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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttattttgtttaataattaaataagagaataatttaaagagctgtggtatatgaaagtttgaaacttaactactgaaacttttgttcactttatcacagATGACAACAGAGCCAAGGGTAGTGGATTAGCTCCATGGCCTGCAAGATTGACTAGTCCTCCTCCTAGATTAGCTGACTTTGGCTATTCAAATGACATGTT

Basic information

species Glycine max
transcript GLYMA10G32470.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G14360.1 (Arabidopsis thaliana), 3'ss of exon 5
tttattttgtttaataattaaataagagaataatttaaagagctgtggtatatgaaagtttgaaacttaactactgaaacttttgttcactttatcacagATGACAACAGAGCCAAGGGTAGTGGATTAGCTCCATGGCCTGCAAGATTGACTAGTCCTCCTCCTAGATTAGCTGACTTTGGCTATTCAAATGACATGTT
                      ||||     ||  |      |  |  |  || | ||  |  |  |   |  |||||   ||| ||    || ||  ||||||| ||| | ||||||| |||||||||||||||||||| ||  | || ||   ||||||||| ||| | ||||| ||||| |||||||  | ||||||
---------------------gtaagttttcaagcttcttctcgcttttcaataacagcgtatattt---cctctgaactcttttttggggttgtcttagATGACCACAAAACCAAGGGAAGTGGATTAGCTCCATGGCCAGCTCGGTTAACCTCTCCTCCTCCCAGACTTGCTGATTTTGGATATTCAACGGGCATGTT

upper sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------------tttattttgtttaataattaaataa-gagaataatttaaagagct-gtggtatatgaaagtttgaaacttaac-----tactgaaacttttgttcactttatcac-agATGACAACAGAGCCAAGGGTAGTGGATTAGCTCCATGGCCTGCAAGATTGACTAGTCCTCCTCCTAGATTAGCTGACTTTGGCTATTCAAATGACATGTT
                 | | || | || | |||   | |   |  | ||| || |  |||| ||| ||| || |  | ||| |   ||       ||| ||   ||| |  || ||   |  ||||||| ||| | ||||||| |||||||| ||||||||||| ||  |||| ||   |||||||||| |  ||||||||||||||||||| | |||||| ||
gtgagttttcattattctatcttcttttcactaacagagtttcgtcattaacttcacaagcttgtgatat-tgcatatctgagaacaaatatgctcactaaattatttttcaacgtttctattagATGACCACAAAACCAAGGGAAGTGGATTGGCTCCATGGCCAGCTCGATTAACCTCTCCTCCTCCTCGGCTAGCTGACTTTGGCTATTCCACTGACATTTT
















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|15813138|gb|BI785413.1|BI785413
EST:     TGCAGTATGGGGAGTAAATATGAAAGCATGCATAACACCTTACAGTGATC                         ATGACAACAGAGCCAAGGGTAGTGGATTAGCTCCATGGCCTGCAAGATTGA
genomic: TGCAGTATGGGGAGTAAATATGAAAGCATGCATAACACCTTACAGTGATCgtgagtactc ... tttatcacagATGACAACAGAGCCAAGGGTAGTGGATTAGCTCCATGGCCTGCAAGATTGA
EST: gi|8827658|gb|BE211388.1|BE211388
EST:     TGCAGTATGGGGAGTAAATATGAAAGCATGCATAACACCTTACAGTGATC                         ATGACAACAGAGCCAAGGGTAGTGGATTAGCTCCATGGCCTGCAAGATTGA
genomic: TGCAGTATGGGGAGTAAATATGAAAGCATGCATAACACCTTACAGTGATCgtgagtactc ... tttatcacagATGACAACAGAGCCAAGGGTAGTGGATTAGCTCCATGGCCTGCAAGATTGA
EST: gi|11688443|gb|BF596119.1|BF596119
EST:     TGCAGTATGGGGAGTAAATATGAAAGCATGCATAACACCTTACAGTGATC                         ATGACAACAGAGCCAAGGGTAGTGGATTAGCTCCATGGCCTGCAAGATTGA
genomic: TGCAGTATGGGGAGTAAATATGAAAGCATGCATAACACCTTACAGTGATCgtgagtactc ... tttatcacagATGACAACAGAGCCAAGGGTAGTGGATTAGCTCCATGGCCTGCAAGATTGA
EST: gi|207694344|gb|GD677407.1|GD677407
EST:     TGCAGTATGGGGAGTAAATATGAAAGCATGCATAACACCTTACAGTGATC                         ATGACAACAGAGCCAAGGGTAGTGGATTAGCTCCATGGCCTGCAAGATTGA
genomic: TGCAGTATGGGGAGTAAATATGAAAGCATGCATAACACCTTACAGTGATCgtgagtactc ... tttatcacagATGACAACAGAGCCAAGGGTAGTGGATTAGCTCCATGGCCTGCAAGATTGA
EST: gi|151399856|gb|EV269727.1|EV269727
EST:     TGCAGTATGGGGAGTAAATATGAAAGCATGCATAACACCTTACAGTGATC                         ATGACAACAGAGCCAAGGGTAGTGGATTAGCTCCATGGCCTGCAAGATTGA
genomic: TGCAGTATGGGGAGTAAATATGAAAGCATGCATAACACCTTACAGTGATCgtgagtactc ... tttatcacagATGACAACAGAGCCAAGGGTAGTGGATTAGCTCCATGGCCTGCAAGATTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtatatgaaagtttgaaacttaactactgaaacttttgttcactttatcacagATGACAACAGAGCCAAGGGTAGTGGATTAGCTCCATGGCCTGCAAGATTGACTAGTCCTCCTCCTAGATTAGCTGACTTTGGCTATTCAAATGACATGTT
                   acttaac  putative branch site (score: 3)
                                  cttttgttcacttt  putative PPT
                 aaacttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttattttgtttaataattaaataagagaataatttaaagagctgtggtatatgaaagtttgaaacttaactactgaaacttttgttcactttatcacagATGACAACAGAGCCAAGGGTAGTGGATTAGCTCCATGGCCTGCAAGATTGACTAGTCCTCCTCCTAGATTAGCTGACTTTGGCTATTCAAATGACATGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - -gctgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actactg