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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcattaagttattttctctagcaatactttgttatgacaatctggtccgattggctcggaatttttggtttaactgccatgtttctttgaatatatatgtatttccggttgtgttccggttctgatttgaacttctgtggattccttgtcccttagGTGAGGAGATCATTTCAGGAGCTCAGCGTGTTCATGTGCCAGAATTTTTGGAACAACGTGCAGCAGCTTGCGGCATTGATGTCAAAACAATATCTTCGTA

Basic information

species Glycine max
transcript GLYMA17G34070.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G34070.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G31180.2 (Arabidopsis thaliana), 3'ss of exon 9
gtaggcattaagttattttctctagcaatactttgttatgacaatctggtccgattggctcggaatttttggtttaactgccatgtttctttgaatatatatgtatttccggttgtgttccggttctgatttgaacttctgtggattccttgtcccttagGTGAGGAGATCATTTCAGGAGCTCAGCGTGTTCATGTGCCAGAATTTTTGGAACAACGTGCAGCAGCTTGCGGCATTGATGTCAAAACAATATCTTCGTA
                                                             | |  | || |  | | | |  | || | |||  | |  |       ||  || || | | |  |  ||||||   |  ||  |    || |  | |||||||||||||||| ||||||||||| ||||| ||| | |||||| | ||||| |||||||||| ||  || |||||||||||||| ||||||||  | ||
-------------------------------------------------------------gtacatctttgagtgatt-cttttttaccttgtgtgttcaca-----ccaattatgctactgcac--atttgatactaagtttacgtgttctgtcctagGTGAGGAGATCATATCAGGAGCTCAACGTGTCCATATCCCAGAAGTCTTGGAGCAACGTGCAGGAGAATGTGGCATTGATGTCAAGACAATATCCACATA

upper sequence: GLYMA17G34070.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv04s0008g03010.t01 (Vitis vinifera), 3'ss of exon 8
gtaggcattaagttattttctctagcaatactttgttatgacaatctggtccgattggctcggaatttttggtttaactgccatgtttctttgaatatatatgtatttccggttgtgttccggttctgatttgaacttctgtggattccttgtcccttagGTGAGGAGATCATTTCAGGAGCTCAGCGTGTTCATGTGCCAGAATTTTTGGAACAACGTGCAGCAGCTTGCGGCATTGATGTCAAAACAATATCTTCGTA
                                                 |   |    | |   || ||| | |||     ||| |||  | | | | | |  |  ||     | |  || || | |  ||| || |||        ||||     ||||||||||||||||| ||||| ||||||||||||||||| || || || |||||| |||||||||  ||||| ||||||||||| || || |||||  | ||
-------------------------------------------------tataaaacacaccatatcttttgcttact---cattttttatggcaaacagacatcgttttttgtttcatcaggatttatttttaaattc--------cctttgtgtttagGTGAGGAGATCATCTCAGGGGCTCAGCGTGTTCATGTACCTGATTTCTTGGAAAAACGTGCAGAGGCTTGTGGCATTGATGTTAAGACTATATCAACATA
















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|254345857|gb|GR859504.1|GR859504
EST:     TTGCTATGACAATCCAGCATACAGCAACTCGTTTGATGTCTTTATTCGAG                         GTGAGGAGATCATTTCAGGAGCTCAGCGTGTTCATGTGCCAGAATTTTTGG
genomic: TTGCTATGACAATCCAGCATACAGCAACTCGTTTGATGTCTTTATTCGAGgtaggcatta ... tgtcccttagGTGAGGAGATCATTTCAGGAGCTCAGCGTGTTCATGTGCCAGAATTTTTGG
EST: gi|6726791|gb|AW311145.1|AW311145
EST:     TTGCTATGACAATCCAGCATACAGCAACTCGTTTGATGTCTTTATTCGAG                         GTGAGGAGATCATTTCAGGAGCTCAGCGTGTTCATGTGCCAGAATTTTTGG
genomic: TTGCTATGACAATCCAGCATACAGCAACTCGTTTGATGTCTTTATTCGAGgtaggcatta ... tgtcccttagGTGAGGAGATCATTTCAGGAGCTCAGCGTGTTCATGTGCCAGAATTTTTGG
EST: gi|17153630|gb|BM143563.1|BM143563
EST:     TCGTTTGATGTCTTTATTCGAG                         GTGAGGAGATCATTTCAGGAGCTCAGCGTGTTCATGTGCCAGAATTTTTGG
genomic: TCGTTTGATGTCTTTATTCGAGgtaggcatta ... tgtcccttagGTGAGGAGATCATTTCAGGAGCTCAGCGTGTTCATGTGCCAGAATTTTTGG
EST: gi|254345856|gb|GR859503.1|GR859503
EST:     TTGCTATGACAATCCAGCATACAGCAACTCGTTTGATGTCTTTATTCGAG                         GTGAGGAGATCATTTCAGGAGCTCAGCGTGTTCATGTGCCAGAATTTTTGG
genomic: TTGCTATGACAATCCAGCATACAGCAACTCGTTTGATGTCTTTATTCGAGgtaggcatta ... tgtcccttagGTGAGGAGATCATTTCAGGAGCTCAGCGTGTTCATGTGCCAGAATTTTTGG
EST: gi|9258964|gb|BE347111.1|BE347111
EST:     TTGCTATGACAATCCAGCATACAGCAACTCGTTTGATGTCTTTATTCGAG                         GTGAGGAGATCATTTCAGGAGCTCAGCGTGTTCATGTGCCAGAATTTTTGG
genomic: TTGCTATGACAATCCAGCATACAGCAACTCGTTTGATGTCTTTATTCGAGgtaggcatta ... tgtcccttagGTGAGGAGATCATTTCAGGAGCTCAGCGTGTTCATGTGCCAGAATTTTTGG
EST: gi|8283577|gb|BE021136.1|BE021136
EST:     TTGCTATGACAATCCAGCATACAGCAACTCGTTTGATGTCTTTATTCGAG                         GTGAGGAGATCATTTCAGGAGCTCAGCGTGTTCATGTGCCAGAATTTTTGG
genomic: TTGCTATGACAATCCAGCATACAGCAACTCGTTTGATGTCTTTATTCGAGgtaggcatta ... tgtcccttagGTGAGGAGATCATTTCAGGAGCTCAGCGTGTTCATGTGCCAGAATTTTTGG
EST: gi|16106116|gb|BI893856.1|BI893856
EST:     TTGCTATGACAATCCAGCATACAGCAACTCGCTTGATGTCTTTATTCGAG                         GTGAGGAGATCATTTCAGGAGCTCAGCGTGTTCATGTGCCAGAATTTTTGG
genomic: TTGCTATGACAATCCAGCATACAGCAACTCGTTTGATGTCTTTATTCGAGgtaggcatta ... tgtcccttagGTGAGGAGATCATTTCAGGAGCTCAGCGTGTTCATGTGCCAGAATTTTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccggttgtgttccggttctgatttgaacttctgtggattccttgtcccttagGTGAGGAGATCATTTCAGGAGCTCAGCGTGTTCATGTGCCAGAATTTTTGGAACAACGTGCAGCAGCTTGCGGCATTGATGTCAAAACAATATCTTCGTA
                  ttctgat  putative branch site (score: 3)
                                        ttccttgtccctt  putative PPT
                       atttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcattaagttattttctctagcaatactttgttatgacaatctggtccgattggctcggaatttttggtttaactgccatgtttctttgaatatatatgtatttccggttgtgttccggttctgatttgaacttctgtggattccttgtcccttagGTGAGGAGATCATTTCAGGAGCTCAGCGTGTTCATGTGCCAGAATTTTTGGAACAACGTGCAGCAGCTTGCGGCATTGATGTCAAAACAATATCTTCGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT