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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catcatgccttttcagaaactgtttttccttccacttgtttcttttttatgtttctattatgctgtgggatactgagaactgttccttccattcttgtagGTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAG

Basic information

species Glycine max
transcript GLYMA05G34790.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G70730.3 (Arabidopsis thaliana), 3'ss of exon 3
catcatgccttttcagaaactgtttttccttccacttgtttcttttttatgtttctatt-atgctgtgggatac----tgagaactgttccttcc--attcttgtagGTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAG
              | | |    | || | ||   ||| || || || | ||     |  ||| |     || |    | ||||    |  ||    | | ||  |||||| || || || || ||||||||||||||||||| |||| || |||||||||||
------------gtaaagatctctcttacctctctttgattgttgttcaggtaaaggtcgatgattgcaaattccatctaagaaagagtatttgttaactttttcagGTGCGACACTTGTGGTTTCTGGTGATGGTCGTTATTATTCAGAGCAAGCTATTCAG
















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|254347113|gb|GR856783.1|GR856783
EST:     TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAG                         GTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTA
genomic: TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAGgtacgaatcc ... attcttgtagGTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTA
EST: gi|193510090|gb|FK472090.1|FK472090
EST:     TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAG                         GTGCAACGCTTGTTGTATCTGGTGA
genomic: TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAGgtacgaatcc ... attcttgtagGTGCAACGCTAGTTGTATCTGGTGA
EST: gi|151396774|gb|EV266647.1|EV266647
EST:     TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAG                         GTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTA
genomic: TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAGgtacgaatcc ... attcttgtagGTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTA
EST: gi|209696727|gb|BW672906.1|BW672906
EST:     TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAG                         GTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTA
genomic: TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAGgtacgaatcc ... attcttgtagGTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTA
EST: gi|193671948|gb|FK616274.1|FK616274
EST:     TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAG                         GTGCAACGCTTGTTGTATCTGGTGATGG
genomic: TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAGgtacgaatcc ... attcttgtagGTGCAACGCTAGTTGTATCTGGTGATGG
EST: gi|213611739|gb|DB958861.1|DB958861
EST:     TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAG                         GTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTA
genomic: TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAGgtacgaatcc ... attcttgtagGTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTA
EST: gi|213617812|gb|DB967258.1|DB967258
EST:     TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAG                         GTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTA
genomic: TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAGgtacgaatcc ... attcttgtagGTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTA
EST: gi|7146923|gb|AW508845.1|AW508845
EST:     AAAAAGTTAGAG                         GTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTA
genomic: AAAAAGTTAGAGgtacgaatcc ... attcttgtagGTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTA
EST: gi|193681003|gb|FK622851.1|FK622851
EST:     TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAG                         GTGCAACGCTTGTTGTATCTGGTGAT
genomic: TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAGgtacgaatcc ... attcttgtagGTGCAACGCTAGTTGTATCTGGTGAT
EST: gi|213605046|gb|DB956379.1|DB956379
EST:     TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAG                         GTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTA
genomic: TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAGgtacgaatcc ... attcttgtagGTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTA
EST: gi|15285957|gb|BI469848.1|BI469848
EST:     TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAG                         GTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTA
genomic: TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAGgtacgaatcc ... attcttgtagGTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTA
EST: gi|6070595|gb|AW099982.1|AW099982
EST:     TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAG                         GTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAAGGAAGCT
genomic: TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAGgtacgaatcc ... attcttgtagGTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAA-GGAAGCT
EST: gi|193484433|gb|FK451139.1|FK451139
EST:     TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAG                         GTGCAACGCTAGTTGTATCTGGTGATGG
genomic: TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAGgtacgaatcc ... attcttgtagGTGCAACGCTAGTTGTATCTGGTGATGG
EST: gi|7684820|gb|AW755468.1|AW755468
EST:     TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAG                         GTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTA
genomic: TAACTTTGTTCAGTCAACATTCAATGCATTAACTGTGGAAAAAGTTAGAGgtacgaatcc ... attcttgtagGTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgtttctattatgctgtgggatactgagaactgttccttccattcttgtagGTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAG
                                  ctgttccttccattct  CT-rich tract
      tttctattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catcatgccttttcagaaactgtttttccttccacttgtttcttttttatgtttctattatgctgtgggatactgagaactgttccttccattcttgtagGTGCAACGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- -catgcct
- - - - - - - - - - - - - tccttcc
- - - - - - - - - - - - - -ccttcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatactg