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)
|
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↵a 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.
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↵b Most significant BLASTIN (N) or BLASTX (X) hit is reported. BLASTX hit reported if top BLASTN hit not associated with a named gene.
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↵c 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.
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↵d Not applicable, as there are no significantly similar (E < 10-5) sequences in non-redundant GenBank nucleotide or amino acid sequence databases.
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↵e 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.
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↵f 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.
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↵g The aligned translations of these two EST clusters differ at 17 of 443 residues (96.2% identity).
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↵h 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).
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↵i The aligned translations of these two EST clusters (238 amino acids) are 84.0% identical.
