Skip to main content

Table 3 Selected cDNAs1 from the liver reverse (enriched for genes down-regulated by heat-shock) SSH library representing immune/stress related genes

From: Heat-shock responsive genes identified and validated in Atlantic cod (Gadus morhua) liver, head kidney and skeletal muscle using genomic techniques

   

BLASTx identification4 of selected transcripts

 

Contig or Sequence ID (Accession Number)

QPCR

# ESTs

Gene Name [Species of best BLASTx Hit]

%ID (aa length of align.)

E-value

Gene Ontology or function of putative orthologue7

154.C1 (ES783183)

Not done

3

Map4k45,6 [Mus musculus]

92% (24/26)

4e-05

Protein amino acid phosphorylation (BP)*

111.C1 (FL634330)

Not done

2

Glutathione peroxidase [Xenopus tropicalis]

55% (30/54)

1e-11

Response to oxidative stress (BP)*

121.C1 (ES782223)

Not done

2

Tetraspanin-6 [Salmo salar]

96% (28/29)

9e-09

G-protein coupled receptor protein signaling pathway (BP)*

129.C1 (ES782343)

Not done

2

Nuclear factor interleukin-3 regulated [Danio rerio]

73% (31/42)

6e-08

Immune response (BP)*

143.C1 (ES782977)

Not done

2

Chaperonin containing TCP1- subunit 34,6 [Salmo salar]

94% (127/134)

7e-67

Protein folding (BP)*

128.C1 (ES782638)

Fig.6B2

2

Nuclear protein 15,6 [Salmo salar]

50% (35/70)

4e-11

Cell growth (BP)*, Acute inflammatory response (BP)*

168.C1 (ES782218)

Fig.6C2

2

Alpha-1-microglobulin/bikunin precursor [Oncorhynchus mykiss]

55% (21/38)

1e-04

Serine-type endopeptidase inhibitor activity (MF), Endopepitidase (MF), Transporter activity (MF)

69.C1 (ES783083)

Fig.6D2

2

Immunoglobulin heavy chain, secretory form5 [Gadus morhua]

97% (137/140)

1e-70

Immune response (BP)*

91.C1 (ES782456)

Not done

2

Lectin [Oncorhynchus mykiss]

48% (25/52)

2e-13

Sugar binding (MF)*

1e08 (ES782565)

Not done

1

Hepcidin precursor5 [Gadus morhua]

98% (78/79)

1e-26

Innate immune response (BP)*

2i08 (ES782607)

Fig.6A2

1

TLR224,6 [Takifugu rubripes]

88% (39/44)

3e-29

Immune response (BP), Inflammatory response (BP)8

7m20 (FL634530)

Not sig.3

1

Interleukin-8 [Melanogrammus aeglefinus]

82% (63/76)

4e-36

Immune response (BP), Cytokine activity (MF)9

7p13 (FL634573)

Not done

1

TNFAIP3 interacting protein 1 [Danio rerio]

86% (74/86)

1e-34

Negative regulation of viral genome duplication (BP)

  1. 1ESTs from the liver reverse library were assembled separately. These cDNAs were not represented by any contig of 2 or more ESTs in any of the 3 forward libraries. For genes represented by multiple contigs in this library, the contig with the highest number of contributing sequences is shown. Possible reasons for the presence of multiple contigs with the same gene name within a given library are provided in the discussion. All SSH contigs and singletons for the liver reverse library, with all BLASTx statistics and GenBank accession numbers, are presented in the Additional file 2, Table S2. The GenBank accession number of one representative EST from each contig is given in this table. The name of this SSH library in the CGP EST database is gmnllrta. Sequence names reflect the plate number and the well number (e.g. 7p13 - plate 7, well p13).
  2. 2These genes showed at least one statistically significant difference between 2 groups and/or time points (e.g. CT at BHS versus CT at CS, or CT at CS versus HS at CS) in at least 1 tissue.
  3. 3This gene was analyzed with QPCR, but the data is not presented because there were no statistically significant differences between groups and/or time-points.
  4. 4Refer to footnote 4 in Table 2.
  5. 5These cDNAs were each represented by one singleton in the liver forward library.
  6. 6Synonyms for protein names were retrieved from the Swiss-Prot Protein Knowledgebase Database http://ca.expasy.org/sprot/: Map4k4: Mitogen-activated protein kinase kinase kinase kinase 4. Chaperonin containing TCP1- subunit 3: CCT3. Nuclear protein 1: Protein p8, Candidate of metastasis 1. TLR22: Toll-like receptor 22.
  7. 7Refer to footnote 7 in Table 2.
  8. 8Other functional annotations associated with this cod EST are: Innate immune response (BP), Receptor activity (MF), Integral part to membrane (CC).
  9. 9Other functional annotations associated with this cod EST are: Extracellular region (CC), Extracellular space (CC).
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us