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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagttagtaactttgtcatgagatttgtgcagtactttaaatgatcttgtgcctgaccaattcaacagtgaactgattgtttgtgtctttccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCAAACATGGCCATGGATATGATGAAGAAAAACC

Basic information

species Glycine max
transcript GLYMA08G44410.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G44410.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g32220.1 (Oryza sativa), 3'ss of exon 2
gaagttagtaactttgtcatgagatt--tgtgcagtacttta--aatgatcttgtgcctgaccaattcaacagtgaactgattgtttgtgtctttccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCAAACATGGCCATGGATATGATGAAGAAAAACC
   | |      ||||   ||| | |    |||| ||||  |  || ||  | | |  | | |  ||      |    |||   ||  ||  |   |  || ||||||| ||  || |   ||| || ||||   | |  |||||  | || ||    ||||| || |||||||||||||||||||| ||||||||||| ||||
-ctgctgaatgttttgatttgatactaacatgcattactccactaacgaa-tcgagtattatcttttgggtgttattttgacctttcttgagta--cgctgtagGAAAACGGATTGCTTCATGTCCCGAAAGAGGAAGCACAGAAAGCTCAGGCTGCCATGTTTTCAGATCCAAACATGGCCATGGACATGATGAAGAAGAACC

upper sequence: GLYMA08G44410.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G014313_T02 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------------gaagttagtaa--ctttgtcatgagatttgtgcagtactttaaatgatcttgtgcctgaccaattcaacagtgaactgattgtttgtgtctttccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCAAACATGGCCATGGATATGATGAAGAAAAACC
                                                                              ||   |  | |  ||| || || |   ||    |  |||  |     | ||   | ||||   | ||      | |   ||    || |||    | || ||||||||||  |  |   ||||||||| |   | |  |||||  | || |||   ||||| ||||||||||||||||||||||| ||||||||||| ||||
gtaattcaccaagtccagttaagaaaggatcaaggaaacgattaagcttaccatgtgcagtaacatgaatgccacgatgagtgtgatgatgcttagttattatgatttca-aacactgaatggactattccacatgacttctccagtgtatatcgtgtttacggtatctagtgactgtagGAAAATGGATTACTTCATGTTCCAAAGGAAGACGCGCAGAAGGCTCAGGCAGCCATGTTTTCTGATCCAAACATGGCCATGGACATGATGAAGAAGAACC

upper sequence: GLYMA08G44410.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G12590.1 (Arabidopsis thaliana), 3'ss of exon 2
gaagttagtaactttgtcatgaga-----tttgtgcagtacttta-aatgatcttgtgcctgaccaattcaacagtgaactgattgtttgtgtctttccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCAAACATGGCCATGGATATGATGAAGAAAAACC
     |  |   ||||  |   ||     | ||| || || |||   ||||   | |   |||   ||     | ||     | | | ||  | | |   ||| |||| |||||| || |   |||||| || ||  | |  || ||||| |||||    ||||| |||||||| ||||||||||||||||||||||||||||| |
--gtctctttgttttgctagaggaagtaatctgttcaatagtttctgatgagtgtat---tgatggatatgg-aatgtgagaagtatgtggttttgtttgttgtagGAGAATGGTTTGCTACATGTTCCCAAGGGAGAAGCTCAAAATCCACAAGCTGCTATGTTTTCTGATCCTAACATGGCCATGGATATGATGAAGAAAAATC

upper sequence: GLYMA08G44410.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0187g00170.t01 (Vitis vinifera), 3'ss of exon 2
gaagttagtaactttgtcatgagatttgtgcagtactttaaatgatcttgtgcc-tgaccaattcaacagtgaactgattgtttgtgtctttccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCAAACATGGCCATGGATATGATGAAGAAAAACC
     |  | |    ||    | | |   ||     |  |      ||| |    ||    |||| |  |  |  |       | ||  |  |||| | ||||||||||  |  ||  |||||| || || ||||  || ||| | || ||||| ||||||||||||||||||||||| ||||||||||||||||| ||||
-ggtcttttgagggagtgcatacactgaagctagcttgcagtgtgccttctcttgtgggttattctaatgccatttatgcacatttgcttgaccatggcagGAAAATGGATTACTGCATGTTCCTAAGGGTCAGGCGCAAAATGCTCAGGCACAAATGTTCTCTGATCCAAACATGGCTATGGATATGATGAAGAAGAACC

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|192306569|gb|FG997239.1|FG997239
EST:     TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAG                         GAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
genomic: TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAGgtttgtttga ... tccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
EST: gi|192312658|gb|FK004346.1|FK004346
EST:     TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAG                         GAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
genomic: TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAGgtttgtttga ... tccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
EST: gi|193464599|gb|FK429699.1|FK429699
EST:     TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAG                         GAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
genomic: TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAGgtttgtttga ... tccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
EST: gi|193609755|gb|FK560755.1|FK560755
EST:     TCGCAAAATTTATTTTTGTAACGAG                         GAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
genomic: TCGCAAAATTTATTTTTGTAACGAGgtttgtttga ... tccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
EST: gi|193451079|gb|FK415693.1|FK415693
EST:     TCGCAAAATTTATTTTTGTAACGAG                         GAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
genomic: TCGCAAAATTTATTTTTGTAACGAGgtttgtttga ... tccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
EST: gi|208254200|gb|GE051670.1|GE051670
EST:     TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAG                         GAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
genomic: TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAGgtttgtttga ... tccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
EST: gi|7042339|gb|AW472233.1|AW472233
EST:     TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAG                         GAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
genomic: TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAGgtttgtttga ... tccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
EST: gi|192312657|gb|FK004345.1|FK004345
EST:     TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAG                         GAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
genomic: TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAGgtttgtttga ... tccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
EST: gi|192323021|gb|FK016752.1|FK016752
EST:     TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAG                         GAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
genomic: TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAGgtttgtttga ... tccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
EST: gi|192294522|gb|FG987451.1|FG987451
EST:     TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAG                         GAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
genomic: TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAGgtttgtttga ... tccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
EST: gi|6913352|gb|AW394882.1|AW394882
EST:     GTATTCCTTCCAAGGCTCTTCGTGCTCGCANAATGTATTTGTGTAACGAG                         GAAAATGGTCTGTTGTTTGTTCCAGAAGGCCCAGG-CCAGAATCCGCAAGC
genomic: TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAGgtttgtttga ... tccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCC-AGGGCCAGAATCCGCAAGC
EST: gi|19053064|gb|BM731731.1|BM731731
EST:     TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAG                         GAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
genomic: TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAGgtttgtttga ... tccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
EST: gi|17023264|gb|BM094298.1|BM094298
EST:     TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAG                         GAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
genomic: TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAGgtttgtttga ... tccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
EST: gi|7588400|gb|AW704196.1|AW704196
EST:     TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAG                         GAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCACAAGCA
genomic: TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAGgtttgtttga ... tccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCA
EST: gi|298181915|gb|HO026090.1|HO026090
EST:     TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAG                         GAAAATGGTCTGTTGTTTGTTCCAAAAGG
genomic: TTATTCCTTCCAAGGCTTTTCGTGCTCGCAAAATTTATTTTTGTAACGAGgtttgtttga ... tccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgtgcctgaccaattcaacagtgaactgattgtttgtgtctttccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCAAACATGGCCATGGATATGATGAAGAAAAACC
                          aactgat  putative branch site (score: 3)
                                         tctttccatt  putative PPT
              aattcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagttagtaactttgtcatgagatttgtgcagtactttaaatgatcttgtgcctgaccaattcaacagtgaactgattgtttgtgtctttccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCAAACATGGCCATGGATATGATGAAGAAAAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - tcatgag
- - - - - - - - - - - - tttgtgc
- - - - - - - - - - - - - - - - - - - - - - - cttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - -ctgacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgt