Table 4 Y-linked gene annotation.

From: Computational identification of Y-linked markers and genes in the grass carp genome by using a pool-and-sequence method

Gene symbol

Scaffold

Ref-Seq (EST) homolog

Amino acid identity with ref

Female-gc-assembly homolog

Domain

Putative function

nsb-y1

Sca704

XP_016118179.147

76%

Yes

Fibronectin type-III, SPRY domains

Microtubule organization and stabilization25

nsb -Y2

Sca811

   

nsb -Y3

 

nacht-y1

Sca704

XP_016362555.147

69%

Yes

NACHT, LRR and PYD domains

Innate immunity and inflammation26

nacht-y2

Sca713

   

rdp-y1

Sca704

XP_014000594.148

71%

Yes

Rve,

RNA-directed DNA polymerase27

RVT_1

rdp-y2

Sca713

rdp-y3

Sca811

rdp-y4 a

Sca971

retro-y1 retro-y2

Sca704

XP_00785969949

74%

Yes

Undefined

Development of the placenta28

un-y1 a

Sca713

CT602791.2

84%

No

Undefined

Undefined

ubq-y a

Sca811

XP_016405694.1

98%

Yes

IBR

Probable E3 ubiquitin-protein ligase29

GW811780.150 EE398743.1

93%

un-y2 a

Sca971

GT224642.150 GR943694.1 GW812769.1 DT343035.1 EG534739.1

95%

No

Undefined

Undefined

  1. Notes: In the cases where the homolog is an annotated gene, we used the homolog gene name as an identifier, otherwise we used the “un-y” as an identifier. Amino acid identity with ref were computed by comparing sequences directly.
  2. aGenes in bold were selected for RT-PCR experiments, as shown in Fig. 6.
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