Texas Xenopus Genome Project/Species Identification

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Target gene

Selection procedure

  • Download CHORI-219 sequences (from NCBI GenBank).
 blat XENLA_CH219.fasta XENTR_mRNA.xenbase20091127.fasta XENTR_mRNA.XENLA_CH219.blat_pslx -out=pslx
  • Parse two BLAT output files with the following criteria.
    1. From X. tropicalis mRNA, only RefSeq (starts sith 'NM_') sequences are considered.
    2. Select X. tropicalis mRNA sequences which hit both CHORI-219 (minimum match length is 200 bp to be called as a 'hit'). I only consider 10 CHORI-219 BACs which we already knew that they are available ('74I8','204L9','197E3','71P23','36I4','35I18','262A22','20I13','206K7','166K18').
    3. Survey each hit blocks. If the hit block is less than 200 bp, discard it. 42 hit blocks from 8 mRNAs are selected.
      • NM_001004837 Unnamed, predicted gene MGC69309 NCBIXenBase
      • NM_001007499 paired-like homeodomain 1 (pitx-1) NCBIXenBase
      • NM_001011405 Homeobox A5 (hoxa5) NCBIXebBase
      • NM_001035121 CCAAT/enhancer binding protein (C/EBP), beta (cebpb) NCBIXenBase
      • NM_001113032 LY6/PLAUR domain containing 6 (lypd6) NCBIXenBase
      • NM_001127429 homeobox A3 (hoxa3) NCBIXenBase
      • NM_001129937 SRY (sex determining region Y)-box 18 (sox18) NCBI XenBase
      • NM_001142220 phosphoribosylformylglycinamidine synthase (pfas) NCBIXenBase
  • Run MUSCLE (version 4.0, with default option) for multiple sequence alignment. I found that most of candidate sequences have duplications. So I filtered them out based on 'Self' mapping information from MUSCLE output (if a sequence is mapped itself longer than 50 bp). Finally 10 fragments are selected.
    • hoxa3 - XENTR_CHORI-219_ID.24.muscle, XENTR_CHORI-219_ID.25.muscle, XENTR_CHORI-219_ID.26.muscle
    • pitx-1 - XENTR_CHORI-219_ID.27.muscle, XENTR_CHORI-219_ID.28.muscle, XENTR_CHORI-219_ID.29.muscle
    • hoxa5 - XENTR_CHORI-219_ID.2.muscle, XENTR_CHORI-219_ID.3.muscle
 $ mus4 -i XENTR_CHORI.fasta -o XENTR_CHORI.muscle 

Here's the example of Self duplication.

>XENTR_NM_001113032_18 gi|163915026|ref|NM_001113032|

  3 + ccaggggtacccagggcacaaataagcactcaccccaaatccccccctaactggccttcaggct 66
      ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
138 + ccaggggtacccagggcacaaataagcactcaccccaaatctccccctaactggccttcaggct 201

 67 + gggcccccttagcccataacaaggttacagatagttagaaacattggg 114
      |||||||||||||||||||||||||||||||||  |||||||||||||
202 + gggcccccttagcccataacaaggttacagatatatagaaacattggg 249