Difference between revisions of "Texas Xenopus Genome Project/Species Identification"

Latest revision as of 16:43, 9 December 2009

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.
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 NCBI XenBase
  - NM_001007499 paired-like homeodomain 1 (pitx-1) NCBI XenBase
  - NM_001011405 Homeobox A5 (hoxa5) NCBI XebBase
  - NM_001035121 CCAAT/enhancer binding protein (C/EBP), beta (cebpb) NCBI XenBase
  - NM_001113032 LY6/PLAUR domain containing 6 (lypd6) NCBI XenBase
  - NM_001127429 homeobox A3 (hoxa3) NCBI XenBase
  - NM_001129937 SRY (sex determining region Y)-box 18 (sox18) NCBI XenBase
  - NM_001142220 phosphoribosylformylglycinamidine synthase (pfas) NCBI XenBase

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

@@ Line 2: / Line 2: @@
 === XENTR_CHORI-219_ID.2 (hoxa5) ===
 * Only cut XENTR - [http://rebase.neb.com/rebase/enz/PsrI.html PsrI](119, 151).
+* Only cut XENLA - None.
 * PCR primer (designed by Primer3)
 <pre>
@@ Line 46: / Line 47: @@
 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
-SEQUENCE SIZE: 363
-INCLUDED REGION SIZE: 363
 </pre>
@@ Line 79: / Line 78: @@
 * [[:xdata:ID/XENTR_CHORI-219_ID.25.muscle|MUSCLE file]]
-== Candidates ==
+=== XENTR_CHORI-219_ID.28 (pitx-1) ===
-=== XENTR_CHORI-219_ID.3 (hoxa5) ===
+* Only cut XENTR - SfaNI(46),TauI(52)
+* Only cut XENLA - BciVI(78),FauI(42),Hpy99I(72)
+* PCR primer
 <pre>
-XENLA_CH219-206K   1 + acaacataggagggccagaaggaaagcgagcccggacagcctacacccgctatcaaactctgga 64
+OLIGO            start  len      tm     gc%   any    3' seq
-XENTR_NM_0010114   1 + acaacataggagggccagaaggaaagcgagcccggacagcctacacccgctaccaaactctgga 64
+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_CH219-206K  65 + gctggaaaaggaatttcatttcaacagatacctgacccgcaggaggagaattgaaatagcccat 128
-XENTR_NM_0010114  65 + gctggaaaaggaatttcatttcaacagatacctgacccgcaggaggaggattgaaatagcccat 128
-                       ************************************************ ***************
-XENLA_CH219-206K 129 + gcactctgtctctctgagaggcaaattaaaatctggttccaaaacaggagaatgaagtggaaaa 192
-XENTR_NM_0010114 129 + gcactctgtctctctgagaggcaaattaaaatctggttccaaaacaggagaatgaagtggaaaa 192
-                       ****************************************************************
-XENLA_CH219-206K 193 + aagacaataaactaaagagtatgagcatggcagcggctgggggtgcatttcgtccttaaatttc 256
-XENTR_NM_0010114 193 + aagacaataaactaaagagtatgagcatggcagcggctgggggtgcatttcgtccttaaatttc 256
-                       ****************************************************************
-XENLA_CH219-206K 257 + ccctccctgaagaatgtactgattcagtattagctaaacctgtatattgtcaccaccactttgt 320
-XENTR_NM_0010114 257 + ccctccctaaagaatgtactgattcagtattagctaaacctgtatattgtcaccaccactttgt 320
-                       ******** *******************************************************
-XENLA_CH219-206K 321 + ataactcttctctgtgacttctgtgaagataccctcctccccaatctcttgtccaccctttatc 384
-XENTR_NM_0010114 321 + ataactcttctctgtgacttctgtgaagataccctcctccctaatatcttgtctaccctttatc 384
-                       ***************************************** *** ******* **********
-XENLA_CH219-206K 385 + ctagcaatgagccttt 400(1)
-XENTR_NM_0010114 385 + ctagcaatgagccttt 400(1)
-                       ****************
 </pre>
-* [[:xdata:ID/XENTR_CHORI-219_ID.3.fasta|FASTA file]]
-* [[:xdata:ID/XENTR_CHORI-219_ID.3.muscle|MUSCLE file]]
-=== XENTR_CHORI-219_ID.24 (hoxa3) ===
-* MUSCLE alignment
-<pre>
-XENLA_CH219-206K   1 + gtcggaccagggaggccattggaggaggaacgccacgtgacagaggggtgccaatgttattctt 64
-XENTR_NM_0011274   1 + gtctgaccagcgaggccattggaggaggaacgccacgtgacagaggggtgccaatgttattctt 64
-                       *** ****** *****************************************************
-XENLA_CH219-206K  65 + tacgggtgtcaagaccctgtcagtttgtgaaataaatattgggaaacaacgaaatgcaaaaagc 128
-XENTR_NM_0011274  65 + tacgggtgtcaagaccctgtcagtttgtgaaataaatattgggaaacaacgaaatgcaaaaagc 128
-                       ****************************************************************
-XENLA_CH219-206K 129 + gacctactacgacagcgctgcgatctatggcggatatccctaccaaggagcaaatggtttcact 192
-XENTR_NM_0011274 129 + gacctactacgacagctctgcgatctatggtggatatccctaccaaggagcaaatggtttcact 192
-                       **************** ************* *********************************
-XENLA_CH219-206K 193 + tataatgcaagtcagcagcaatatcctccttcctcatctctgctggaaagtgaatatcatcgac 256
-XENTR_NM_0011274 193 + tataatgcaagtcagcagcaatatcctccttcctcatctctgctggaaactgaatatcatcgac 256
-                       ************************************************* **************
-XENLA_CH219-206K 257 + ctgcctgctccctgcagtcacctggcagcgctgtgccccatctcaaggccaatgacatcaatga 320
-XENTR_NM_0011274 257 + ctgcctgctccctgcagtcacctggcagcgcagtgccccatcacaaggccaatgacatcaacga 320
-                       ******************************* ********** ****************** **
-XENLA_CH219-206K 321 + aagttgtatgagaagtatcagcagtcaatcaagtcaagccccggtcattcccgagcagcagccc 384
-XENTR_NM_0011274 321 + aagttgtatgagaaccattaacagtcaatcaaaccaagccccggtcattcccgagcagcagccc 384
-                       **************  ** * ***********  ******************************
-XENLA_CH219-206K 385 + acaccacaagggccgccaccctctgtgtccccaccacaaaccaccagcaatgcagccacagcct 448
-XENTR_NM_0011274 385 + acaccgcaagggccgccaccctctgtgtccccaccacaaaccaccagcaatgcagccacagcct 448
-                       ***** **********************************************************
-XENLA_CH219-206K 449 + cctccaacaaggccacaggcatcaactcacctaccatgtcaaagcagattttcccttggatgaa 512
-XENTR_NM_0011274 449 + cctccaacaaggccacaagcatcacctcacctaccatgtcaaagcagattttcccttggatgaa 512
-                       ***************** ****** ***************************************
-XENLA_CH219-206K 513 + agagtcccggcagaacacaa 532(1)
-XENTR_NM_0011274 513 + agaatcccgacagaacacga 532(1)
-                       *** ***** ******** *
-</pre>
-=== XENTR_CHORI-219_ID.26 (hoxa3) ===
-* MUSCLE alignment
-<pre>
-XENLA_CH219-206K   1 + aacaaacaccaccctggcgcctatggtgtgcctgcaccctacccaagcccccacaacagctgtc 64
-XENTR_NM_0011274   1 + aacaaacaccaccctagcgcgtatggcgtgcctgcaccctacccaagcccccacaacagctgcc 64
-                       *************** **** ***** *********************************** *
-XENLA_CH219-206K  65 + ctccccaccaaaaaagatacagcggaactgctgcggtcaccccagaatatgagccccatcctct 128
-XENTR_NM_0011274  65 + ctccccaccaaaagagatacagcgggactgctgcggtcacccctgaatatgagccacatcctct 128
-                       ************* *********** ***************** *********** ********
-XENLA_CH219-206K 129 + ccaacaaggcaacggagcttatgggaatcctcatgtacagggaagccccgtttatgtaggggga 192
-XENTR_NM_0011274 129 + ccaacaaagcagcggagcttatgggaatccgcatgtacagggaagccccgtttatgtagggggg 192
-                       ******* *** ****************** ********************************
-XENLA_CH219-206K 193 + aactatgtggagaccatgactaattctggaccatccatgtttggtttgtctcatctctctcatt 256
-XENTR_NM_0011274 193 + aactatgtggagaccatgactaattctggaccatccatgtttggtttgtctcatctctctcatt 256
-                       ****************************************************************
-XENLA_CH219-206K 257 + cctcatcgaacatggactacagtggagccggacccatgaacagtggtcaccaccatggaccttg 320
-XENTR_NM_0011274 257 + cctcatcgaacatggactacagtggagccggacccatgaacagtggtcaccaccatggaccctg 320
-                       ************************************************************* **
-XENLA_CH219-206K 321 + tgactcccacactacatacacagacttatctgctcaccacaatcctcagggaagaattcaggaa 384
-XENTR_NM_0011274 321 + tgactctcaccctacatacacggacttatctgctcaccacaatcctcagggaagaattcaggaa 384
-                       ****** *** ********** ******************************************
-XENLA_CH219-206K 385 + gcccccaaattaacacatttgtaatggccatggagacaaataatcccctcttttc 439(1)
-XENTR_NM_0011274 385 + gcccccaaattaacacatttgtaatgatcgtggagacaaattttccccttttttc 439(1)
-                       **************************  * ***********  ****** *****
-</pre>
-=== XENTR_CHORI-219_ID.27 (pitx-1) ===
-* MUSCLE alignment
-<pre>
-XENLA_CH219-166K   1 + agaaagaacgaaccggggagccaaaaggagaggacgggaatggggatgatcccagcaagaaaaa 64
-XENTR_NM_0010074   1 + agaaagaacgaagtggggagccaaagggagaggacggcaatggggatgatcccacaaagaaaaa 64
-                       ************  *********** *********** ****************  ********
-XENLA_CH219-166K  65 + gaagcagaggagacaaaggactcactttaccagccagcagctgcaggagctggaggccactttc 128
-XENTR_NM_0010074  65 + gaagcagaggagacaaaggactcactttaccagccagcagctgcaggagctggaggccactttc 128
-                       ****************************************************************
-XENLA_CH219-166K 129 + cagaggaaccgatatccagacatgagcatgagagaggagattgctgtatggaccaatctgactg 192
-XENTR_NM_0010074 129 + cagaggaaccgctacccagacatgagcatgagagaggagatcgctgtatggaccaatctgactg 192
-                       *********** ** ************************** **********************
-XENLA_CH219-166K 193 + aggccagggtcagggt 208(1)
-XENTR_NM_0010074 193 + aggccagggtcagggt 208(1)
-                       ****************
-</pre>
-=== XENTR_CHORI-219_ID.28 (pitx-1) ===
-* MUSCLE alignment
 <pre>
 XENLA_CH219-166K   1 + tggttcaagaaccgccgagccaagtggaggaagagggagcggaaccagcagatggacctgtgta 64
 XENTR_NM_0010074   1 + tggttcaagaaccgcagagccaagtggaggaagagggagcggaaccagcagatggacctgtgca 64
                         *************** ********************************************** *
+                                                               >>>>>>>>>>>>>>>>>>>
 XENLA_CH219-166K  65 + agaatggttacgtgccccagttcagcgggctcatgcagccgtacgacgagatgtacgcaggata 128
 XENTR_NM_0010074  65 + agaatggctacgtgccccagttcagcggcctgatgcagccctacgatgagatgtacgctggcta 128
@@ Line 222: / Line 99: @@
 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)
                         ************************* ***** ******** ****** *******
 </pre>
+* [[:xdata:ID/XENTR_CHORI-219_ID.28.fasta|FASTA file]]
+* [[:xdata:ID/XENTR_CHORI-219_ID.28.muscle|MUSCLE file]]
-=== XENTR_CHORI-219_ID.29 (pitx-1) ===
+== Candidates ==
-* MUSCLE alignment
+=== XENTR_CHORI-219_ID.3 (hoxa5) ===
-<pre>
+* [[:xdata:ID/XENTR_CHORI-219_ID.3.fasta|FASTA file]]
-XENLA_CH219-166K   1 + atcagcggctcctccctcaactcagccatgtcttctactggttgtccctatggaccccctggtt 64
+* [[:xdata:ID/XENTR_CHORI-219_ID.3.muscle|MUSCLE file]]
-XENTR_NM_0010074   1 + atcagcagctcctccctcaactccgccatgtcttctactgcttgtccctatggcccccccggct 64
-                       ****** **************** **************** ************ ***** ** *
-XENLA_CH219-166K  65 + ccccctacacggtttaccgggacacttgtaactccagtctggcaagcctgagactgaaatccaa 128
+=== XENTR_CHORI-219_ID.24 (hoxa3) ===
-XENTR_NM_0010074  65 + ccccatacacggtatacagggacacttgtaactcgagtttggccagcctgagactgaaatccaa 128
+* [[:xdata:ID/XENTR_CHORI-219_ID.24.fasta|FASTA file]]
-                       **** ******** *** **************** *** **** ********************
+* [[:xdata:ID/XENTR_CHORI-219_ID.24.muscle|MUSCLE file]]
-XENLA_CH219-166K 129 + gcagcactccaccttcggctacagcagcctccagagcccggcctccagcctcaatgcttgccaa 192
+=== XENTR_CHORI-219_ID.26 (hoxa3) ===
-XENTR_NM_0010074 129 + gcagcactccacctttggctacagtagcctgcagagcccggcctccagcctcaatgcctgccag 192
+* [[:xdata:ID/XENTR_CHORI-219_ID.26.fasta|FASTA file]]
-                       *************** ******** ***** ************************** *****
+* [[:xdata:ID/XENTR_CHORI-219_ID.26.muscle|MUSCLE file]]
-XENLA_CH219-166K 193 + tataacagttgatagactcccc 214(1)
+=== XENTR_CHORI-219_ID.27 (pitx-1) ===
-XENTR_NM_0010074 193 + tataacagttgatagactcccc 214(1)
+* [[:xdata:ID/XENTR_CHORI-219_ID.27.fasta|FASTA file]]
-                       **********************
+* [[:xdata:ID/XENTR_CHORI-219_ID.27.muscle|MUSCLE file]]
-</pre>
+=== XENTR_CHORI-219_ID.29 (pitx-1) ===
+* [[:xdata:ID/XENTR_CHORI-219_ID.29.fasta|FASTA file]]
+* [[:xdata:ID/XENTR_CHORI-219_ID.29.muscle|MUSCLE file]]
 == Selection procedure ==

Difference between revisions of "Texas Xenopus Genome Project/Species Identification"

Latest revision as of 16:43, 9 December 2009

Contents

Designed

XENTR_CHORI-219_ID.2 (hoxa5)

XENTR_CHORI-219_ID.25 (hoxa3)

XENTR_CHORI-219_ID.28 (pitx-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

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