Texas Xenopus Genome Project/Species Identification
From Marcotte Lab
Contents |
Target fragments
XENTR_CHORI-219_ID.2 (hoxa5)
- PsrI cut only XENTR sequence (position 119, 151).
- 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.3 (hoxa5)
- MUSCLE alignment
XENLA_CH219-206K 1 + acaacataggagggccagaaggaaagcgagcccggacagcctacacccgctatcaaactctgga 64 XENTR_NM_0010114 1 + acaacataggagggccagaaggaaagcgagcccggacagcctacacccgctaccaaactctgga 64 **************************************************** *********** 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) ****************
XENTR_CHORI-219_ID.24 (hoxa3)
- MUSCLE alignment
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) *** ***** ******** *
XENTR_CHORI-219_ID.25 (hoxa3)
- MUSCLE alignemtn
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.26 (hoxa3)
- MUSCLE alignment
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) ************************** * *********** ****** *****
XENTR_CHORI-219_ID.27 (pitx-1)
- MUSCLE alignment
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) ****************
XENTR_CHORI-219_ID.28 (pitx-1)
- MUSCLE alignment
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) ************************* ***** ******** ****** *******
XENTR_CHORI-219_ID.29 (pitx-1)
- MUSCLE alignment
XENLA_CH219-166K 1 + atcagcggctcctccctcaactcagccatgtcttctactggttgtccctatggaccccctggtt 64 XENTR_NM_0010074 1 + atcagcagctcctccctcaactccgccatgtcttctactgcttgtccctatggcccccccggct 64 ****** **************** **************** ************ ***** ** * XENLA_CH219-166K 65 + ccccctacacggtttaccgggacacttgtaactccagtctggcaagcctgagactgaaatccaa 128 XENTR_NM_0010074 65 + ccccatacacggtatacagggacacttgtaactcgagtttggccagcctgagactgaaatccaa 128 **** ******** *** **************** *** **** ******************** XENLA_CH219-166K 129 + gcagcactccaccttcggctacagcagcctccagagcccggcctccagcctcaatgcttgccaa 192 XENTR_NM_0010074 129 + gcagcactccacctttggctacagtagcctgcagagcccggcctccagcctcaatgcctgccag 192 *************** ******** ***** ************************** ***** XENLA_CH219-166K 193 + tataacagttgatagactcccc 214(1) XENTR_NM_0010074 193 + tataacagttgatagactcccc 214(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