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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttccaatcagtaacttttgatgttaaaatattccatgttgagagaagaaggggtattctagtgttatgttgtctgcttgtctgactgaacttcattccatcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATAT

Basic information

species Glycine max
transcript GLYMA03G42370.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 5
gtatgttccaatcagtaacttttgatgttaaa-atattccatgt-tgagagaagaaggggtattctagtgttatgttgtctgcttgtctgactgaacttcattccatcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATAT
         | |||    | ||  || | | | ||| |   | | | |  |    |||  | ||  |    | |  |  |||    | | | |  |  |||     | | | ||| |||||| | ||||| || ||||||||||||||  |||| || ||||||||||||||||||||||||||||||||||| || || |||||||||||||||
---------agtcatatgccttctatatcatatatagtttgtatgtcattgttctaggtctgttgaaccactgtactcactg----tataaattcatctcacgt--ttaatgcagTGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGACCCAAGTGTTACCATGATGACAGTTGAGGAAAAACCTGATGTGACATAT

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 5
gtatgttccaatcagtaacttttgatgttaaaatattccatgttgagagaagaaggggtattctagtg-ttatgttgtctgcttgtctg-actgaacttcattccat-cat--ttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATAT
                 || | || ||||     ||| ||  ||| | || |  |   | ||  |||  |||| || ||   | |  || | ||    |||| |  |  ||  | ||| |||||| ||||||| || || |||||||||||  |||| ||||| ||||| || || |||||||||||||| || ||||| || || |||||||| || 
-------------ttccacatatgttgtttg--cattgcac-ttgtgtgatgctgt--tcttgaagtaattatattatcaattggattgtattgtttctcatcctgtgtatcatacagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGATCCCAGCGTTACCATGATGACTGTGGAAGAAAAACCAGATGTGACTTAC

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 5
gtatgttccaatcagtaacttttgatgttaaaatattccatgttgagagaagaaggggtattctagtgttatgttgtctgcttgtctgactgaacttcattccatcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATAT
      | |  | | |  || |    | |    ||||   |   ||   |        | |||     |  ||    ||  ||||  ||    ||  | |    |  || ||| |||||| | ||||| || ||||||||||| || || || |||||||||||||||||||||||||||||||| || || || ||||| |||||||| || 
------ttcggttattt-ctctgcgcgctgtgctatttt-taccgaataagttgaaccttttcccacctagtgaaaact--ttgt--gatctcaca-cgtatgcttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGACCCAAGTGTTACCATGATGACCGTGGAGGAAAAGCCAGATGTGACGTAC

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 5
gtatgttccaatcagtaacttttgatgttaaaatattccatgttga-gagaagaaggggtattctagtgttatgttgtctgcttgtctgactgaacttcattccatcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATAT
     ||    | | |      || ||||    ||||        | |||  |||  | |  ||   |  |       ||  || ||| |||| | |        |  || ||| |||||| | ||||| || ||||||||||| || || || |||||||||||||||||||||||||||||||| || || || ||||| |||||||| || 
-----ttttggttatttctccatg-tgttgtgctattattcccgaatgagttgaactgtttctcacctagtgaaaaaacta-ttatctcactggattc-------ttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGACCCAAGTGTTACCATGATGACTGTGGAGGAAAAGCCAGATGTGACGTAC

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 5
gtatgttccaatcagtaacttttgatgt-taaaatattccatgttgagagaagaaggggtattctagtgttatgttgtctgcttgtctgactgaacttcattccatcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATAT
               |  ||||  | |  |  | |    |||  |    |  |       |||    |||| |  ||| | ||||| || || | |  ||| |   |||| |||||||||| |||| ||||||||||||||||||||  |||| ||||| ||||| |||||||| |||||||||||||| |||||||| || ||||||||||||
-------------gatgcctttaaaggcatgtacttcctcataatttttgtggtgaaaaaatttatttgtt-taatgtgttcttgtttgtctcaccaacatgctgccattgcagGGTTGATCGAAATAAATATCAGATTCAAATTCCCTTGCCCCCAAAGATTGATCCAAGTGTAACCATGATGACAGTAGAAGAGAAACCGGATGTGACATAT

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------------------gtatgt-tccaatcag---taactttt---gatgttaaaat-attcca-tgttgagagaagaagg-ggtattctag---tgttatgttgtctgc----ttgtctgactgaacttcattccatcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATAT
                                                                      || || || | |  |   | |||| |   || |||    | | | || | | ||  |||| ||  | |  |  |    || ||| ||||  |     ||  ||   |       | |  |    | |||||| ||||||||||| ||||| || || |||||| ||||||| || |||||||| || ||||| ||||||||||| || || ||||| ||||| || || 
gtacgttttcttaacttctcgttctactttatactcggttcctgagtgagctgtattgatcatgtgaagataggtctctagttgggcctcacttgtctggacgttcgttttactgcagtatcgaaggaaggagatgatgattaaaagctggtattttgttcgagatgttaactttttcggtcataatatacatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTAC

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|208278974|gb|GE076611.1|GE076611
EST:     ACCGACATTGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGA
genomic: ACCGACATTGAGGAAGGGATGCGTGTTGGgtatgttcca ... atcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGA
EST: gi|192301329|gb|FG990219.1|FG990219
EST:     CTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGA
genomic: CTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGGATGCGTGTTGGgtatgttcca ... atcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGA
EST: gi|213602675|gb|DB956611.1|DB956611
EST:     CTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGA
genomic: CTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGGATGCGTGTTGGgtatgttcca ... atcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGA
EST: gi|213589227|gb|DB957759.1|DB957759
EST:     CTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGA
genomic: CTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGGATGCGTGTTGGgtatgttcca ... atcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGA
EST: gi|151405667|gb|EV275481.1|EV275481
EST:     CTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGA
genomic: CTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGGATGCGTGTTGGgtatgttcca ... atcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGA
EST: gi|209702899|gb|BW667434.1|BW667434
EST:     CTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGA
genomic: CTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGGATGCGTGTTGGgtatgttcca ... atcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGA
EST: gi|193314171|gb|FK280098.1|FK280098
EST:     CTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGA
genomic: CTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGGATGCGTGTTGGgtatgttcca ... atcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGA
EST: gi|208215664|gb|GE008516.1|GE008516
EST:     CTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAACAAATATCAGATTCAAATTCCACTG
genomic: CTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGGATGCGTGTTGGgtatgttcca ... atcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTG
EST: gi|208127872|gb|GD924022.1|GD924022
EST:     TGGGCGACAAAGTTTTCACCCACCGACATTGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGA
genomic: TGGGCGACAAAG-TTTCACCCACCGACATTGAGGAAGGGATGCGTGTTGGgtatgttcca ... atcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGA
EST: gi|213600299|gb|DB970277.1|DB970277
EST:     CTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGGATGCGTGTTGN                         GGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGA
genomic: CTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGGATGCGTGTTGGgtatgttcca ... atcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattctagtgttatgttgtctgcttgtctgactgaacttcattccatcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATAT
                         gtctgac  putative branch site (score: 3)
                                         ttccatc  putative PPT
          ttatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttccaatcagtaacttttgatgttaaaatattccatgttgagagaagaaggggtattctagtgttatgttgtctgcttgtctgactgaacttcattccatcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC