Download Supplemental Figure Legends Fig. S1. Gene synteny between IFNd

Supplemental Figure Legends
Fig. S1. Gene synteny between IFNd and CD79b in zebrafish and Atlantic
salmon. The salmon IFNd gene was identified by TBLASTN in the genomic
sequence with GenBank Accession no. AGKD01088706, which was annotated
(GenBank accession no. BK008598) using the Fgenesh program
(http://softberry.com). CD79b was found in the same sequence. Zebrafish IFNd/
φͶ (GenBank GeneID:100302089) was found linked to a gene (GenBank
accession no. LOC100329481), which was identified as CD79b antigen
(immunoglobulin-associated beta) by BLAST search. Other genes in the same cluster
are scn4αα (sodium channel, voltage-gated, type IV, alpha, a) and ghrhr2 (growth
hormone-releasing hormone receptor second type).
Fig. S2. Comparison of amino acid sequences of full length IFNa, IFNb, IFNc
and IFNd translated from cDNA.
A. Multiple alignment of IFNa1 (AY216594), IFNb (JX524152), IFNc (JX524153)
and IFNd (JX524151) by the Clustal W program. Shaded amino acids show identity
to the consensus sequence. Positions of cysteines, which are putatively involved in
disulphide bridges are marked with stars. Exon boundaries are indicated with arrows.
B. Percentage amino acid identity between the sequences. The IFNb cloned in the
present work is most similar to the sequence encoded by the IFNb2 gene (99.5%) and
the cloned IFNc is most similar to the sequence encoded by the IFNc1 gene (99.5%)
where the genomic sequences are described by Sun et al. (8).
Fig. S3. Atlantic salmon type I IFN promoter regions.
A. Putative IRF binding elements in the Atlantic salmon IFNd promoter region.
Potential transcription factor binding sites in the 1000 nucleotide sequence upstream
of the open reading frame of the IFNd gene (GenBank accession no. BK008598) was
identified by the MatInspector program (www.genomatix.de). Two IRF-binding
motifs and two TATA-boxes were identified as indicated by grey shading, but no Ǧ
κ„‹†‹‰•‹–‡•™‡”‡‹†‡–‹ˆ‹‡†ǤŠ‡’”‡•‡…‡‘ˆ–™‘Ǧ„‘š‡•ƒ‡•–Š‡
–”ƒ•…”‹’–‹‘•–ƒ”–•‹–‡—…‡”–ƒ‹ƒ•ƒŽ•‘•‡‡‹–Š‡’”‘‘–‡”‘ˆ–Š‡”ƒ‹„‘™
–”‘—–†‰‡‡ȋͳͲȌǤ B. Overview of putative IRF and NF-B binding elements in
the proximal promoter regions of IFNa1, IFNb2, IFNc1 and IFNd. Potential
transcription factor binding sites in the 500 nucleotide sequence upstream of the open
reading frame of the genes were identified by the MatInspector program as described
by Sun et al. (8). The specific IRF binding sites detected by the MatInspector program
is based on sequence preferences of mammalian IRFs and are merely shown to
illustrate differences in IRF binding sites. (+) and (-) indicate the DNA-strand for the
binding sites.
Supplemental figure 1
IFN 4
CD79b
IFNd
CD79b
ghrhr2
scn4 zebrafish Chr. 12
Atl. salmon AGKD01088706
Supplemental figure 2
A
*
*
*
*
B
IFNd
IFNc
IFNb
37.4%
25.3%
30.4%
IFNb
30.2%
30.7%
-
IFNc
25.6%
-
-
IFNa1
Supplemental figure 3
A
TTTTCGATCTGCTTCAGATGATATTCATGATGCCACACAGCCTGAGGCTCAAATCAAAGT
GTATTTGTCATGTGCGCCGAATTCAACAACCTTACAGTGAAATGCTTACTTACAGGCAAT
AACCAATAGTGCAAAAAAAGGTATTAGGTGAACAATAGGTAAGTAAAGAAATAAAAAGAA
IRF-E
AGTGAAAAATAACACACAATGCAAATAGTCCGGGTAGCCATTTGATTACCTGTTCAGGAG
TCTTGCTTGGGGGTAAAAACTGTTGAGAAGCCTTTTTGTCCTAGACCTGGCACTCCGGTA
CCGCTTGTCATGCGATAGTAGATAAGAACATTCTATGACTGGGGTGGTTGGTTCTATTAA
GTAAAAAAAAAAATAAAATAGGCCTACGTTTTTTAAAATTAATAACATTATGGGCTTAAT
ATAAATAATATATTTTTGTTCAGTGGTTAAAGTAGCCCAATTTCAATGGCTACTAAATGA
AATAAAACAAATAGGCTAGTTAAAATCATATTGAATAGCCTACATTAATATTTACAGAAA
ATGACTCGGAAAAAATACATGTAAACGAAGCCTACAGAAAATTGCAAACAATTGCAATTT
ATAGCCTCAGCTCAGGCCATGCAAATCGGAAAAAGTGTCTCAAACATGTTTAGATGCGTT
CTAGCGTCCTATTCAGCTGGCTTGGTATGACATTTACAGTAGCCTATTCGATGTGTGTGA
ATATTTCTAAAAATAATACATTGACTTTCCAAACACTGTAAAACATAAACGAATATAAAT
IRF-E
GTCGTGGTAAATATGTGCTCTTAATTGTTTTCCAACCGTCGCAGGTACGGAAAGTGAAAC
AGGTATTGGCTTCACCCTATTCGTTTTGAGAAACTATAAAGGTCGCATTCCTACAGGTAA
TATGGTATACCTAAACATTAGTAACAAGACAGTTACAATTGCCTATTTTGTATTACAAAG
ATATACTTTTTTTGCTCCACGTCTTGTTTTCATTACCAACATG
-941
-881
-821
-761
-701
-641
-581
-521
-461
-401
-341
-281
-221
-161
-101
-41
B
IRF7(+)
NF-kB
IRF3(-)
TATA
IRF7(-)
IFNa1
IRF2(+)
IRF7(+)
TATA
IFNb
IRF3(-)
IRF1(+)
IRF2(-)
IFNc
TATA
IRF2(+) TATA
IFNd
- 500
- 400
- 300
- 200
nucleotides upstream of ATG
-100
-1