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 5'  3'   
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcgtttcgttattttagagtagagacggttagttatgttgcggggtttacatttatgaacatctactcttgcgaattgtttaatatctcgttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTGACGCTGAGCTGAAGCTCGTGGGGGAGTATGGTCTCCGCAACAAGCGTGA

Basic information

species Physcomitrella patens
transcript PP1S14_31V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S14_31V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EDO97033 (Chlamydomonas reinhardtii), 3'ss of exon 1
ttcgtttcgttattttagagtagaga--cggttagttatg--ttgcggggtttacatttatgaacatctactcttgcgaattgtttaatatctcgttt-tcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTGACGCTGAGCTGAAGCTCGTGGGGGAGTATGGTCTCCGCAACAAGCGTGA
| | | |||| || | | | | ||| | | | || | || | || || | | || |||||||| ||||||||||||||||| || | || | ||||||||||| || ||||||||||||||||| || || |||||||| || ||||||||||| ||
-----agccagagctcagaggcgacgcccagctcgacatgagtgggaatacgtgcaacttcaaatggaagcgacgctgatttttggcttgggctgtgcactgcagATGGCAAGACCTTCAAGAAGCCCCGGCGTCCTTATGAGAAGGAGCGCCTGGACGCTGAGCTGAAGCTTGTCGGCGAGTATGGCCTGCGCAACAAGCGCGA

upper sequence: PP1S14_31V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ11758 (Selaginella moellendorffii), 3'ss of exon 1
ttcgtttcgttattttagagtagagacggttagttatgttgcggggtttacatttatgaacatctactcttgcgaattgtttaatatctcgttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTGACGCTGAGCTGAAGCTCGTGGGGGAGTATGGTCTCCGCAACAAGCGTGA
| | | | || || | | | || | | || || ||||||||| || || ||||||||||| || |||| |||||||||||||| || ||||| ||||| ||||| ||||| |||||||| || ||||||||||| ||
----------------------------------------gtaagtctctccttctcgatcgcat-tgcgcccgtgccgatcgatccggtgtgc-cgcagATGGGAAAACTTTCAAGAAGCCACGGCGGCCATTCGAGAAGGAGCGCCTGGACGCGGAGCTCAAGCTGGTGGGCGAGTATGGCCTGCGCAACAAGCGCGA

upper sequence: PP1S14_31V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ31761 (Selaginella moellendorffii), 3'ss of exon 1
ttcgtttcgttattttagagtagagacggttagttatgttgcggggtttacatttatgaacatctactcttgc-gaattgtttaatatctcgttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTGACGCTGAGCTGAAGCTCGTGGGGGAGTATGGTCTCCGCAACAAGCGTGA
|| | || | | | || | | | || | | | |||||||||| || || |||||||||||||| |||| |||||||||||||| || ||||| ||||| ||||| ||||| |||||||| ||||| |||||||| ||
---------------------------------------------gtaagtctcgattcgcgctggcagtcgccgggatcatggatttggtggtgtcgcagATGGGAAAACTTTCAAGAAGCCGCGGCGGCCATTCGAGAAGGAGCGCCTGGACGCGGAGCTCAAGCTGGTGGGCGAGTATGGGCTCCGGAACAAGCGAGA

upper sequence: PP1S14_31V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ13465 (Selaginella moellendorffii), 3'ss of exon 1
ttcgtttcgttattttagagtagagacggttagttatgttgcggggtttacatttatgaacatctactcttgcgaattgtttaatatctcgttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTGACGCTGAGCTGAAGCTCGTGGGGGAGTATGGTCTCCGCAACAAGCGTGA
| | | | || || | | | || | | || || ||||||||| || || ||||||||||| || |||| |||||||||||||| || ||||| ||||| ||||| ||||| |||||||| || ||||||||||| ||
----------------------------------------gtaagtctctccttctcgatcgcat-tgcgcccgtgccgatccatccggtgtgc-cgcagATGGGAAAACTTTCAAGAAGCCACGGCGGCCATTCGAGAAGGAGCGCCTGGACGCGGAGCTCAAGCTGGTGGGCGAGTATGGCCTGCGCAACAAGCGCGA

upper sequence: PP1S14_31V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ38391 (Selaginella moellendorffii), 3'ss of exon 1
ttcgtttcgttattttagagtagagacggttagttatgttgcggggtttacatttatgaacatctactcttgc-gaattgtttaatatctcgttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTGACGCTGAGCTGAAGCTCGTGGGGGAGTATGGTCTCCGCAACAAGCGTGA
|| | || | | | | || | | | || | | | |||||||||| || || |||||||||||||| |||| ||||| |||||||| || ||||| ||||| ||||| ||||| |||||||| ||||| |||||||| ||
---------------------------------------------gtaagtctcgattcgcgcttgcagtcgccgggatcatggatttggtggtgtcgcagATGGGAAAACTTTCAAGAAGCCGCGGCGGCCATTCGAAAAGGAGCGCCTGGACGCGGAGCTCAAGCTGGTGGGCGAGTATGGGCTCCGGAACAAGCGAGA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|162206616|gb|FC382374.1|FC382374
EST:     TTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: TTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|162221676|gb|FC397901.1|FC397901
EST:     CTTTGCAAGNCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: CTTTGCAAG-CTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|22491657|gb|BU051580.1|BU051580
EST:     GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|162272057|gb|FC447851.1|FC447851
EST:     GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|162247658|gb|FC420570.1|FC420570
EST:     TCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: TCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|18341470|gb|BJ173505.1|BJ173505
EST:     GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACNTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|19784999|gb|BQ040255.1|BQ040255
EST:     CTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: CTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|162215217|gb|FC390803.1|FC390803
EST:     GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|22492118|gb|BU052041.1|BU052041
EST:     GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|162244711|gb|FC425445.1|FC425445
EST:     GCTTCCGGAANT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: GCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|19789711|gb|BQ041466.1|BQ041466
EST:     TTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: TTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|22492156|gb|BU052072.1|BU052072
EST:     GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|162278883|gb|FC454934.1|FC454934
EST:     GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|67702183|gb|BJ962416.1|BJ962416
EST:     GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|162241367|gb|FC416998.1|FC416998
EST:     CTTTGCAAGCCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: CTTTGCAAG-CTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|37852085|gb|BJ610093.1|BJ610093
EST:     GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|67578437|gb|BJ950604.1|BJ950604
EST:     GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|162272058|gb|FC447852.1|FC447852
EST:     GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|100362884|gb|BY947577.1|BY947577
EST:     GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGGGAAGGAGCGTCTCG
genomic: GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|18325105|gb|BJ157101.1|BJ157101
EST:     GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|67720679|gb|BJ970938.1|BJ970938
EST:     GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|18336648|gb|BJ168671.1|BJ168671
EST:     AACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: AACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|162241366|gb|FC416997.1|FC416997
EST:     GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|162221675|gb|FC397900.1|FC397900
EST:     GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|162278884|gb|FC454935.1|FC454935
EST:     GCTTTGC-AGCTTTTTCTC-ACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|162215216|gb|FC390802.1|FC390802
EST:     GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: GCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
EST: gi|162244712|gb|FC425446.1|FC425446
EST:     GCTTCCGGAACT                         ATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG
genomic: GCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 26 (upstream exon), 34 (downstream exon)
Score: 14

CTCTTTCAAGCTCGAGCTCTTGGAAGCAGCTTTGCAAGCTTTTTCTCAACATGGTGCACGTCGCCAGCTTCCGGAACTgttagtctct ... gttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTGACGCTGAGCTGAAGCTCGTGGGGGAGTATGGTCTCCGCAACAAGCGTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttacatttatgaacatctactcttgcgaattgtttaatatctcgttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTGACGCTGAGCTGAAGCTCGTGGGGGAGTATGGTCTCCGCAACAAGCGTGA
                                 gtttaat  putative branch site (score: 14)
 tctcgttttc  CT-rich tract
 aattgtttaatatct  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcgtttcgttattttagagtagagacggttagttatgttgcggggtttacatttatgaacatctactcttgcgaattgtttaatatctcgttttcgcagATGGAAAGACCTTCAAGAAGCCGCGCAGGCCGTTCGAGAAGGAGCGTCTTGACGCTGAGCTGAAGCTCGTGGGGGAGTATGGTCTCCGCAACAAGCGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC