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An organized view of the transcripome



Library:20911 (dbEST ID)

NICHD_XGC_tropLimb_m

Library Description

Organism:Xenopus (Silurana) tropicalis
Strain:TGA IC
Developmental stage:Metamorphic
Tissue:Limb
Vector:pCS107
Cloning site 1:SalI
Cloning site 2:NotI
Lab host:ElectroMAX DH10B T1 Phage Resistant cells

This library was made from dT primed cDNA and cloned into pCS107 vector. The work was done at DOE Joint Genome Institute. Poly A RNA were primed with 5' GACTAGTTCTAGATCGCGAGCGGCCGCCCTTTTTTTTTTTTTTT 3'. CDNA were ligated to SalI adapter (5' TCGACCCACGCGTCCG and 5'CGGACGCGTGGG), digested with NotI, size fractionated in 1.1% agarose gel electrophoresis and ligated into NotI and SalI digested pCS107 vector.

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

Gene Content Analysis

15,402 ESTs from this library were grouped into 3,138 UniGene entries (putative genes) [UniGene build #52, 23-Feb-2013]. EST counts for each entry may be used to calculate an approximate expression level in transcripts per million (TPM).

ESTs TPM   UniGene Entry
480 31165 Str.65949 Uncharacterized LOC496414.
355 23049 Str.6694 Parvalbumin.
266 17270 Str.65307 Myosin light chain, phosphorylatable, fast skeletal muscle.
210 13635 Str.65118 Ferritin, heavy polypeptide 1.
206 13375 Str.67961 Creatine kinase, muscle.
205 13310 Str.66708 Myosin, light chain 1, alkali; skeletal, fast.
195 12661 Str.63027 Parvalbumin, gene 1.
180 11687 Str.68815 Actin, alpha 1, skeletal muscle.
167 10843 Str.66747 Actin, alpha, cardiac muscle 1.
160 10388 Str.11303 Collagen, type 1, alpha 2.
118 7661 Str.5739 Ribosomal protein S3.
117 7596 Str.5631 Troponin C type 2 (fast).
114 7402 Str.45491 Transcribed locus, strongly similar to NP_001017795.1 eef1a1b gene product [Danio rerio].
113 7337 Str.55829 Myosin, heavy chain 3, skeletal muscle, embryonic.
109 7077 Str.64787 Ribosomal protein S2.
98 6363 Str.5646 Ribosomal protein, large, P0.
94 6103 Str.41468 Troponin I type 2 (skeletal, fast).
93 6038 Str.84743 Ribosomal protein L10.
93 6038 Str.24478 Myosin, heavy chain 7, cardiac muscle, beta.
92 5973 Str.20603 Keratin 5, gene 4.
91 5908 Str.65140 Ribosomal protein L10a.
91 5908 Str.6170 Secreted protein, acidic, cysteine-rich (osteonectin).
88 5714 Str.52164 Ribosomal protein L7.
87 5649 Str.40721 Ribosomal protein S8.
84 5454 Str.5620 Troponin T type 3 (skeletal, fast).
82 5324 Str.52469 Ribosomal protein S3A.
80 5194 Str.5526 Tropomyosin 2 (beta).
79 5129 Str.8252 Ribosomal protein L7a.
75 4869 Str.6969 Ribosomal protein S6.
73 4740 Str.65146 Ribosomal protein S4, X-linked.
73 4740 Str.643 Ribosomal protein L3.
73 4740 Str.47263 Ribosomal protein S5.
69 4480 Str.37180 Eukaryotic translation elongation factor 1 alpha 1.
68 4415 Str.1774 Ribosomal protein L6.
62 4025 Str.54515 Collagen, type II, alpha 1.
61 3961 Str.46989 Ribosomal protein L13a.
60 3896 Str.7118 Ribosomal protein L8.
60 3896 Str.66716 ATPase, Ca++ transporting, cardiac muscle, fast twitch 1.
60 3896 Str.66310 Ribosomal protein S9.
60 3896 Str.62377 Ribosomal protein L9.
59 3831 Str.47654 Ribosomal protein L15.
59 3831 Str.20174 Ribosomal protein L13.
58 3766 Str.64795 Tumor protein, translationally-controlled 1.
58 3766 Str.33529 Ribosomal protein L18a.
58 3766 Str.32162 Eukaryotic translation elongation factor 2, gene 1.
54 3506 Str.6701 Guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1.
54 3506 Str.6666 Actin, gamma 1.
52 3376 Str.68478 Calsequestrin 1 (fast-twitch, skeletal muscle).
52 3376 Str.36098 Ribosomal protein L17.
51 3311 Str.68813 Transcribed locus, strongly similar to NP_001121485.1 LOC100158585 gene product [Xenopus (Silurana) tropicalis].
51 3311 Str.41589 Peptidylprolyl isomerase A (cyclophilin A).
46 2987 Str.84923 Keratin 6.
46 2987 Str.21675 Myelin protein zero.
45 2922 Str.64764 Transcribed locus, strongly similar to NP_001079367.1 nuclease-sensitive element-binding protein 1 [Xenopus laevis].
45 2922 Str.26251 Cold inducible RNA binding protein.
44 2857 Str.68855 Uncharacterized LOC100158585.
44 2857 Str.6703 Ribosomal protein SA.
44 2857 Str.65589 Ribosomal protein L18.
42 2727 Str.75415 Keratin, type II cytoskeletal 5-like.
42 2727 Str.68861 Collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV, autosomal dominant).
42 2727 Str.68467 Tropomyosin 3.
40 2597 Str.47464 Eukaryotic translation elongation factor 1 gamma.
40 2597 Str.20527 Actin, alpha sarcomeric/cardiac.
39 2532 Str.62376 Ribosomal protein S7.
33 2143 Str.68636 Actinin, alpha 3.
33 2143 Str.44232 Glyceraldehyde-3-phosphate dehydrogenase.
33 2143 Str.27192 Ribosomal protein, large, P1.
31 2013 Str.69009 Myosin-4-like.
31 2013 Str.47152 Ribosomal protein S10.
30 1948 Str.10997 Follistatin-like 1.
29 1883 Str.69076 Collagen alpha-1(II) chain-like.
29 1883 Str.5826 NME/NM23 nucleoside diphosphate kinase 2.
29 1883 Str.49960 Keratin-3, type I cytoskeletal 51 kDa-like.
28 1818 Str.65738 Ribosomal protein L19.
28 1818 Str.65054 Aldolase A, fructose-bisphosphate.
28 1818 Str.60300 Uncharacterized protein MGC75752.
28 1818 Str.45917 Triosephosphate isomerase 1.
27 1753 Str.6036 Ferritin mitochondrial.
27 1753 Str.36828 Ribosomal protein L11.
26 1688 Str.58346 Decorin.
26 1688 Str.35930 Uncharacterized LOC549476.
25 1623 Str.2884 Nascent polypeptide-associated complex alpha subunit.
24 1558 Str.17078 Ribosomal protein L12.
23 1493 Str.68526 Cold shock domain protein A.
23 1493 Str.41716 Tropomyosin 1 (alpha).
23 1493 Str.20553 Ribosomal protein L5.
22 1428 Str.8396 Eukaryotic translation elongation factor 1 beta 2.
22 1428 Str.68745 Collagen, type V, alpha 3.
22 1428 Str.55489 Ribosomal protein S27a.
22 1428 Str.47687 Y box binding protein 1.
21 1363 Str.84724 Transcribed locus, strongly similar to XP_002940696.1 PREDICTED: keratin, type I cytoskeletal 47 kDa-like [Xenopus (Silurana) tropicalis].
21 1363 Str.6222 Annexin A2.
20 1299 Str.68996 Keratin-3, type I cytoskeletal 51 kDa-like.
20 1299 Str.66839 Spondin 2, extracellular matrix protein.
20 1299 Str.65317 Ribosomal protein S15.
20 1299 Str.46761 Collagen alpha-1(VI) chain-like.
19 1234 Str.75428 Ribosomal protein S24.
19 1234 Str.65384 Transcribed locus, strongly similar to NP_033739.1 actin, cytoplasmic 2 [Mus musculus].
19 1234 Str.43578 Vimentin.
19 1234 Str.20 LSM12 homolog.

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Source: NCBI UniGene

EST Sequences

15,889 EST sequences from this library have been submitted to the public sequence database as of 23-Feb-2013.

Source: NCBI GenBank

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

Keywords

  • limb
  • metamorphosis
  • non-normalized
  • bulk

Source: NCBI Clone Registry



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