Gene Search

Vertebrate TimeCapsule

Vertebrate TimeCapsule (VTcap) is a publicly available gene database for investigations aimed at elucidating the evolutionary process of the vertebrate developmental systems. Sequence data derived from large-scale sequencing analyses in emerging model organisms are deposited. The detailed information of the analyses, the BLAST search and a sophisticated keyword search are available in this data base.

VTcap EST Project

The VTcap EST project aims to develop a gene database to represent evolution and development.
The goal of the project is to provide a fundamental database to investigate evolution and development by combination with other environmental data.

Image archive

Polypterus Summary

 

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Species:  Polypterus senegalus
Stage:  fertilized egg - early neurula
Tissue:  whole
cDNA Library Kit: Stratagene ZAP cDNA Synthesis Kit
Cloning Vector: pBluescript SK(-)

Plasmid Amplification: 

GE TempliPhi
Sequence Reaction Chemistory:  ABI BigDye Terminator v.3.1
Sequence Primer:  Forward: T3, Reverse: T7, M13
DNA Sequencer: ABI 3730xl
Sequence Prefix: Pos_gW

 

Sequences Included in database
ESTs are from GRAS EST Project through 12 JUL 2008

  17,110 EST, 5' read
  17,226 EST, 3' read
  10,034 EST both read

  34,336 total sequences
Build Method: Transcript Based

Alignments between all transcript sequences are used to generate clusters of sequences originating from the same gene. However, the obviously redundant sequences (same clone name) are not used.

 

  

Hagfish Summary

 

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Species:  Eptatretus burgeri
   
Stage and Tissue: embryo - whole
cDNA Library Kit: Stratagene ZAP cDNA Synthesis Kit
Cloning Vector: pDNR-LIB
Host: DH10B

Plasmid Amplification: 

GE TempliPhi
Sequence Reaction Chemistory:  ABI BigDye Terminator v.3.1
Sequence Primer:  M13-20
DNA Sequencer: ABI 3730xl
Sequence Prefix: Eb_eW
   
Stage and Tissue: adult - brain
RT Primer: Random hexamer
DNA Sequencer: Roche 454 FLX
Sequence Prefix: Eb_aB_F1
   

 

Sequences Included in database
  4,025 Eb_eW
  157,457 Eb_aB_F1
  23,884 Eb_EST (GenBank EST entries)
  450 Eb_NA (GenBank nucleotide entries)
  1 Eb_mitochondrion (GenBank entry)
  185,817 total sequences
 

Cloudy Dogfish Summary

 

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Species:  Scyliorhinus torazame
   
Stage and Tissue: embryo stage31 - whole
cDNA Library Kit: Stratagene ZAP cDNA Synthesis Kit
Cloning Vector: pBluescript II SK(+)
Host: DH10B

Plasmid Amplification: 

GE TempliPhi
Sequence Reaction Chemistory:  ABI BigDye Terminator v.3.1
Sequence Primer:  Forward: T3, Reverse: T7, M13
DNA Sequencer: ABI 3730xl
Sequence Prefix: St_e31W
   
Stage and Tissue: embryo stage23-28+31 - whole
RT Primer: Random hexamer
DNA Sequencer: Roche 454 FLX
Sequence Prefix: St_eW_F1
   
Sequences Included in database
  2,945 St_e31W
  162,877 St_eW_F1
  165,822 total sequences