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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtttaaattttctcatggtgaagtttcttgccactatctctgtatgctgtttattttttttagaaaactcaaatatttgattttggtgtttgcctcagGTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG

Basic information

species Glycine max
transcript GLYMA09G38010.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38010.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os12g10784.3 (Oryza sativa), 3'ss of exon 9
---ttgtttaaattttctcatggtgaagtttcttgccactatctctgtatgctgtttattttttttagaaaactcaaatatttgattttggtgtt-tgcctcagGTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG
   || ||| |||| ||| |     |   ||      ||  | |   |  ||| |  | | |  | | |  ||    |   |||||   | | ||     ||||||||||||| |||| ||  | |||||||||||||||||||| |||
tattttttttaattctcttaacccaataatttcatagacc-tttgaattagctatcaactatggt-atagtacgtggaccattgatg--gatattacatttcagGTAGCTGATGTAACGCATGCTCTACAACAGCCTGCTGGAAAAAAG

upper sequence: GLYMA09G38010.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G16340.2 (Arabidopsis thaliana), 3'ss of exon 9
---------------ttgtttaaattttctcatggtgaagtttcttgccactatctctgtatgctgtttattttttttagaaaactcaaatatt-tgattttggtgtttgcctcagGTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG
               || ||    ||||||  | |||    ||  |  |      |  |  |  |  ||   | ||||   | ||||  ||| | | |||| | | || || |||||| |||||||||||||| ||| ||||||| ||||| || ||||||
gtgagttaatattgcttcttgttcttttcttgttgtgggagtttatatcttggctttggctttatactttgatgtttt--gacactcgtataatataatttagttattggcttcagGTTGCTGATATAACTCATTCATTACAACAACCTGCAGGCAAGAAG
















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|192326691|gb|FK018878.1|FK018878
EST:     TTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATT                         GTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG
genomic: TTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATTgtaagtaaat ... tttgcctcagGTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG
EST: gi|208275338|gb|GE079372.1|GE079372
EST:     TTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATT                         GTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG
genomic: TTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATTgtaagtaaat ... tttgcctcagGTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG
EST: gi|23063937|gb|BU578710.1|BU578710
EST:     TTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATT                         GTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG
genomic: TTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATTgtaagtaaat ... tttgcctcagGTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG
EST: gi|58017972|gb|CX704714.1|CX704714
EST:     TTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATT                         GTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG
genomic: TTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATTgtaagtaaat ... tttgcctcagGTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG
EST: gi|208262320|gb|GE059681.1|GE059681
EST:     TTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATT                         GTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG
genomic: TTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATTgtaagtaaat ... tttgcctcagGTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG
EST: gi|58021325|gb|CX708066.1|CX708066
EST:     TTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATT                         GTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG
genomic: TTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATTgtaagtaaat ... tttgcctcagGTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG
EST: gi|57575913|gb|CX548884.1|CX548884
EST:     TTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATT                         GTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG
genomic: TTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATTgtaagtaaat ... tttgcctcagGTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG
EST: gi|151406834|gb|EV276649.1|EV276649
EST:     TTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATT                         GTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG
genomic: TTGTTGATCCACGTAACTTGGAGTGGATGAGAGAAGCCAATTGTCCCATTgtaagtaaat ... tttgcctcagGTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctgtttattttttttagaaaactcaaatatttgattttggtgtttgcctcagGTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG
                               atttgat  putative branch site (score: 5)
                                             tttgcctc  putative PPT
      tttattttttttagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtttaaattttctcatggtgaagtttcttgccactatctctgtatgctgtttattttttttagaaaactcaaatatttgattttggtgtttgcctcagGTAGCTGATATAACTCACTCACTACAACAGCCTGCTGGAAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG