Table 3.
Largest EST Clusters in Select Single-Tissue, Nonnormalized Atlantic Salmon Libraries/Library Groupsa
| Tissue (library)a | Total ESTs | ESTs in cluster | BLASTbE-value | Length (% identity)c | GenBank hit acc. no.b | Gene identification (species) of top BLAST hitb |
|---|---|---|---|---|---|---|
| Brain | 1161 | 23 | (X) 1.5E-60 | 113 (95.6%) | P28770 | Ependymin I (Oncorhynchus mykiss) |
| 19 | (X) 2.9E-128 | 221 (99.5%) | P28772 | Ependymin II (Salmo salar) | ||
| 17 | (X) 7.2E-10 | 119 (29.1%) | 062680 | Membrane attack complex inhibition factor (Sus scrofa) | ||
| 15 | (X) 5.6E-6 | 97 (32.9%) | P06906 | Myelin basic protein (Pan troglodytes) | ||
| 8 | n/ad | n/ad | n/ad | unknown | ||
| Esophagus | 749 | 88 | (X) 1.3E-24 | 111 (58.9%) | BAA86981 | Novel member of chitinase family (Homo sapiens)e |
| 32 | (X) 4.8E-59 | 315 (59.9%) | BAA86981 | Novel member of chitinase family (H. sapiens)e | ||
| 9 | (X) 4.7E-58 | 154 (75.3%) | AAD56283 | Pepsinogen A form IIa (Pseudopleuronectes americanus) | ||
| 8 | (X) 0 | 461 (99.5%) | AAG38613 | Elongation factor 1 α (S. salar) | ||
| 8 | (X) 9.3E-83 | 175 (97.7%) | CAA37852 | Creatine kinase (O. mykiss) | ||
| Gill | 2308 | 14 | (X) 1.6E-64 | 116 (98.2%) | AAG17525 | β-2 microglobulin (S. salar) |
| 13 | (X) 5.6E-132 | 244 (100%) | CAA49726 | MHC Class II β chain (S. salar) | ||
| 11 | (X) 6.6E-22 | 62 (62.9%) | AAG30024 | C-type lectin 2-1 (O. mykiss) | ||
| 10 | (N) 0 | 346 (99.1%) | BG936357 | unknown spleen clone SS1-0729 (S. salar) | ||
| 9 | (N) 0 | 876 (98.4%) | BG934637 | unknown kidney clone SK1-0954 (S. salar) | ||
| Head kidney (lower MW) | 784 | 57 | (X) 1.2E-79 | 148 (94.5%) | CAA65945 | β globinA (S. salar)f |
| 53 | (X) 1.1E-83 | 148 (100%) | CAA49580 | β globinB (S. salar)f | ||
| 41 | (X) 2.0E-82 | 148 (97.9%) | CAA65945 | β globinC (S. salar)f | ||
| 7 | (X) 1.1E-83 | 148 (100%) | CAA65945 | β globinD (S. salar)f | ||
| 7 | (X) 4.6E-66 | 119 (100%) | CAA65944 | α globin (S. salar) | ||
| Head kidney (higher MW) | 867 | 24 | (X) 9.4E-146 | 252 (100%) | 042161 | β actin (S. salar) |
| 5 | (X) 0 | 443 (96.2%) | A46533 | Immunoglobulin heavy chain constant region (S. salar)g | ||
| 4 | (X) 1.1E-141 | 287 (100%) | S21175 | dnaK-type molecular chaperone hsc71 (O. mykiss) | ||
| 4 | (X) 0 | 443 (100%) | A46533 | Immunoglobulin heavy chain constant region (S. salar)g | ||
| 4 | (N) 0 | 695 (99.7%) | AJ424426 | unknown kidney clone k09F03 (S. salar) | ||
| Mixed gut (stomach, mid, & hind) | 3753 | 47 | (X) 1.9E-85 | 239 (79.1%) | JH0472 | Apolipoprotein A-I (S. salar) |
| 20 | (X) 0 | 330 (97.8%) | AAK69705 | Procathepsin B (O. mykiss) | ||
| 18 | (X) 3.8E-34 | 76 (92.1%) | CAC45057 | Type II keratin E2 (O. mykiss) | ||
| 17 | (X) 0 | 461 (99.5%) | AAG38613 | Elongation factor 1 α (S. salar) | ||
| 16 | (X) 4.8E-89 | 325 (51.6%) | CAC87888 | Toad pancreatic chitinase (Bufo japonicus) | ||
| Ovary | 2664 | 13 | (X) 1.2E-48 | 139 (59.7%) | AAO43606 | Serum lectin isoform 2 (S. salar)h |
| 11 | (X) 4.3E-48 | 139 (59.1%) | AAO43606 | Serum lectin isoform 2 (S. salar)h | ||
| 6 | n/ad | n/ad | n/ad | unknown | ||
| 5 | n.ad | n/ad | n/ad | unknown | ||
| 5 | (X) 1.5E-16 | 127 (41.0%) | P56733 | Avidin-related protein 3 (Gallus gallus) | ||
| Pituitary Gland | 2883 | 123 | (N) 0 | 545 (98.5%) | X84787 | Prolactin (S. salar) |
| 96 | (N) 6.5E-166 | 1084 (94.9%) | X69809 | Proopiomelanocortine B (O. mykiss) | ||
| 48 | (N) 5.9E-73 | 173 (94.7%) | X69808 | Proopiomelanocortine A (O. mykiss) | ||
| 44 | (X) 1.0E-26 | 50 (100%) | AAA49558 | Growth hormone (S. salar) | ||
| 43 | (X) 3.1E-60 | 114 (100%) | AAA49407 | Gonadotropin-I α (Oncorhynchus keta) | ||
| Pyloric caeca (lower MW) | 329 | 8 | (X) 5.1E-123 | 262 (98.0%) | AAA88542 | Apolipoprotein A-I (S. salar)i |
| 7 | (X) 9.9E-67 | 268 (49.2%) | CAB65320 | Apolipoprotein E (O. mykiss) | ||
| 5 | (X) 9.7E-55 | 254 (46.0%) | BAB40965 | 28 kD-1e apolipoprotein (Anguilla japonica) | ||
| 5 | (X) 8.1E-27 | 129 (44.1%) | AAF61069 | Galectin (Paralichthys olivaceus) | ||
| 4 | (X) 3.9E-100 | 238 (92.4%) | JH0472 | Apolipoprotein A-I (S. salar)i | ||
| Pyloric caeca (higher MW) | 716 | 16 | (X) 1.2E-48 | 168 (58.2%) | AAG53688 | Selenoprotein Pa (Danio rerio) |
| 10 | (X) 4.5E-141 | 286 (86.4%) | AAG02508 | MHC Class I heavy chain (O. mykiss) | ||
| 8 | (X) 1.4E-32 | 122 (53.2%) | AAL85339 | Meprin A α; PABA peptide hydrolase (H. sapiens) | ||
| 7 | (N) 2.0E-12 | 115 (84.3%) | BG935597 | unknown liver clone SL1-0959 (S. salar) | ||
| 6 | (X) 3.8E-34 | 76 (92.1%) | CAC45057 | Type II keratin E2 (O. mykiss) |
Compiled using the August 16, 2003 version of the GRASP EST database and excluding ribosomal and mitochondrial EST clusters. For notes on libraries and library groups, see Table 2.
Most significant BLASTIN (N) or BLASTX (X) hit is reported. BLASTX hit reported if top BLASTN hit not associated with a named gene.
Extent of BLAST hit aligned region, and percent identity over the aligned region. Length (and percent identity) refers to amino acids if BLASTX reported, and nucleic acids if BLASTN reported.
Not applicable, as there are no significantly similar (E < 10-5) sequences in non-redundant GenBank nucleotide or amino acid sequence databases.
The C-terminal 111 amino acids of the aligned translations of these 2 EST contigs are 85.6% identical, indicating 2 distinct forms of the gene.
The aligned translations of β globins A, B, and C differ from the translation of β globin D at 8 of 148 (94.6% identity), 2 of 148 (98.6% identity), and 3 of 148 (98.0% identity) residues, respectively.
The aligned translations of these two EST clusters differ at 17 of 443 residues (96.2% identity).
The aligned translations of these two EST clusters differ at four of 139 residues (97.1% identity). They are ∼60% identical, at the amino acid level, to a third ovary lectin cluster containing four ESTs (not shown in table).
The aligned translations of these two EST clusters (238 amino acids) are 84.0% identical.