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An organized view of the transcripome



Library:15520 (dbEST ID)

p4civp

Library Description

Organism:Sus scrofa

Funding: A grant from the Monsanto Company to the University of Missouri. Genetic Source: Slaughterhouse-derived oocytes were collected, and after cumulous cell removal were used for germinal vesicle stage oocytes, or were matured in vitro (with cumulus cells attached), in vitro fertilized and cultured. In vivo produced 4-cell and blastocyst stage embryos were collected on days 3 and 6, respectively. Zonae Pellucidae were removed from the embryos prior to mRNA isolation. Expanded descriptions of how the tissues were collected can be found at the following URL: http://genome.rnet.missouri.edu/Swine/Methods.html. Library Construction (PCR Protocol): The amount of mRNA that was recovered from oocytes and embryos was quite limiting and was not sufficient for library production with a standard protocol. Therefore, PCR-based protocol was utilized for producing libraries. Poly-A RNA was isolated by using the MicroPoly(A) Pure kit from Ambion (cat. #1918). The mRNA was reverse transcribed with a NotI-tag-dT18 oligonucleotide and a SMART oligonucleotide (Clontech) modified to contain a SalI site to generate full-length cDNA with a sequence complementary to the SMART oligonucleotide. Sequences within the SMART and dT oligonucleotides were used as primers to amplify the cDNAs by PCR with pfu turbo polymerase (Stratagene). The resulting PCR products were purified, digested with NotI and SalI and size fractionated by using a Chroma Spin-400 followed by a Chroma Spin-1000 column (Clontech). Purified cDNA from each PCR reaction was ligated into the pCMV-SPORT6 vector. Preliminary Library Characterization: Randomly chosen clones from each library were analyzed by restriction digestion to determine average insert size (96 clones) and by sequencing (~3 96-well plates) to confirm library quality [e.g. the presence of short polyA+ tails, genomic DNA contamination (must be <1%), ribosomal RNA clones (must be <1%), etc.] and to provide a sequence database representing the predominant clones in each library. The clones were sequenced at the University of Missouri-Columbia DNA Core Facility. Bioinformatics work was performed by GK Springer's bioinformatics group (WG Spollen, JE Ries, A Guillen) in Computer Science and Health Management and Informatics Departments at the University of Missouri-Columbia. Clone Requests: Requests for clones should be made to the Director of the University of Missouri DNA Core facility at: porcine@rnet.missouri.edu.

Source: DNA Core Facility (Bovine Project), University of Missouri-Columbia

Gene Content Analysis

632 ESTs from this library were grouped into 221 UniGene entries (putative genes) [UniGene build #42, 19-Jun-2012]. EST counts for each entry may be used to calculate an approximate expression level in transcripts per million (TPM).

ESTs TPM   UniGene Entry
48 75949 Ssc.842 Ribosomal protein S21.
47 74367 Ssc.32215 Casein kinase 2, beta polypeptide.
29 45886 Ssc.79019 Transcribed locus.
22 34810 Ssc.53738 Ribosomal phosphoprotein large PO subunit.
19 30063 Ssc.49527 Karyopherin alpha 7 (importin alpha 8).
10 15823 Ssc.31296 Transcribed locus, strongly similar to NP_034610.1 heat shock protein HSP 90-alpha [Mus musculus].
10 15823 Ssc.2866 Transcribed locus, strongly similar to NP_001005767.1 presenilins-associated rhomboid-like protein, mitochondrial precursor [Mus musculus].
9 14241 Ssc.953 Transcribed locus, strongly similar to XP_003122631.1 PREDICTED: cytochrome c oxidase subunit 8A, mitochondrial-like isoform 1 [Sus scrofa].
9 14241 Ssc.42200 Nuclear receptor subfamily 5 group A member 2 (nr5a2).
8 12658 Ssc.2261 Ribosomal protein L10.
8 12658 Ssc.1606 Rho guanine nucleotide exchange factor 7-like.
7 11076 Ssc.55115 Transcribed locus, strongly similar to XP_003357670.1 PREDICTED: RRP15-like protein-like [Sus scrofa].
7 11076 Ssc.16638 Solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6.
7 11076 Ssc.11211 Transcribed locus, strongly similar to NP_054761.1 anaphase-promoting complex subunit 15 [Homo sapiens].
6 9494 Ssc.23186 Ribosomal protein S10.
6 9494 Ssc.11141 Transcribed locus, strongly similar to NP_064335.1 signal peptidase complex catalytic subunit SEC11A [Mus musculus].
5 7911 Ssc.68277 Transcribed locus, strongly similar to NP_001003860.1 protein BUD31 homolog [Danio rerio].
5 7911 Ssc.53888 Ribosomal protein S3.
5 7911 Ssc.53861 Transcribed locus, strongly similar to NP_001004224.1 B-cell receptor-associated protein 31 [Rattus norvegicus].
5 7911 Ssc.43337 Transcribed locus, strongly similar to XP_001064168.2 PREDICTED: zinc finger protein 618 [Rattus norvegicus].
5 7911 Ssc.29580 CDC28 protein kinase regulatory subunit 1B.
5 7911 Ssc.2716 Malonyl-CoA-acyl carrier protein transacylase, mitochondrial-like.
5 7911 Ssc.23221 Ovarian and testicular apolipoprotein N.
5 7911 Ssc.17653 39S ribosomal protein L46, mitochondrial-like.
4 6329 Ssc.93748 Transcribed locus, strongly similar to NP_035995.1 poly(rC)-binding protein 1 [Mus musculus].
4 6329 Ssc.61929 Transcribed locus, strongly similar to XP_003131832.1 PREDICTED: nuclear speckle splicing regulatory protein 1-like [Sus scrofa].
4 6329 Ssc.43634 Transcribed locus, strongly similar to NP_002887.2 RNA-binding protein 4 isoform 1 [Homo sapiens].
4 6329 Ssc.43281 Transcribed locus, moderately similar to XP_002945200.1 PREDICTED: ribosomal RNA large subunit methyltransferase N-like [Xenopus (Silurana) tropicalis].
4 6329 Ssc.43255 Transcribed locus.
4 6329 Ssc.43243 Transcribed locus, strongly similar to NP_001164108.1 SLIT-ROBO Rho GTPase-activating protein 2 isoform c [Homo sapiens].
4 6329 Ssc.43241 Transcribed locus, strongly similar to XP_003481392.1 PREDICTED: hypothetical protein LOC100737583 [Sus scrofa].
4 6329 Ssc.43236 Fas (TNFRSF6) binding factor 1.
4 6329 Ssc.41936 Transcribed locus, weakly similar to XP_003390961.1 PREDICTED: elongation factor G 2-like, partial [Amphimedon queenslandica].
4 6329 Ssc.31669 Transcribed locus, strongly similar to XP_003359532.2 PREDICTED: transforming acidic coiled-coil-containing protein 1, partial [Sus scrofa].
4 6329 Ssc.2957 Transcribed locus, strongly similar to NP_036980.1 ferritin heavy chain [Rattus norvegicus].
4 6329 Ssc.23777 Transcribed locus, strongly similar to NP_060762.3 glutamyl-tRNA(Gln) amidotransferase subunit A, mitochondrial [Homo sapiens].
4 6329 Ssc.1320 Lectin, galactoside-binding, soluble, 1.
3 4747 Ssc.98899 Transcribed locus, strongly similar to XP_003642851.1 PREDICTED: F-box/LRR-repeat protein 20 isoform 2 [Gallus gallus].
3 4747 Ssc.97443 Transcribed locus, strongly similar to XP_003130598.3 PREDICTED: chaperone activity of bc1 complex-like, mitochondrial-like isoform 1 [Sus scrofa].
3 4747 Ssc.97066 Spectrin beta protein (pAZSP 3' end).
3 4747 Ssc.7335 Transcribed locus, strongly similar to NP_989928.1 eukaryotic translation initiation factor 2 subunit 2 [Gallus gallus].
3 4747 Ssc.7111 Ribonucleotide reductase M2.
3 4747 Ssc.6682 Transcribed locus, strongly similar to NP_005830.2 serine/arginine repetitive matrix protein 1 [Homo sapiens].
3 4747 Ssc.6520 Transcribed locus, strongly similar to XP_002725277.2 PREDICTED: pterin-4-alpha-carbinolamine dehydratase 2 [Rattus norvegicus].
3 4747 Ssc.5928 Transcribed locus, strongly similar to NP_057017.1 coiled-coil domain-containing protein 72 [Homo sapiens].
3 4747 Ssc.54089 Protein disulfide isomerase family A, member 6.
3 4747 Ssc.53780 Ribosomal protein L8.
3 4747 Ssc.52888 Par-6 partitioning defective 6 homolog beta.
3 4747 Ssc.43253 Transcribed locus, weakly similar to NP_001007766.1 NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial [Danio rerio].
3 4747 Ssc.43244 Transcribed locus, strongly similar to XP_003128403.2 PREDICTED: hypothetical protein LOC100153390 [Sus scrofa].
3 4747 Ssc.43232 Transcribed locus.
3 4747 Ssc.37849 Activating transcription factor 4 (tax-responsive enhancer element B67).
3 4747 Ssc.2776 Transcribed locus, strongly similar to NP_001032867.1 dynactin subunit 5 [Rattus norvegicus].
3 4747 Ssc.27275 Apoptosis-related protein.
3 4747 Ssc.25131 H/ACA ribonucleoprotein complex subunit 2-like.
3 4747 Ssc.21125 Oral-facial-digital syndrome 1.
3 4747 Ssc.20849 Transcribed locus, strongly similar to NP_940915.1 PHD finger protein 20-like protein 1 isoform 3 [Homo sapiens].
3 4747 Ssc.20481 Transcribed locus, strongly similar to XP_001927704.4 PREDICTED: pumilio domain-containing protein KIAA0020-like [Sus scrofa].
3 4747 Ssc.19951 C6orf49 mRNA, partial sequence.
3 4747 Ssc.18668 Uncharacterized LOC100152160.
3 4747 Ssc.12177 Uncharacterized protein C21orf59-like.
3 4747 Ssc.11948 Transcribed locus, strongly similar to NP_001073965.2 retrograde Golgi transport protein RGP1 homolog [Homo sapiens].
3 4747 Ssc.10989 Son3 protein.
3 4747 Ssc.10393 Makorin ring finger protein 1.
2 3165 Ssc.96417 NEDD4 family-interacting protein 2-like.
2 3165 Ssc.908 Transcribed locus, strongly similar to XP_428428.3 PREDICTED: LOW QUALITY PROTEIN: 26S proteasome non-ATPase regulatory subunit 11 [Gallus gallus].
2 3165 Ssc.81692 Transcribed locus.
2 3165 Ssc.80753 Transcribed locus.
2 3165 Ssc.74011 Transcribed locus, weakly similar to XP_002161322.1 PREDICTED: hypothetical protein [Hydra magnipapillata].
2 3165 Ssc.6730 Transcribed locus, strongly similar to NP_062132.2 complement component 1 Q subcomponent-binding protein, mitochondrial precursor [Rattus norvegicus].
2 3165 Ssc.6644 Transcribed locus.
2 3165 Ssc.5729 Transcribed locus, strongly similar to NP_000283.1 phosphorylase b kinase regulatory subunit alpha, liver isoform [Homo sapiens].
2 3165 Ssc.55555 ATPase, Ca++ transporting, plasma membrane 1.
2 3165 Ssc.55376 Transcribed locus, strongly similar to NP_033058.2 RNA-binding protein 4 [Mus musculus].
2 3165 Ssc.55223 Transcribed locus, strongly similar to NP_932096.1 cytochrome b-c1 complex subunit 9 [Mus musculus].
2 3165 Ssc.53708 Ribosomal protein L3.
2 3165 Ssc.52880 Transcribed locus, strongly similar to XP_003361280.1 PREDICTED: LOW QUALITY PROTEIN: zinc finger and BTB domain-containing protein 40 [Sus scrofa].
2 3165 Ssc.50004 Tight junction protein 2 (zona occludens 2).
2 3165 Ssc.4908 Mitochondrial ribosomal protein S11.
2 3165 Ssc.4589 PRELI domain containing 1.
2 3165 Ssc.4428 Transcribed locus, strongly similar to NP_001026637.1 transmembrane protein 11, mitochondrial [Gallus gallus].
2 3165 Ssc.43317 Transcribed locus.
2 3165 Ssc.43237 Transcribed locus, strongly similar to NP_054740.3 afadin- and alpha-actinin-binding protein isoform 1 [Homo sapiens].
2 3165 Ssc.43229 Transcribed locus, strongly similar to XP_003132814.3 PREDICTED: hypothetical protein LOC100513760 [Sus scrofa].
2 3165 Ssc.43222 Transcribed locus, strongly similar to NP_036760.1 protein kinase C gamma type [Rattus norvegicus].
2 3165 Ssc.42728 Polo-like kinase 3.
2 3165 Ssc.41966 Transcribed locus, strongly similar to NP_036222.3 microtubule-actin cross-linking factor 1 isoform a [Homo sapiens].
2 3165 Ssc.41951 Transcribed locus.
2 3165 Ssc.41849 Transcribed locus.
2 3165 Ssc.41809 Transcribed locus, strongly similar to NP_001070011.1 protein regulator of cytokinesis 1 [Bos taurus].
2 3165 Ssc.4094 Mitochondrial ribosomal protein L55.
2 3165 Ssc.36628 Transcribed locus, strongly similar to NP_008646.1 cytochrome b [Sus scrofa].
2 3165 Ssc.32154 Transcribed locus, strongly similar to NP_002681.1 DNA polymerase beta [Homo sapiens].
2 3165 Ssc.31505 Transcribed locus, strongly similar to NP_032236.1 histone H3.3 [Mus musculus].
2 3165 Ssc.29975 Transcribed locus.
2 3165 Ssc.2922 RNA-binding protein 40-like.
2 3165 Ssc.28982 Transcribed locus.
2 3165 Ssc.2647 Adiponectin receptor 2.
2 3165 Ssc.26446 Transcribed locus, strongly similar to NP_001026322.1 methionine aminopeptidase 1 [Gallus gallus].
2 3165 Ssc.20133 Thy-1 cell surface antigen.

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Source: NCBI UniGene

EST Sequences

1,264 EST sequences from this library have been submitted to the public sequence database as of 19-Jun-2012.

Source: NCBI GenBank

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

Keywords

  • embryonic tissue
  • pre-implantation embryo

Source: NCBI Clone Registry



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