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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatttgtgtgtgataggtttatatgtagagtatttttttttgttgccactattatttatgtttgtgacaaccatctttaatttgtgttattccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTG

Basic information

species Glycine max
transcript GLYMA15G00380.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G00380.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g27960.1 (Oryza sativa), 3'ss of exon 9
---tgatttgtg--tgtgataggtttatatgtagagt----atttttttttgttgccac---tattatttatgtt-tgtgacaaccatctttaatttgtgttattccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTG
   || || | |    |  |||  |  | ||||  ||    | ||| |    || | |    | ||| || | |  | |      |||  | | | ||  | | |  || ||||||||||| || || |||||||||||  | ||||||||  |||||||||| ||||||||||| || || ||||||||||| || ||  |     
gtgtgtttagagaacttattagcatcctctgtattgttcatactttatacaattacaagagatcttacttttatgatctagtgcacattctaattctgaataaatgtttccagGAAGGAACATCGAACTATTTTAAAGGCCTTATGCTTATCTTATGCTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTCAA

upper sequence: GLYMA15G00380.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G040017_T01 (Zea mays), 3'ss of exon 10
tgatttgtgtgtgataggtttatatgtagagtatttttttttgttgccactattatttatgtttgtgac--aaccatctttaatttgtgttattccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTG
 ||   ||         ||||   |  |  |   ||  ||||||  | | | | |  ||  ||||  |    ||| | |  ||| |   |  ||| |||||||| || ||  | || || || |||||  | ||||| || ||||| ||||||||||||||||||||||| || || ||||| || ||  ||    
-gaccagttatcatcttgtttcatttcaccgagattggttttgt-acgaatttgagctacatttggtatctgaccctgtgcaatgtacttgtttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAA

upper sequence: GLYMA15G00380.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 11
tgatttgtgtgtgataggtttatatgtagagtatttttttttgttg-ccactattatttatgtt-tgtgacaaccatctttaatttgtgttattccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTG
 ||   ||          |||   |  ||||   | |||| | | |  |     |   | || | | ||||  |||| |  |||     |  ||| |  ||||| || ||  | || || || |||||  | ||||| || ||||| ||||||||||||||||||||||| || || || || || ||  ||    
-gaccagttatcatcttatttcatttcagagatctgttttgtatggatctgagctgcatttgatatctgacc-ccatttgcaatgcacttgtttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA

upper sequence: GLYMA15G00380.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G053004_T03 (Zea mays), 3'ss of exon 9
----------------------tgatttgtgtgtgataggtttatatgtagagtatttttttttgttgccactattatttatgtttgtgacaaccatctttaatttgtgttat---tccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTG
                           | |      |   | | ||| |  |||   |      | ||    | |    ||| |||    | |   | || | ||| |  |||   |  || |||||||| || ||||| |||||||||||  | ||||| ||  ||||||| || ||||||||||| || ||||| || ||||| |||||| |     
gtatgcttacagaacaaagcaacatcctattctattttcctctgtatatgaagttactacacgggctgtt-ttgtagcctatttttagttctaatgttttcattttattatatatgtttttccagGAAGGCACATCAAACTATTTTAAAGGTCTTATGCTCATCTTATGCTACCTCATAGTTGCTGCAAGCTTTTTTGTCCATGTCGACCCTGATGCAA

upper sequence: GLYMA15G00380.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 10
tgatttgtgtgtgataggtttatatgtagagt--atttttttttgttgccactattatttatgtttg---tgacaaccatctttaatttgtgttattccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTG
     |||   | | || ||||| |    | |  |||| ||||   ||     ||||||| | |||    |||  |     || | ||||  ||  |  ||||||||||| || ||||| ||||||||||| ||||||||||| ||||||||||| |||||||| ||||| ||||| |||||||| ||||||| ||  |
----atgtacat-agagctttatcttcctaatcaatttattttccgtgtataaattatttcttttttacctgatgaattcattaattttggctttgtatttgcagGAAGGGACATCAAACTATTTTAAAGGTTTGATGCTTATTCTATGCTATCTCATAGTTGCAGCCAGCTTTTTTGTACATGTTGACCCTACAAAGG

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|8825719|gb|BE209385.1|BE209385
EST:     AGACTGCCACACTTTTTATCACTGTGTTAGTAGTTGCATTTATGATGCAG                         GAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTA
genomic: AGACTGCCACACTTTTTATCACTGTGTTAGTAGTTGCATTTATGATGCAGgtatgttatt ... ttccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTA
EST: gi|21887557|gb|BQ740770.1|BQ740770
EST:     AGACTGCCACACTTTTTATCACTGTGTTAGTAGTTGCATTTATGATGCAG                         GAAAGAACCTCAAATTATTTTAGAGGGTTGATGCTTATACTATGCTATCTA
genomic: AGACTGCCACACTTTTTATCACTGTGTTAGTAGTTGCATTTATGATGCAGgtatgttatt ... ttccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTA
EST: gi|209715668|gb|BW674354.1|BW674354
EST:     AGACTGCCACACTTTTTATCACTGTGTTAGTAGTTGCATTTATGATGCAG                         GAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTA
genomic: AGACTGCCACACTTTTTATCACTGTGTTAGTAGTTGCATTTATGATGCAGgtatgttatt ... ttccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTA
EST: gi|208033744|gb|GD828239.1|GD828239
EST:     AGACTGCCACACTTTTTATCACTGTGTTAGTAGTTGCATTTATGATGCAG                         GAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTA
genomic: AGACTGCCACACTTTTTATCACTGTGTTAGTAGTTGCATTTATGATGCAGgtatgttatt ... ttccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTA
EST: gi|208047251|gb|GD844348.1|GD844348
EST:     AGACTGCCACACTTTTTATCACTGTGTTAGTAGTTGCATTTATGATGCAG                         GAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTA
genomic: AGACTGCCACACTTTTTATCACTGTGTTAGTAGTTGCATTTATGATGCAGgtatgttatt ... ttccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTA
EST: gi|13481337|gb|BG510680.1|BG510680
EST:     AGACTGCCACACTTTTTATCACTGTGTTAGTAGTTGCATTTATAATGCAG                         GAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTA
genomic: AGACTGCCACACTTTTTATCACTGTGTTAGTAGTTGCATTTATGATGCAGgtatgttatt ... ttccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTA
EST: gi|208112415|gb|GD911504.1|GD911504
EST:     GACTGCCACTACTTTTTATCACTGTGTTAGTAGTTGCATTTATGATGCAG                         GAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTA
genomic: GACTGCCAC-ACTTTTTATCACTGTGTTAGTAGTTGCATTTATGATGCAGgtatgttatt ... ttccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccactattatttatgtttgtgacaaccatctttaatttgtgttattccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTG
                              ctttaat  putative branch site (score: 4)
                                          ttattcctt  putative PPT
     tattatttatgtttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatttgtgtgtgataggtttatatgtagagtatttttttttgttgccactattatttatgtttgtgacaaccatctttaatttgtgttattccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC