weakly similar to NP_073199.1 prolactin-inducible protein homolog precursor [Rattus norvegicus].
23 1617 Pmn.2738 Transcribed locus, strongly similar to NP_990284.1 ubiquitin-40S ribosomal protein S27a [Gallus gallus].
22 1546 Pmn.6855 Transcribed locus, strongly similar to NP_001026156.1 heterogeneous nuclear ribonucleoproteins A2/B1 [Gallus gallus].
22 1546 Pmn.3636 Transcribed locus, strongly similar to NP_001093115.1 60S ribosomal protein L22-like 1 [Homo sapiens].
22 1546 Pmn.16315 Transcribed locus, strongly similar to NP_064335.1 signal peptidase complex catalytic subunit SEC11A [Mus musculus].
21 1476 Pmn.8100 Transcribed locus, moderately similar to NP_032522.2 galectin-7 [Mus musculus].
21 1476 Pmn.7404 Transcribed locus, moderately similar to NP_001078821.1 apolipoprotein C-II [Rattus norvegicus].
21 1476 Pmn.16296 Transcribed locus, strongly similar to NP_001009480.1 cytochrome b-c1 complex subunit 6, mitochondrial [Rattus norvegicus].
21 1476 Pmn.126 Transcribed locus, strongly similar to NP_034490.1 glutathione S-transferase Mu 5 [Mus musculus].
21 1476 Pmn.1192 Transcribed locus, strongly similar to NP_035421.2 60S ribosomal protein L7 [Mus musculus].
20 1406 Pmn.785 Transcribed locus, strongly similar to NP_034075.2 cytochrome c oxidase subunit 7A2, mitochondrial precursor [Mus musculus].
20 1406 Pmn.5328 Transcribed locus, strongly similar to NP_057016.1 proteasome maturation protein [Homo sapiens].
20 1406 Pmn.3351 Transcribed locus, moderately similar to XP_001074466.1 PREDICTED: similar to ATP synthase, H+ transporting, mitochondrial F0 complex, subunit f, isoform 2 [Rattus norvegicus].
20 1406 Pmn.2311 Transcribed locus, strongly similar to NP_001032423.1 40S ribosomal protein S19 [Rattus norvegicus].
20 1406 Pmn.2060 Transcribed locus, strongly similar to NP_058974.1 proteasome subunit alpha type-1 [Rattus norvegicus].
19 1335 Pmn.774 Transcribed locus, strongly similar to NP_031615.1 calmodulin [Mus musculus].
19 1335 Pmn.7354 Transcribed locus, moderately similar to XP_001478505.1 PREDICTED: ATP synthase subunit g, mitochondrial-like [Mus musculus].
19 1335 Pmn.6934 Transcribed locus, moderately similar to NP_803421.1 3-ketoacyl-CoA thiolase, mitochondrial [Mus musculus].
19 1335 Pmn.3889 Transcribed locus, strongly similar to NP_032186.2 glutathione peroxidase 1 [Mus musculus].
19 1335 Pmn.3557 Transcribed locus, strongly similar to NP_033118.1 40S ribosomal protein S17 [Mus musculus].
19 1335 Pmn.2690 Transcribed locus, moderately similar to NP_081234.2 SRA stem-loop-interacting RNA-binding protein, mitochondrial precursor [Mus musculus].
19 1335 Pmn.2450 Transcribed locus, strongly similar to NP_003964.3 60S ribosomal protein L14 [Homo sapiens].
18 1265 Pmn.6580 Transcribed locus, strongly similar to NP_001001969.1 lymphocyte antigen 6 complex G6C [Rattus norvegicus].
18 1265 Pmn.6427 Transcribed locus, strongly similar to XP_002664732.1 PREDICTED: ribosomal protein S5-like [Danio rerio].
18 1265 Pmn.3321 Transcribed locus, strongly similar to XP_416113.1 PREDICTED: similar to Rps16 protein [Gallus gallus].
18 1265 Pmn.2462 Transcribed locus, strongly similar to XP_002726835.1 PREDICTED: ribosomal protein L35a-like [Rattus norvegicus].
18 1265 Pmn.2316 Transcribed locus, strongly similar to NP_001002079.1 40S ribosomal protein S13 [Danio rerio].
18 1265 Pmn.2133 Transcribed locus, strongly similar to NP_035424.1 activated RNA polymerase II transcriptional coactivator p15 [Mus musculus].
18 1265 Pmn.2066 Transcribed locus, strongly similar to NP_001002097.1 probable protein BRICK1 [Danio rerio].
17 1195 Pmn.8545 Transcribed locus, moderately similar to NP_001012359.1 angiogenin, ribonuclease, RNase A family, 5 [Rattus norvegicus].
17 1195 Pmn.6691 Transcribed locus, strongly similar to NP_059068.1 lysozyme C-2 precursor [Mus musculus].
17 1195 Pmn.5258 Transcribed locus, strongly similar to NP_958818.1 60S ribosomal protein L17 [Rattus norvegicus].
17 1195 Pmn.4933 Transcribed locus, moderately similar to XP_003364122.1 PREDICTED: 6.8 kDa mitochondrial proteolipid-like [Equus caballus].
17 1195 Pmn.423 Transcribed locus, strongly similar to NP_058977.1 proteasome subunit alpha type-4 [Rattus norvegicus].
17 1195 Pmn.2811 Transcribed locus, strongly similar to XP_002725396.1 PREDICTED: cytochrome c, somatic-like [Rattus norvegicus].
17 1195 Pmn.2546 Transcribed locus, strongly similar to NP_038725.1 transthyretin [Mus musculus].
17 1195 Pmn.2380 Transcribed locus, strongly similar to NP_056591.1 microfibrillar-associated protein 5 precursor [Mus musculus].
17 1195 Pmn.2163 Transcribed locus, strongly similar to NP_061341.1 60S acidic ribosomal protein P1 [Mus musculus].
17 1195 Pmn.1116 Transcribed locus, strongly similar to NP_033182.1 selenoprotein W [Mus musculus].
16 1125 Pmn.9860 Transcribed locus.
16 1125 Pmn.8991 Transcribed locus, moderately similar to NP_038741.1 keratin-associated protein 15-1 [Mus musculus].
16 1125 Pmn.7785 Transcribed locus, strongly similar to NP_036099.1 proteasome subunit alpha type-7 [Mus musculus].
16 1125 Pmn.7133 Transcribed locus, strongly similar to NP_035826.1 voltage-dependent anion-selective channel protein 3 isoform 2 [Mus musculus].
16 1125 Pmn.5381 Transcribed locus, strongly similar to NP_476443.1 ADP/ATP translocase 2 [Rattus norvegicus].
16 1125 Pmn.5117 Transcribed locus, strongly similar to NP_031856.1 acyl-CoA-binding protein isoform 2 [Mus musculus].
16 1125 Pmn.4729 Transcribed locus, strongly similar to NP_079655.1 cytochrome c oxidase subunit 7B, mitochondrial precursor [Mus musculus].
16 1125 Pmn.4094 Transcribed locus, strongly similar to NP_001013079.1 adenine phosphoribosyltransferase [Rattus norvegicus].
16 1125 Pmn.2725 Transcribed locus, strongly similar to NP_062798.1 actin-related protein 2/3 complex subunit 3 [Mus musculus].
16 1125 Pmn.2542 Transcribed locus, strongly similar to NP_058975.1 proteasome subunit alpha type-2 [Rattus norvegicus].
16 1125 Pmn.2333 Transcribed locus, strongly similar to NP_000981.1 60S ribosomal protein L27a [Homo sapiens].
16 1125 Pmn.205 Transcribed locus, strongly similar to NP_058030.1 histone H2A.Z [Mus musculus].
16 1125 Pmn.16616 Transcribed locus, moderately similar to NP_036644.1 beta-2-microglobulin precursor [Rattus norvegicus].
16 1125 Pmn.16385 Transcribed locus, strongly similar to NP_000977.1 60S ribosomal protein L24 [Homo sapiens].
16 1125 Pmn.1513 Transcribed locus, moderately similar to XP_002725066.1 PREDICTED: rCG31129-like [Rattus norvegicus].
16 1125 Pmn.1138 Transcribed locus, strongly similar to NP_001016.1 40S ribosomal protein S23 [Homo sapiens].
16 1125 Pmn.10008 Transcribed locus, strongly similar to NP_032616.1 mesoderm-specific transcript protein [Mus musculus].
15 1054 Pmn.9166 Transcribed locus.
15 1054 Pmn.6900 Transcribed locus, strongly similar to NP_037036.1 annexin A1 [Rattus norvegicus].
15 1054 Pmn.5641 Transcribed locus, strongly similar to NP_062723.1 gamma-aminobutyric acid receptor-associated protein [Mus musculus].
15 1054 Pmn.4573 Transcribed locus, strongly similar to XP_344047.2 PREDICTED: similar to Ubiquitin-conjugating enzyme E2 L3 (Ubiquitin-protein ligase L3) (Ubiquitin carrier protein L3) (UbcM4) [Rattus norvegicus].
15 1054 Pmn.4331 Transcribed locus, strongly similar to XP_002726748.1 PREDICTED: mitochondrial ribosomal protein L33-like [Rattus norvegicus].
15 1054 Pmn.3720 Transcribed locus, strongly similar to NP_033120.1 40S ribosomal protein S4, X isoform [Mus musculus].
15 1054 Pmn.3709 Transcribed locus, moderately similar to NP_001005534.1 succinate dehydrogenase complex, subunit C [Rattus norvegicus].
15 1054 Pmn.3604 Transcribed locus, strongly similar to NP_035016.1 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 4 [Mus musculus].
15 1054 Pmn.3518 Transcribed locus, moderately similar to NP_037288.1 cathepsin L1 preproprotein [Rattus norvegicus].
15 1054 Pmn.2569 Transcribed locus, strongly similar to NP_001005528.1 40S ribosomal protein S25 [Rattus norvegicus].
15 1054 Pmn.1735 Transcribed locus, strongly similar to NP_001185781.1 forkhead box protein J3 isoform 2 [Homo sapiens].
15 1054 Pmn.16720 Transcribed locus, weakly similar to NP_001020745.1 hypothetical protein LOC433492 [Mus musculus].
15 1054 Pmn.1663 Transcribed locus, strongly similar to NP_001395.1 elongation factor 1-gamma [Homo sapiens].
15 1054 Pmn.16466 Transcribed locus, strongly similar to NP_001988.1 ubiquitin-like protein fubi and ribosomal protein S30 precursor [Homo sapiens].
15 1054 Pmn.10096 Transcribed locus, strongly similar to NP_001029296.1 microfibril-associated glycoprotein 4 [Rattus norvegicus].
14 984 Pmn.7638 Transcribed locus, strongly similar to NP_115877.2 cornifelin [Homo sapiens].
14 984 Pmn.7381 Transcribed locus, strongly similar to NP_110459.1 fatty acid-binding protein, brain [Rattus norvegicus].
14 984 Pmn.7096 Transcribed locus, moderately similar to NP_058709.2 glutathione S-transferase alpha-1 [Rattus norvegicus].
14 984 Pmn.611 Transcribed locus, strongly similar to NP_998369.1 40S ribosomal protein S20 [Danio rerio].
14 984 Pmn.5614 Transcribed locus, strongly similar to NP_001003447.1 60S ribosomal protein L15 [Danio rerio].
14 984 Pmn.4087 Transcribed locus, strongly similar to NP_001124478.1 signal peptidase complex subunit 1 [Rattus norvegicus].
14 984 Pmn.4074 Transcribed locus, strongly similar to XP_001069423.2 PREDICTED: Ngg1 interacting factor 3 like 1 binding protein 1-like [Rattus norvegicus].
14 984 Pmn.3637 Transcribed locus, strongly similar to NP_001017582.1 small nuclear ribonucleoprotein Sm D2 [Danio rerio].
14 984 Pmn.3225 Transcribed locus, strongly similar to NP_005457.2 mediator of RNA polymerase II transcription subunit 6 [Homo sapiens].
14 984 Pmn.3167 Transcribed locus, strongly similar to NP_001091274.1 interferon induced transmembrane protein 3 [Xenopus laevis].
14 984 Pmn.2939 Transcribed locus, strongly similar to NP_778166.2 39S ribosomal protein L22, mitochondrial precursor [Mus musculus].
14 984 Pmn.2299 Transcribed locus, strongly similar to NP_057182.1 brain protein 44-like protein [Homo sapiens].
14 984 Pmn.2291 Transcribed locus, strongly similar to NP_000984.1 60S ribosomal protein L31 isoform 1 [Homo sapiens].
14 984 Pmn.16719 Transcribed locus, strongly similar to NP_998515.1 ras homolog gene family, member Ac [Danio rerio].
14 984 Pmn.10881 Transcribed locus, strongly similar to NP_001005550.1 NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial precursor [Rattus norvegicus].
13 914 Pmn.8523 Transcribed locus, strongly similar to NP_082280.2 titin isoform N2-B [Mus musculus].
13 914 Pmn.8251 Transcribed locus, moderately similar to NP_037033.1 protein AMBP precursor [Rattus norvegicus].

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Source: NCBI UniGene

EST Sequences

15,987 EST sequences from this library have been submitted to the public sequence database as of 09-Mar-2010.

Source: NCBI GenBank

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



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