Texas Xenopus Genome Project/Species Identification
From MarcotteLab
Contents |
Designed
XENTR_CHORI-219_ID.2 (hoxa5)
- Only cut XENTR - PsrI(119, 151).
- Only cut XENLA - None.
- PCR primer (designed by Primer3)
OLIGO start len tm gc% any 3' seq LEFT PRIMER 24 20 59.99 45.00 2.00 0.00 caagagccacaaatcaagca RIGHT PRIMER 221 20 59.92 50.00 5.00 1.00 agatccatgccattgtagcc
XENLA_CH219-206K 1 + gtgctatagacgcgcaaaacgaccaagagccacaaatcaagcacacatatcaaaaaacaaatga 64
XENTR_NM_0010114 1 + gtgctatagacgcgcaaaacgaccaagagccacaaatcaagcacacatatcaaaaaacaaatga 64
****************************************************************
>>>>>>>>>>>>>>>>>>>>
XENLA_CH219-206K 65 + gctcttattttgtaaactcattttgcggtcgctatccaaatggcccggactaccagttacataa 128
XENTR_NM_0010114 65 + gctcttattttgtaaactcattttgcggtcgctatccaaatggcccggactaccagttacataa 128
****************************************************************
XENLA_CH219-206K 129 + ttatggagatcagagctcggtgagcgagcaatacagggatacaacgagcatgcattccagcagg 192
XENTR_NM_0010114 129 + ttatggagatcacagctcggtgaacgagcaatacagggatacaacgagcatgcattccagcagg 192
************ ********** ****************************************
XENLA_CH219-206K 193 + tacggatacggctacaatggcatggatctcagcgttgggcgctcagcttccaaccactttagtg 256
XENTR_NM_0010114 193 + tacggatacggctacaatggcatggatctcagcgttgggcgctcagcttccaaccactttagtg 256
****************************************************************
<<<<<<<<<<<<<<<<<<<<
XENLA_CH219-206K 257 + ccaatgacagagcaaggaattatccatccaatccgagctcctctacagagccaaggtataacca 320
XENTR_NM_0010114 257 + ccaatgacagagcaaggaattatccatccaatccgagctcctctacagagccaaggtataacca 320
****************************************************************
XENLA_CH219-206K 321 + acctgcagcctct 333(1)
XENTR_NM_0010114 321 + acctgcagcgtct 333(1)
********* ***
XENTR_CHORI-219_ID.25 (hoxa3)
- Only cut XENTR - BccI(136), BfiI(110), BglII(21), BstEII(140), Eco57I(72), Eco57MI(72), MboII(78), MmeI(115), PflMI(134), PleI(118), Tsp45I(99), TspDTI(59), TspRI(123,178)
- Only cut XENLA - BciVi(136,167), BspMI(156), EcoP15I(193), HphI(136), MslI(105), NspI(157), SacI(44,122), SphI(157), TspGWI(157)
- PCR primer
OLIGO start len tm gc% any 3' seq LEFT PRIMER 161 20 60.21 50.00 7.00 2.00 cctcaccgagaggcaaatta RIGHT PRIMER 351 20 59.68 60.00 5.00 3.00 gaggctcataggggacactg
XENLA_CH219-206K 1 + gtgagagctgtgcaggagacaaaagtcccccggggcaatcctcttccaaaagggcccgcactgc 64
XENTR_NM_0011274 1 + gtgagagttgtgctggagacaaaagccccccggggcaatcctcttccaagagggcccgcactgc 64
******* ***** *********** *********************** **************
XENLA_CH219-206K 65 + ttacacaagcgctcagctggtagaactggaaaaagagttccactttaacagatacctgtgcaga 128
XENTR_NM_0011274 65 + ttacacaagcgctcagctggtagaactggaaaaagagttccactttaacagatacctgtgcaga 128
****************************************************************
XENLA_CH219-206K 129 + cccaggagggtggagatggccaatctactcaacctcaccgagaggcaaattaagatctggtttc 192
XENTR_NM_0011274 129 + cccaggagggtggagatggccaatctgctcaacctcaccgagaggcaaattaagatctggtttc 192
************************** *************************************
>>>>>>>>>>>>>>>>>>>>
XENLA_CH219-206K 193 + agaacaggcgaatgaaatacaaaaaggatcaaaaagggaaatccatgatgacctcttcaggagg 256
XENTR_NM_0011274 193 + agaacaggcgaatgaaatacaaaaaggatcaaaaagggaaatccatgatgacctcttcaggagg 256
****************************************************************
XENLA_CH219-206K 257 + acagtcaccatgtaggagcccggtgccagctccatctgttggaggttacctaaactctatgcat 320
XENTR_NM_0011274 257 + gcagtcaccatgtaggagcccagtgccgactccatctgttggaggttacctaaactctatgcat 320
******************** ***** ***********************************
XENLA_CH219-206K 321 + tctttggtaaacagtgtcccctatgagcctcagtctccccctg 363(1)
XENTR_NM_0011274 321 + tctttggtaaacagtgtcccctatgagcctcagtctcccccag 363(1)
***************************************** *
<<<<<<<<<<<<<<<<<<<<
XENTR_CHORI-219_ID.28 (pitx-1)
- Only cut XENTR - SfaNI(46),TauI(52)
- Only cut XENLA - BciVI(78),FauI(42),Hpy99I(72)
- PCR primer
OLIGO start len tm gc% any 3' seq LEFT PRIMER 42 20 60.12 55.00 5.00 2.00 gaaccagcagatggacctgt RIGHT PRIMER 194 20 59.84 50.00 4.00 0.00 aaggtgaagctcttggtgga
XENLA_CH219-166K 1 + tggttcaagaaccgccgagccaagtggaggaagagggagcggaaccagcagatggacctgtgta 64
XENTR_NM_0010074 1 + tggttcaagaaccgcagagccaagtggaggaagagggagcggaaccagcagatggacctgtgca 64
*************** ********************************************** *
>>>>>>>>>>>>>>>>>>>
XENLA_CH219-166K 65 + agaatggttacgtgccccagttcagcgggctcatgcagccgtacgacgagatgtacgcaggata 128
XENTR_NM_0010074 65 + agaatggctacgtgccccagttcagcggcctgatgcagccctacgatgagatgtacgctggcta 128
******* ******************** ** ******** ***** *********** ** **
XENLA_CH219-166K 129 + cccctacaacaactgggccacaaaaagcctcacccctgcccccctgtccaccaagagcttcacc 192
XENTR_NM_0010074 129 + cccgtacaacaactgggccaccaaaagcctcacccctgcccccctgtccaccaagagcttcacc 192
*** ***************** ******************************************
<<<<<<<<<<<<<<<<<<
XENLA_CH219-166K 193 + ttcttcaactccatgagtcccttgtcttcccagtccatgttctccggccccagctccatctctt 256
XENTR_NM_0010074 193 + ttcttcaactccatgagtccgctgtcctcccagtccatgttctctggccccagctccatctctt 256
******************** **** ***************** *******************
<<
XENLA_CH219-166K 257 + ccatgagcatgccctccagcatgggtcactctgcggtgccaggcatggccaactc 311(1)
XENTR_NM_0010074 257 + ccatgagcatgccctccagcatgggccactcggcggtgcccggcatgcccaactc 311(1)
************************* ***** ******** ****** *******
Candidates
XENTR_CHORI-219_ID.3 (hoxa5)
XENTR_CHORI-219_ID.24 (hoxa3)
XENTR_CHORI-219_ID.26 (hoxa3)
XENTR_CHORI-219_ID.27 (pitx-1)
XENTR_CHORI-219_ID.29 (pitx-1)
Selection procedure
- Download X. tropicalis mRNA sequences from XenBase (Nov. 27, 2009 version).
- xdata:ID/XENTR_mRNA.xenbase20091127.fasta.gz 17 MB, gzipped.
- Download CHORI-219 sequences (from NCBI GenBank).
- xdata:ID/XENLA_CH219.fasta.gz 6.5 MB, gzipped. (CHORI-219 sequences. 29 BAC sequences from X. laeves genome)
- Run BLAT (version 3.4, with default option) to known CHORI BAC sequences.
- xdata:ID/XENTR_mRNA.XENLA_CH219.blat_pslx.gz 1.2 MB, gzipped.
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.
- From X. tropicalis mRNA, only RefSeq (starts sith 'NM_') sequences are considered.
- 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').
- 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
