Finding Selenoproteins in

Parus major


Llauradó M, Miquel M, Solà M.

  • ABSTRACT
  • INTRODUCTION
    • Selenoproteins
    • Synthesis of selenoproteins
    • Selenoprotein families
    • Parus major
  • MATERIALS & METHODS
    • Genome selection
    • Obtention of queries
    • Queries selection
    • Region of interest extraction
    • Exonerate/GeneWise
    • SECIS elements
    • Automatization process
  • RESULTS
    • Selenoproteins
    • Machinery
  • DISCUSSION
  • CONCLUSION
  • REFERENCES
  • ACKNOWLEDGEMENTS
  • CONTACT US





RESULTS

The next table shows our results regarding the presence of genes encoding for selenoproteins in the Parus major genome.

Selenoproteins

Family Protein ID BLAST Scaffold Exonerate Gene location T-Coffee Alignment Seblastian SECIS
Sel15 Sel15 SPP00001043_2.0 CM003718.2 16502160-16522708 Sec-Sec
Pos: 68
DIO DIO1 SP00001030_2.0 CM003715.1 51076976-51077473 (-) Sec-Sec Pos: 125
DIO2 SPP0000203_2.0 CM003715.1
CM003718.2
41683167-41694923 (-)
26378673-26380350 (-)
Sec-Sec Pos: 132
Sec-Sec Pos: 132

DIO3 SPP0000203_2.0 CM003715.1
CM003718.2
41683167-41694923 (-)
26378673-26380350 (-)		 Sec-Sec Pos: 132
Sec-Sec Pos: 132

GPx GPx3 SPP00001033_2.0 CM003723.1 6318505-6319524 (-) Sec-Sec Pos: 36
SelI SelI SPP00001048_2.0 CM003710.1
CM003736.1
CM003714.1
SelK SelK SPP00001044_2.0 CM003722.1 6871848-6874402 (-) Sec-Sec Pos: 93
SelN SelN SPP00001049_2.0 CM003732.1 25828-38381 (+) Sec-Sec Pos: 400
SelO SelO(1) SPP00001050_2.0 CM003714.1 18647850-18653164(+) Sec-Sec Pos: 364
SelO(3) SPP00001052_2.0 CM003714.1 18641791-18653164(+) Sec-Sec Pos: 630
SelP SelP(1) SPP00001054_2.0 CM003718.2
CM003740.1
21852842-21864716 (-)
13447051-13450224 (-)
Multiple Sec

SelP(2) SPP00001055_2.0 CM003740.1
CM003718.2
13400940-13450317 (-)
21863208-21864758 (-)
Sec-Sec Pos: 55
Sec-Sec Pos: 39

SelT SelT SPP00001059_2.0 CM003719.1 24733340-24783451 (-) Sec-Sec Pos: 41
SelU SelU1 SPP00001060_2.0 CM003716.2 17811084-17814856 (+) Sec-Sec Pos: 88
TXNRD TXNRD SPP00001061_2.0 CM003714.1
CM003725.1
52413690-52434923
7361031-7371968
Sec-Sec Pos: 513
Sec-Sec Pos: 319

TXNRD2 SPP00001062_2.0 CM003725.1
CM003714.1
7341820-7371969
52420613-52424682
Sec-Sec Pos: 513
Sec-Sec Pos: 345

TXNRD3 SPP00001063_2.0 CM003722.1
CM003725.1
10204350-10220494
7361031-7371969
Sec-Sec Pos: 604
Sec-Sec Pos: 325



Return

Machinery

This table shows the presence of the genes encoding the machinery proteins.

Family Protein ID BLAST Scaffold Exonerate Gene location T-Coffee
eEFsec eEFsec SPP00001064_2.0 CM003722.1 9037272-9201435 (-)
GPx GPx7 SPP00001034_2.0 CM003718.2
CM003740.1
CM003722.1

25661213-25653369(-)
16443643-16445924(+)
6466180-6466320(+)

GPx8 SPP00001035_2.0 CM003740.1
CM003718.2
CM003722.1

16443643-16445918(+)
25651212-25653363(+)
6466180-6466314(+)

MsrA MsrA SPP00001036_2.0 CM003711.1 110712620-110728407(-)
MSRB MSRB1 SPG00000952_2.0 CM003724.1 14785400-14786173(-)
MSRB3 SPG00000953_2.0 CM003714.1
CM003710.1
31947720-31991589(+)
17493801-17493893(-)
PSTK PSTK SPP00001065_2.0 CM003716.2 30190025-30193073 (+)
SBP2 SBP2(1) SPP00001037_2.0 CM003720.1
CM003740.1
SBP2(2) SPP00001038_2.0 CM003740.1
CM003720.1
40465249-40483332(+)
9811238-9817756(-)
SBP2(3) SPP00001039_2.0 CM003720.1 9811097-9811315(-)
SECp43 SECp43 SPP00001066_2.0 CM003732.1
CM003710.1
CM003735.1
CM003711.1
SecS SecS(1) SPP00001041_2.0 CM003712.1 50928949-50935813(+)
SecS(2) SPP00001042_2.0 CM003712.1 50926536-50946093(+)
SelH SelH SPP00001047_2.0
SelK SelK(2) SPP00001045_2.0
SelK(3) SPP00001046_2.0
SelO SelO(2) SPP00001051_2.0 CM003710.1
CM003714.1
16118970-16138256(+)
18642151-18647978(+)
SelO(4) SPP00001053_2.0 CM003714.1
CM003710.1
18641860-18643715(+)
16118967-16119381(+)
SEPHS SEPHS SPP00001040_2.0 CM003714.1 5925269-5944698(-)
↑