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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattcagaatccattgacttcacccttatgttttttctaacttatgtgcattattttttgtcttctcccttgattatttggttttcggtctaaaatatgcatacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGTGACTACCTTTCCGTGAAAGGACCTAAG

Basic information

species Glycine max
transcript GLYMA03G00920.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G00920.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g59930.1 (Oryza sativa), 3'ss of exon 3
-----gtatattcagaatccattgacttcacccttatgttttttctaacttatgtgcattattttttgtcttctcccttgattatttggttttcggtctaaaatatgcatacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGTGACTACCTTTCCGTGAAAGGACCTAAG
      | |||||||  ||  |  |||  |    |   | |||   ||     |  |||    || |||      |    |  |||||   ||     |    |   ||||    |||||||||| |||||||| |||||||||||||||||||| |||   |||||||| ||  | || ||||| |||||||||
gtaaattgtattcagt-tctttatactgtatgaatgcttgtttgtcaatcctggaacatatcgttatgtgccacacaagcaggatttgccatttaactt----ttctcataatgcagATGTACCCTCAAGGAAGAATGTCACACCATTTCCGTGAAATGAAAGTTGGTGATTATATGTCTGTGAAGGGACCTAAG

upper sequence: GLYMA03G00920.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatattcagaatccattgacttcacccttatgttttttct-aacttatgtgcattattttttgtcttctcccttgattatttggttttcggtctaaaatatgcatacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGTGACTACCTTTCCGTGAAAGGACCTAAG
                  |  |   |    ||   |||||| |||||     | |  |||||    |      ||  || |      |||  || ||||         | |||||||| || |||||| ||||||| || |||||| | |||||||||||||| ||| | ||| |||| || ||||| |||
------------------gtatatgcttaaatacattttctcaacttg---acttggtttttgaattcgggtgttccttctccctaattcaatcgaaaaatgctgccaaatagATGTATCCGCAAGGACGGATGTCTCATCATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAG

upper sequence: GLYMA03G00920.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0056g01150.t01 (Vitis vinifera), 3'ss of exon 3
gtatattcagaatccattgacttcacccttatgttttttctaacttatgtgcattattttttgtcttctcccttgattatttggttttcggtctaaaatatgcatacat-tagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGTGACTACCTTTCCGTGAAAGGACCTAAG
     ||   |    |||    | |   |  ||   ||  ||| |    |   |||||| ||   || || | |    || || | |  | | |    | | | |  |  |||||||| |||||||||||||||||||| ||||| || ||||||||||| ||||| || ||  | || || ||||| |||
----gtttgtatctgatt---cttatattattggacttcgtaattggctttatttatttatttatttgtctcatttaaatctg-tgtctgctatgtgtttttcctgtaaatagATGTATCCACAAGGAAGGATGTCACATCATTTTCGAGAGATGCGTGTAGGTGATTATCTGGCTGTAAAGGGACCCAAG

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|192301598|gb|FG994782.1|FG994782
EST:     CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG                         ATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
genomic: CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
EST: gi|213587981|gb|DB971456.1|DB971456
EST:     CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG                         ATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
genomic: CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
EST: gi|213617616|gb|DB969328.1|DB969328
EST:     CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG                         ATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
genomic: CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
EST: gi|209728695|gb|BW655402.1|BW655402
EST:     CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG                         ATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
genomic: CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
EST: gi|151407227|gb|EV277042.1|EV277042
EST:     CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG                         ATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
genomic: CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
EST: gi|10236160|gb|BE805048.1|BE805048
EST:     CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG                         ATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
genomic: CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
EST: gi|151394787|gb|EV264658.1|EV264658
EST:     CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG                         ATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
genomic: CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
EST: gi|13251953|gb|BG362856.1|BG362856
EST:     TTTTGAACTAGTTATTAAG                         ATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
genomic: TTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
EST: gi|58021619|gb|CX708360.1|CX708360
EST:     CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG                         ATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
genomic: CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
EST: gi|298183643|gb|HO028856.1|HO028856
EST:     CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG                         ATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
genomic: CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
EST: gi|151401464|gb|EV271278.1|EV271278
EST:     CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAATTATTAAG                         ATGTACCCACAAGGAAAGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
genomic: CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
EST: gi|193418380|gb|FK385180.1|FK385180
EST:     CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG                         ATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
genomic: CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
EST: gi|298174935|gb|HO014852.1|HO014852
EST:     CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG                         ATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
genomic: CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
EST: gi|151403993|gb|EV273803.1|EV273803
EST:     CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG                         ATGTACCCACAGGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
genomic: CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
EST: gi|298189804|gb|HO038207.1|HO038207
EST:     CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG                         ATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
genomic: CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
EST: gi|13788917|gb|BG651508.1|BG651508
EST:     CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG                         ATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
genomic: CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
EST: gi|37995436|gb|CF807025.1|CF807025
EST:     CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG                         ATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
genomic: CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
EST: gi|18690778|gb|BM519626.1|BM519626
EST:     CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG                         ATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
genomic: CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
EST: gi|298186113|gb|HO036746.1|HO036746
EST:     CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG                         ATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
genomic: CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
EST: gi|151399348|gb|EV269219.1|EV269219
EST:     CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG                         ATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
genomic: CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT
EST: gi|298178943|gb|HO024678.1|HO024678
EST:     CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG                         ATGTACCCACAAGGAAGGATGTCACACCATTTCTGTGAGATGCGTGTTGGT
genomic: CTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAGgtatattcag ... catacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgtcttctcccttgattatttggttttcggtctaaaatatgcatacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGTGACTACCTTTCCGTGAAAGGACCTAAG
                                 gtctaaa  putative branch site (score: 3)
               ttgattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattcagaatccattgacttcacccttatgttttttctaacttatgtgcattattttttgtcttctcccttgattatttggttttcggtctaaaatatgcatacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGTGACTACCTTTCCGTGAAAGGACCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG