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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccatatctgggaaacatgatctgatgttcagttattcttatattctctattcatgtctctgtattttgttgatgatagttttttgtcattttgttgcagCTCCTGAAGTAGTTGAGAAGCCTGGGGATAACTCATTGGCTAGGCTGAAATTTTTGTACACTCAAGCAAAAGATCTTTCAGAAAGTGAAGCAAG

Basic information

species Glycine max
transcript GLYMA16G07460.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G07460.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G40550.2 (Arabidopsis thaliana), 3'ss of exon 1
--tccatatctgggaaacatgatctgatgttcagttattcttatattctctattcatgtctctgtattttgttgatgatagtttt-ttgtcattttgttgcagCTCCTGAAGTAGTTGAGAAGCCTGGGGATAACTCATTGGCTAGGCTGAAATTTTTGTACACTCAAGCAAAAGATCTTTCAGAAAGTGAAGCAAG
  |    || | |||  |||||  | |  || |   |   | || |    || | ||   | |  ||  || | |    || ||| |||| || ||| ||||||||||||  |||||||||||||||| ||||  ||||| || | ||| ||   |||||||| |||||| ||||| || ||||||| ||||| || 
agttttgattttggat-catgaagtaa--ttaaagaaaattaatctagattagtgattaatttagatactgctaaattaagctttgttgtaatgttgatgcagCTCCTGAGATAGTTGAGAAGCCTGGTGATATTTCATTAGCAAAGCTTAAGAATTTGTACATTCAAGCGAAAGAGCTCTCAGAAAATGAAGTAAC

upper sequence: GLYMA16G07460.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G27460.2 (Arabidopsis thaliana), 3'ss of exon 1
tccatatctgg-gaaacatgatctgatgttcagttattcttatattctctattcatgtctctgtattttgttgatgatagttttttgtcattttgt--tgcagCTCCTGAAGTAGTTGAGAAGCCTGGGGATAACTCATTGGCTAGGCTGAAATTTTTGTACACTCAAGCAAAAGATCTTTCAGAAAGTGAAGCAAG
 ||  || ||| |  |   ||| | | ||    ||   | | || |   |||  |  |   || ||| | | | |||   || | | |   ||     |||||| || ||  |||||||||||||||| ||||  |||||| | | ||| |||  |||||||| |||||||||||| |||||||||||||||| || 
-cctcatttggtggtatcagatataa-gtattattgagcctctaatacttatctac-ttggtgaattatctggctgactcttgtgtatgtgttgaaaatgcagCGCCGGAGATAGTTGAGAAGCCTGGTGATATTTCATTGTCAAAGCTTAAAAATTTGTACATTCAAGCAAAAGAGCTTTCAGAAAGTGAAGTAAC
















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|151405976|gb|EV275791.1|EV275791
EST:     AGAGGATATTCTGTCGGAGATCAACAAACTTCACAAGAAGCTTCAAGCAA                         CTCCTGAAGTAGTTGAGAAGCCTGGGGATAACTCATTGGCTAGGCTGAAAT
genomic: AGAGGATATTCTGTCGGAGATCAACAAACTTCACAAGAAGCTTCAAGCAAgtaagtttct ... tttgttgcagCTCCTGAAGTAGTTGAGAAGCCTGGGGATAACTCATTGGCTAGGCTGAAAT
EST: gi|208179556|gb|GD973587.1|GD973587
EST:     AGAGGATATTCTGTCGGAGATCAACAAACTTCACAAGAAGCTTCAAGCAA                         CTCCTGAAGTAGTTGAGAAGCCTGGGGATAACTCAT
genomic: AGAGGATATTCTGTCGGAGATCAACAAACTTCACAAGAAGCTTCAAGCAAgtaagtttct ... tttgttgcagCTCCTGAAGTAGTTGAGAAGCCTGGGGATAACTCAT
EST: gi|151411026|gb|EV280837.1|EV280837
EST:     AGAGGATATTCTGTCGGAGATCAACAAACTTCACAAGAAGCTTCAAGCAA                         CTCCTGAAGTAGTTGAGAAGCCTGGGGATAACTCATTGGCTAGGCTGAAAT
genomic: AGAGGATATTCTGTCGGAGATCAACAAACTTCACAAGAAGCTTCAAGCAAgtaagtttct ... tttgttgcagCTCCTGAAGTAGTTGAGAAGCCTGGGGATAACTCATTGGCTAGGCTGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctattcatgtctctgtattttgttgatgatagttttttgtcattttgttgcagCTCCTGAAGTAGTTGAGAAGCCTGGGGATAACTCATTGGCTAGGCTGAAATTTTTGTACACTCAAGCAAAAGATCTTTCAGAAAGTGAAGCAAG
                      tgttgat  putative branch site (score: 4)
                                  ttttttgtcatttt  putative PPT
                                  ttttttgtcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccatatctgggaaacatgatctgatgttcagttattcttatattctctattcatgtctctgtattttgttgatgatagttttttgtcattttgttgcagCTCCTGAAGTAGTTGAGAAGCCTGGGGATAACTCATTGGCTAGGCTGAAATTTTTGTACACTCAAGCAAAAGATCTTTCAGAAAGTGAAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - -catgatc
- - - - - - - - - - - tgatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgatg