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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG

Basic information

species Physcomitrella patens
transcript PP1S87_129V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os05g43570.1 (Oryza sativa), 3'ss of exon 6
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgt-catagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
                                     | |   ||  ||| |   |  | ||| |||   | |  | ||||||| |  |||  | |   |     || | |      || | |  | || |||    | ||         ||| |||| |||||||||||||| || || ||||| ||||| |||||||| || || |||||||||||||| ||||| ||||| ||||||||
-------------------------------------gccacgttggcaagt---gaatatgtacatgagtctagttttctaggctctcatcaatatatg-----gtagta------tgcttagttatactcttt--tttt---------tttggcatgcagGCATATTCAACGGTTGGTACTCCTGATTACATTGCTCCAGAGGTTCTGCTGAAGAAAGGATATGGAATGGAATGTGACTG

upper sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os12g19290.1 (Oryza sativa), 3'ss of exon 5
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
                                               | ||       | |   | | ||| |||  |     ||||  | |  | |||      ||||| |   ||  | || | |   ||    |  | |              | ||||| ||||||||||| || || || ||||| |||||||| || |||||  |||||||||| ||||| ||||||||||||| 
---------------------------------------------gtcgatagaaaattgtagaaaaaatggcatggtaatcatttgtttgccaaagagcct---tggcagtgtgttttttatgtatttactttcatgataat-------------tgcagGCTTATTCAACAGTTGGTACACCTGATTACATTGCTCCGGAGGTACTATTGAAGAAAGGATATGGAATGGAGTGTGACTT

upper sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G375904_T01 (Zea mays), 3'ss of exon 5
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
                                      |     |||  ||| |  |||||  ||||    ||  ||||| | |  ||       |  || ||  ||   | |  |||| ||| | ||||| ||| | |||  |||            |||||||| ||||||||||| || || |||||||||||||| ||||| || ||||||||||| ||||| | ||||||||||||
--------------------------------------tgtctatcaagattccccccttttccataagcttc--cttcttgctgcgct------gaggtacacttga-gcacagttga-catgtttaatcgcaatt-ttgggaca------------cagGCATACTCAACAGTCGGTACACCTGATTATATTGCTCCAGAAGTGCTACTGAAGAAAGGATATGGAACGGAGTGTGACTG

upper sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
                                                             ||||   ||  ||| ||     ||| |     || || |  |  |     |      ||| | |  |    |||||  | |  |   | | ||||    ||| || || || ||||| || ||||| || || ||||| ||||| || |||||||||||||| |||||||| ||||||||
-------------------------------------------------------------gtcagtaat--catttt-----tttaccacttgatgactcgatctcttgatatgcaaatctttttga----caagtgatcattctg-gctgcgca----gGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG

upper sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA10G04410.2 (Glycine max), 3'ss of exon 6
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacaga-ggagtgcaag----tggcactccattgatcatctgtaatctcaagtattgacacaaagtttcg-catt-cagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
                                                                     | |  | || | ||| |  |||   | || ||  |||    ||    || |    |  | | | |   |  ||| |     || || |   |||| ||||| ||||| ||||| || || ||||||||||||||||| ||||| ||  |||||||||| ||||||||||| ||||| ||
--------------------------------------------------------------------ttatagtattttgggtatctatatgaatggtgtttaagatagtgttcttcgacatcttttttttgagtgcttgtaatttttgaatgtgtaaacattgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG

upper sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA13G18670.2 (Glycine max), 3'ss of exon 5
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactcca---ttgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
                                                              ||||  ||   || || |   | |   |  | ||   |  |  | |   || |    |  |  | |||  |   || | |||| |   |     |  | ||||| ||||| ||||| || || ||||||||||||||||| ||||| ||  |||||||||| ||||||||||| ||||| ||
-------------------------------------------------------------ttcatt-atactattttgtgtatatatgtggatagtgtttaagatagtgttctacatctttttgtgtgtgtttgtaatttttga-atgtataaatgt-tgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG

upper sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 5
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaat-ctcaagtattgacacaaagtttcgcatt-cagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
                                                          ||||  |   |  || | ||||   ||||  |   |     |||      | ||   ||||  | ||   |   |  |   ||  |      ||    | | ||||| ||||| |||||||| || || || |||||||| || ||||| || ||||||||||| ||||| ||||| ||||| ||
---------------------------------------------------------atttggta---acctcttgttctgactttgttt-tggcaagttgctgac--ccctgttttgacaaactacgacatttgaagcttttctttcttttcaatactgcagGCCTATTCTACAGTCGGAACACCTGACTATATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG

upper sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA02G00580.2 (Glycine max), 3'ss of exon 6
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcat-agatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
                                                   || |||||  ||  | | | ||  ||||     ||  |   || | ||           |||  || |||     | | | | |  | ||    |   |      || ||||| ||||| ||||| || || || |||||||||||||| ||||| || ||||||||||| |||||  |||| ||||| ||
---------------------------------------------------ttttgcctcagttttgacaagttttctttccccttctcgc-catacgata---------actatatagattgatggcattttaagcttttctttctttgcaata-atgcagGCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG

upper sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 5
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
                                                          |||| |  || | | |     |   ||| |       |  || | | ||  |||  || |||     | | | | |  | ||    |   |      || ||||| ||||| ||||| || || || |||||||||||||| ||||| || ||||||||||| |||||  |||| ||||| ||
---------------------------------------------------------ttttgcctcagttttgacaagttttctttccccctgtggctgtacga-tg--actatatagattgatggcattttaagcttttctttctttgcaata-atgcagGCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG

upper sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 5
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
                                              ||| ||  |  | |  |    ||  |  | ||      ||||  ||    | ||     || ||  | |  |  ||| || ||| |    | ||  ||     |  ||||    ||| ||||| |||||||| || || || |||||||| || ||||| || ||||||||||| ||||| ||||| ||||| ||
----------------------------------------------acatttggtaacctcttgtctgactttgttttgacaagttgctgacccctgtgt-----tgacaaactacgg--catttgaaattttttttcttttca----ataccgca----gGCCTATTCTACAGTCGGAACACCTGACTATATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG

upper sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT2G20470.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
                                                                      || |   |  |  ||  | |      || |   | | |   | |        | |||  ||| |    || |||||   | || |   ||||| ||||| ||||| ||||| |||||||| || ||||| ||||| ||| |||||||||||||||||||||||||||||||
----------------------------------------------------------------------gtaaggcttcatattcacctttga--gattttcaatagagtttctccctctgtgtgtg-tctga----ttaacaca---tgtcacga-cagGCTTATTCCACAGTTGGCACACCAGATTACATAGCTCCAGAAGTTCTGTTGAAGAAAGGCTATGGGATGGAGTGTGACTG

upper sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT1G30640.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
                                                          |||| |||  || || | |   || ||   ||    ||   |  |  || |  | |  | || ||| |        |  || |       || |  |  |||||| | ||| ||||| || ||||| ||||| ||||| ||||| || |||||||||||||| ||||| ||||||||||| ||
----------------------------------------------------------tttg-cattaatctcctttggaagtttcctatttt-agttatttatatgacctttccat-ataatcggagcgtaataagatggctctttcgtgtatcgatcagGCTTTTTCTACAGTAGGAACTCCCGATTACATTGCCCCTGAGGTGCTGCTGAAGAAAGGGTATGGAATGGAGTGTGATTG

upper sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 6
--gtaatcttctttgcattcc-attttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
  |   |  || ||   |||   || ||   |  ||  | | |   || |  |  ||   | ||    ||    || | |   || ||| |  || ||    |  ||||          || |||  |  |  || |   | ||| |     | ||   | ||||| ||||| ||||| || ||||| || ||||||||||| |||||  || |||||||||| ||||| ||||| ||||| ||
gtgagtttatcgttcttttcttgttctgagatttctacttgccagattgaacaaatc-atcattactttattcatcttatggaagtttttctcactgata--tataagt------tttctgttcaaatacag-cttattaagtgaaatgc--tatcaattgcagGCTTATTCTACAGTTGGAACTCCTGACTATATTGCTCCAGAAGTTTTGTTGAAGAAAGGATATGGCATGGAATGTGATTG

upper sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
                                                                 | ||   ||  |  |   |||| ||| | |     |  | |||   |   ||||   |||||  | | |  ||| |        | |   ||  |||| ||||||||||| || ||||| || || ||||| || |||||||||||||||||||| ||||| ||||||||||| ||
----------------------------------------------------------gccactctggactacacttcttttatttgaataaaaatctcaggtattggatatattttga--gtctgttttgt-atttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG

upper sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 5
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
                                                      |  ||||||      ||| ||     | ||||    |       | || |   |||    |  | |  | | | | || || | |||| |      | |   | ||||| ||||| || || || || || || || |||||||| ||||| ||||| |||||||| ||||||||||||||||| ||
------------------------------------------------------tcactttgtttcctctgttataagaaatgtttatgcaggaccctgcgctaactgcat---aagggtt-tatatcaactaaacttttgatattggaatac---tgcagGCCTATTCTACTGTTGGTACCCCTGACTACATTGCTCCAGAAGTGCTGCTTAAGAAAGGATATGGGATGGAGTGTGATTG

upper sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 5
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
                                                                                                | | | |  | | ||| | ||         |  || | | | ||  |  |  |||    |  ||||| |||||||| ||||| || ||||||||||||||||| ||||| || |||||||| || || |||||||||||||| ||
------------------------------------------------------------------------------------------------gtgcgtagcttgtacttcctt---------ttgtcccgatttttatctaagtgttctttaa-cagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTG

upper sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 5
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
                                                                                                | | | |  | | ||| | ||         |  || | | | || |   ||  || |     ||||| |||||||| ||||| || ||||||||||||||||| ||||| || |||||||| || || |||||||||||||| ||
------------------------------------------------------------------------------------------------gtgcgtagcttgtacttcctt---------ttgtcccga-tttttatctaagtttcctttaacagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTG

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: 16 (upstream exon), 25 (downstream exon)
Score: 2

AGATCCTCTAAATCCCAGGCAGCATAGATCTGCTTCACCCGGACCAAGGCGAACACAGCAGGAACAGCTACTTCACTGGCAAAGGAACAGACGAATGCTGgtaatcttct ... tcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
                              tattgac  putative branch site (score: 2)
                           aagtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA