Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgatttgaaacgatttaattgccgcgtgattgtagttgggttagacagcaaattaggtctattatattgaaggccttgatattccactgaactcagtcgcttttggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAATTGAACCGGTACATTCCCACAGCAGCTGCTTTTGGAGGTATGTGTATTG

Basic information

species Physcomitrella patens
transcript PP1S323_56V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S323_56V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os09g17840.1 (Oryza sativa), 3'ss of exon 5
-gtaattgat-ttgaaacgatttaattgccgcgtgattgtagttgggttagacagcaaattaggtctattatattgaaggccttgatattccactgaactcagtcgcttttggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAATTGAACCGGTACATTCCCACAGCAGCTGCTTTTGGAGGTATGTGTATTG
  || ||  | ||||   ||| |||||      |  ||||       ||| | |   || |     || ||  |  |    ||    | |||| |        ||  |     | |||||||||||||||||| | ||||||||||| ||||| || ||| | |||| |||||||||| | ||||| ||||| || ||||| ||||| ||  |||| ||||
gatatttagtgttgaggtgatctaattagtctatatttgt-------ttacatacagaaatg---ttactaagtcca---tctatgaactccatt--------tctttgccaatataacagGAACAACAAATGGTGATGCCTGGCCATCGTGAGTCAAACTTGCAGAAGGAATTGAACAGATACATCCCCACTGCTGCTGCATTTGGTGGAGTGTGCATTG

upper sequence: PP1S323_56V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os09g17830.1 (Oryza sativa), 3'ss of exon 5
gtaattgatttgaaacgatttaattgccgcgtgattgtagttg-ggttagacagcaaattaggtctattatattgaaggccttgatattccactgaactcagtcgcttt--tggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAATTGAACCGGTACATTCCCACAGCAGCTGCTTTTGGAGGTATGTGTATTG
               | || || | |  |  |  ||   |||| ||| |   |  |   ||  |   ||   |  |||||| |       |  | |||||  |  || |     | ||||||||||| |||||| | ||||||||||| ||||| || ||| | |||| |||||||||| | ||||| ||||| || ||||| ||||| ||  |||| ||||
--------------tctatata-tagtgggatatttagtgttgaggtgatctaatagtctatattggtttactcaaaggccat-------ctataaactccatttctatgtcactataacagGAACAGCAAATGGTGATGCCTGGCCATCGTGAGTCAAACTTGCAGAAGGAATTGAACAGATACATCCCCACTGCCGCTGCATTTGGTGGAGTGTGCATTG

upper sequence: PP1S323_56V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 5
gtaattgatttgaaacgatttaattgccgcgtgattgtagttgggttagacagcaaattaggtctattatattgaaggccttgatattccactgaactcagtcgcttttggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAATTGAACCGGTACATTCCCACAGCAGCTGCTTTTGGAGGTATGTGTATTG
                   | |  ||  | |  | |||  |    || |    | ||||| |   | |   |      |  | |  |   |     ||| | | ||     ||   ||||||||||||||| | ||||| || || ||||| || ||| | |||| |||| ||||||| ||||| ||||| || ||||| ||||| ||  | || || |
-------------------taacgtgttgagctactgttttatatttggctcactaattatgcaaactcactatgcaacaattacctgtgatcatcctctgacactggatattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAACTGAACCGATACATCCCCACTGCTGCTGCATTTGGTGGAGTATGCATCG

upper sequence: PP1S323_56V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G130987_T04 (Zea mays), 3'ss of exon 5
gtaattgatttgaaacgatttaattgccgcgtgattgtagttgggttagacagcaaattaggtctattatattgaaggccttgatattccactgaactcagtcgcttttggttta-acagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAATTGAACCGGTACATTCCCACAGCAGCTGCTTTTGGAGGTATGTGTATTG
              || || ||||  |    ||||| |      |     |||   |  || | |  |||   | ||   ||| ||  |   ||| |           |  | ||  ||||||||||||||| | ||||| ||||| ||||| || ||| | |||| |||| | ||||| ||||| ||||| || ||||| ||||| ||| | || ||||
-------------tacaatataat--cttaatgatttttcacatgcctatcagttga--agatttggtatggagcag--tttgctaacctg-tgatcctgacactggatattatatgcagGAACAACAAATGGTGATGCCAGGCCATCGTGAGTCGAACTTGCAGAAGGAACTTAACCGATACATCCCCACTGCTGCTGCATTTGGTGGTGTATGCATTG

upper sequence: PP1S323_56V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA06G32680.1 (Glycine max), 3'ss of exon 6
gtaattgatttgaaacgatttaattgccgcgtgattgtagttgggttagacagcaaattaggtctattatattgaaggccttgatattccactga-actcagtcgcttttggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAATTGAACCGGTACATTCCCACAGCAGCTGCTTTTGGAGGTATGTGTATTG
                    || |||  |  ||     || |   | ||         |   |||||||| |||      |  || |||   ||  |||   |   ||||   ||  ||||||||||||||| | |||||||| || || ||||| ||| | ||||  ||| ||||||| ||||||||||| || || || |||||||| || ||||| |
-------------------atatttgtagtttgtagtaagattcatgagctcaatgcctgaatctattatgttgtttat-taaattttcggttgtcactttttttttttttaatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAACTGAACCGATACATTCCCACCGCGGCAGCATTTGGAGGCATATGTATCG

upper sequence: PP1S323_56V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 6
gtaattgatttgaaacgatttaattgccgcgtgattgtagttgggttagacagcaaattaggtctattatattgaaggccttgatattccactgaactcagt-cgcttttggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAATTGAACCGGTACATTCCCACAGCAGCTGCTTTTGGAGGTATGTGTATTG
                 ||  ||| |         |||| |   | ||     ||||| |  | |||  ||||  | | |   | |||    ||  | || | |  |||||   |  ||||||||||||||| | |||||||| |||||||| || ||| | ||||  ||  ||||||| ||||||||||| || || || |||||||| || ||||| |
-----------------atcaaatagaaattcatctgtattaaagataccagacaaatgaactttatc-tatt--atgtcggtaaattttggtggtcacaatacatttttgaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAGCTGAACCGATACATTCCCACGGCCGCAGCATTTGGAGGCATCTGTATCG

upper sequence: PP1S323_56V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA12G17950.1 (Glycine max), 3'ss of exon 6
gtaattgatttgaaacgatttaattgccgcgtgattgtagttgggttagacagcaaattaggtctattatattgaaggccttgatattccactgaactcagtcgcttttggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAATTGAACCGGTACATTCCCACAGCAGCTGCTTTTGGAGGTATGTGTATTG
                  | || ||        | |  |  |||| | |||      ||  |  ||||| | |    |     ||| |  | |        | | ||||   ||  ||||||||||||||| | |||||||| || || || || ||| | ||||  ||| ||||||| ||||||||||| || || || |||||||| || |||||||
-----------------ctgtagtttgtagaaaaatcca--tgggctggacctatttttttgcttattaaaatttctgttgctataatgtatttcttgtttttgttttttaatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAGTCAAACTTGCAGAAAGAACTGAACCGATACATTCCCACTGCCGCAGCATTTGGAGGCATATGTATTG

upper sequence: PP1S323_56V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT1G78720.1 (Arabidopsis thaliana), 3'ss of exon 5
gta-attgatttgaaacgatttaattgccgcgtgattgtagttgggttagacagcaaattaggtctattatattgaaggccttgatattccactgaactcagtcgcttttggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAATTGAACCGGTACATTCCCACAGCAGCTGCTTTTGGAGGTATGTGTATTG
|||  ||  ||||       || ||  || | || |   ||    |||    | | ||||       ||   |     || |   |||  | || || |  ||     ||  |||  |||||||| |||||| | |||||||| ||||| || || |||||||| | |||| ||||||| ||||||||||| || || |||||||| ||| ||||||| |
gtatgtttgtttg-------ttgatcacc-cttgttctaagcaaagttgcggatccaattcttatctttgggtcttttgcatgactataactcttaaatttgtgttgattttttt--cagGAACAGCAAATGGTAATGCCTGGTCACCGAGACTCAAACCTTCAAAAGGAACTGAACCGATACATTCCCACGGCTGCAGCTTTTGGTGGTCTGTGTATCG

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|37828092|gb|BJ586104.1|BJ586104
EST:     GGATCGAAGTGTCAGGATCTTCTGCGCGANATGTTGCCAAGCAGCTCAAG                         GAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
genomic: GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAGgtaattgatt ... ggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
EST: gi|18341392|gb|BJ173427.1|BJ173427
EST:     GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAG                         GAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
genomic: GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAGgtaattgatt ... ggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
EST: gi|208371446|gb|DC955782.1|DC955782
EST:     GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAG                         GAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
genomic: GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAGgtaattgatt ... ggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
EST: gi|37847016|gb|BJ605024.1|BJ605024
EST:     GGATCGAAGTGTCAGGATCTTCTGCGCGAGATTTTGCCAAGCAGCTCAAG                         GAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
genomic: GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAGgtaattgatt ... ggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
EST: gi|37821396|gb|BJ579462.1|BJ579462
EST:     GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAG                         GAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
genomic: GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAGgtaattgatt ... ggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
EST: gi|37832704|gb|BJ590716.1|BJ590716
EST:     AGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAG                         GAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
genomic: AGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAGgtaattgatt ... ggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
EST: gi|37821747|gb|BJ579813.1|BJ579813
EST:     GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAG                         GAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
genomic: GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAGgtaattgatt ... ggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
EST: gi|208370161|gb|DC951760.1|DC951760
EST:     GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAG                         GAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
genomic: GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAGgtaattgatt ... ggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
EST: gi|208374672|gb|DC948644.1|DC948644
EST:     GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAG                         GAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
genomic: GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAGgtaattgatt ... ggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
EST: gi|37827746|gb|BJ585758.1|BJ585758
EST:     GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAG                         GAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
genomic: GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAGgtaattgatt ... ggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
EST: gi|37837683|gb|BJ595691.1|BJ595691
EST:     GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAG                         GAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
genomic: GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAGgtaattgatt ... ggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
EST: gi|37829525|gb|BJ587537.1|BJ587537
EST:     GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAG                         GAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
genomic: GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAGgtaattgatt ... ggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
EST: gi|37822184|gb|BJ580250.1|BJ580250
EST:     GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAG                         GAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
genomic: GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAGgtaattgatt ... ggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
EST: gi|7047224|gb|AW477118.1|AW477118
EST:     GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAG                         GAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
genomic: GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAGgtaattgatt ... ggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
EST: gi|18338671|gb|BJ170695.1|BJ170695
EST:     GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAG                         GAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
genomic: GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAGgtaattgatt ... ggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
EST: gi|37821435|gb|BJ579501.1|BJ579501
EST:     GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAG                         GAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
genomic: GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAGgtaattgatt ... ggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
EST: gi|37834254|gb|BJ592266.1|BJ592266
EST:     GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAG                         GAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
genomic: GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAGgtaattgatt ... ggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
EST: gi|18337235|gb|BJ169259.1|BJ169259
EST:     GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAG                         GAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA
genomic: GGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAGgtaattgatt ... ggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAA

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: 35 (upstream exon), 35 (downstream exon)
Score: 13

CTTCTACTTGACCTTCATGCTTACTGCTTGTGCGCTCTTCTCCAAGACCTGGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAGgtaattgatt ... ggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAATTGAACCGGTACATTCCCACAGCAGCTGCTTTTGGAGGTATGTGTATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattatattgaaggccttgatattccactgaactcagtcgcttttggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAATTGAACCGGTACATTCCCACAGCAGCTGCTTTTGGAGGTATGTGTATTG
              ccttgat  putative branch site (score: 13)
                ttgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgatttgaaacgatttaattgccgcgtgattgtagttgggttagacagcaaattaggtctattatattgaaggccttgatattccactgaactcagtcgcttttggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAATTGAACCGGTACATTCCCACAGCAGCTGCTTTTGGAGGTATGTGTATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG