Characterization of the OmyY1 Region on the Rainbow Trout Y Chromosome
Table 2
List of predicted nonrepetitive transcribed genes in rainbow trout physical map contig #6256 with corresponding EST’s in at least one database. EST designations in bold had the highest homology to OmyY1 linked sequence, and those sequences were used for homology and coverage analyses.
Gene name
4 × 44 K salmonid oligo array designation
cGRASP EST cluster contig annotation
GenBank Annotation
Miller draft rainbow trout genome scaffold
Miller scaffold homology (base pair identities)
Coverage in Miller scaffold
OmyY1 contig (Illumina unless noted)
OmyY1 contig homology (base pair identities)
Coverage within OmyY1 contig
PCR amplification in BAC clone
Transcribed gene in OmyY1 contig?
Oncorhynchus mykiss sdY
AB626896.1
n/a
n/a
n/a
454 contig_3
3270/3273
100%
143K08/223F06
Yes
F-Box/WD repeat containing protein 2 (FBXW2)
C262R066/ C179R024
Contig53026
MMSRT112A/ 121C (overlap)
2319/2326
100%
Contig_2
2319/2326
100%
RT450D22/ RT492A21
Yes
Unknown (Some homology to laminin subunit beta-1-like)
omyk-BX860091
MMSRT112A/ 121C (overlap)
747/778
100%
Contig_2
747/778
100%
Likely
Na/K/2Cl co-transporter (nkcc1a)
C029R137
omyk-CR375193
MMSRT112A
832/843
100%
Contig_2
832/843
100%
RT450D22
Yes
Oocyte protease inhibitor-1 (opi-1)
Contig59765
MMSRT010A/ 121C
919/940, 883/906
97%, 94%
Contig_2
883/906
94%
Likely in MMSRT010A scaffold
Unknown
omyk-CB488087
MMSRT010A/ 121C
315/315, 311/315
100%, 100%
Contig_2
311/315
100%
Likely in MMSRT010A scaffold
Unknown (Some homology to Sec16A)
Contig22207
MMSRT104C
1193/1197
100%
Contig_28
1193/1197
100%
Yes
cAMP-responsive element-binding protein 3-like protein 4 (cr3l4)
