Representative Transcript and Protein Sets

[RTS: Representative Transcript Set]

rts-transcripts.fasta:
  Representative transcript sequences
  Fasta file

  (header)
  >[RepTransID] [Nucleotide SeqID] [NT Length] [Definition]

  RepTransID:       Identifier assigned to each representative transcript
  Nucleotide SeqID: gb=(GenBank or RefSeq accession)  or
	            ri=(RIKEN Clone ID)
  NT Length:        length=(NT length)
  Definition:       GenBank, RefSeq or FANTOM2 definition of the sequence


rts-transcripts.txt:
  Representative transcript information
  Tab-delimited text file

  1. Rep Trans ID
  2. Nucleotide SeqID
  3. RIKEN Clone ID
  4. Description line from GenBank or RefSeq, or if a FANTOM2 sequence is selected, the Curated Gene Name
  5. NT Length
  6. MGI ID
  7. LocusLink ID
  8. MGI Gene Symbol
  9. MGI Gene Name



[RPS: Representative Protein Set]

rps-proteins.fasta:
  Representative protein sequences
  Fasta file

  (header)
  >[RepProteinID] [Protein SeqID] [CDS Length] [Definition]

  RepProteinID:  Identifier assigned to each representative protein
  Protein SeqID: spid=(SWISS-PROT accession),
		 gp=(GenPept/RefSeq-NP accession) or
		 ri=(RIKEN Clone ID)
  CDS Length:    cdslen=(CDS length)
  Definition:    SWISS-PROT, GenPept, RefSeq or FANTOM2 definition


rps-proteins.txt:
  Representative protein information
  Tab-delimited text file

  1. Rep Protein ID
  2. Protein SeqID
  3. RIKEN Clone ID
  4. Description line from GenBank or RefSeq, or if a FANTOM2 sequence is selected, the Curated Gene Name
  5. CDS Length
  6. MGI ID
  7. LocusLink ID
  8. MGI Gene Symbol
  9. MGI Gene Name


[VPS: Variant-based representative Protein Set]

vps-proteins.fasta:
  Variant-based representative protein sequences
  Fasta file

  (header)
  >[VPS ProteinID] [Protein SeqID] [CDS Length] [Definition]

  VPSProteinID:  Identifier assigned to each variant-based representative protein
  Protein SeqID: spid=(SWISS-PROT accession),
		 gp=(GenPept/RefSeq-NP accession)
		 ri=(RIKEN Clone ID)
		 rps=(Rep Prot ID) (spid=.. , gp=.. or ri=..)
  CDS Length:    cdslen=(CDS length)
  Definition:    SWISS-PROT, GenPept, RefSeq or FANTOM2 definition

vps-proteins.txt:
  Variant-baesd representative protein information
  Tab-delimited text file

  1. VPS Protein ID
  2. Protein SeqID
  3. RIKEN Clone ID
  4. Description line from GenBank or RefSeq, or if a FANTOM2 sequence is selected, the Curated Gene Name
  5. CDS Length
  6. MGI ID
  7. LocusLink ID
  8. MGI Gene Symbol
  9. MGI Gene Name


[Additional Information]

allseqs.txt:
  1. Representative Transcript ID (T#*) (Rep Trans ID)
  2. SeqID (GenBank/RefSeq Accession) of Representative Transcript
  3. FANTOM2 Clone ID of Representative Transcript (if FANTOM2 clone)
  4. Representative Protein ID (P#*) (Rep Protein ID)
  5. SeqID (GenPept/RefSeq/SwissProt Accession) of Rep Protein
  6. FANTOM2 Clone ID of Representative Protein (if FANTOM2 clone)

  7. All SeqIDs (GenBank/RefSeq Accession) in the TU
  8. All FANTOM1     Clone IDs in the TU
  9. All FANTOM2-new Clone IDs in the TU