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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgggcaacagtattcagactgcagctcaaaactagttttagtcatacaatttataattcacttgtcactagaaattatctccagcaatttttgataagctccctgaaatatattcactgtttttgattgtccagAGAAATTCCGCGAGATATATAACTTTGCTTTTGGCTGGGCAAAAGAGAAG

Basic information

species Glycine max
transcript GLYMA15G41570.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G41570.2 (Glycine max), 3'ss of exon 7
lower sequence: AT3G12760.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatgggcaacagtattcagactgcagctcaaaactagttttagtcatacaatttataattcacttgtcactagaaattatctccagcaatttttgataagctccctgaaatatattcactgt---ttttgattgtccagAGAAATTCCGCGAGATATATAACTTTGCTTTTGGCTGGGCAAAAGAGAAG
                  |    | |  |  |  |    ||   | ||    ||||  |||   |||     |   ||| || |     || || | | |  |   || ||| | ||   |||   |||   || | |||| || ||||  |||||||| |||||||||||||| ||||| |||||||||
----------------gtaaggagaaaattgagtcgccattcttttatctggtttacgatttgattg-----atggattgtccc-----atgttagctgacatatgtgtaatgtttttcttgtgcatttatctttttcagAAAAGTTCCATGAGATATACAACTTTGCTTTTGGGTGGGCGAAAGAGAAG

upper sequence: GLYMA15G41570.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv19s0085g00630.t01 (Vitis vinifera), 3'ss of exon 7
gtatgggcaacagtattcagactgcagctcaaaactagttttagtcatacaatttataattcacttgtcacta-gaaattatctccagcaatttttgataagctccctgaaatatattcactgtttttgattgt---ccagAGAAATTCCGCGAGATATATAACTTTGCTTTTGGCTGGGCAAAAGAGAAG
                                      |||| || |||     | | |||   |    |||  || | ||        || ||||| |    ||      | || ||  |||||| | | | |   ||||| || ||||| |||||||| |||||||||||||||||||| ||||| |||
-------------------------------------cttttggtaatag----tttgatttgatcagtactgtgagaataatagattgaacttttggtcttttcttgctgaaatgttgtctgtttcttactatattccagAAAAGTTCCGTGAGATATACAACTTTGCTTTTGGCTGGGCTAAAGAAAAG
















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|7692163|gb|AW760277.1|AW760277
EST:     TAAGTTCCGTGAAAAGATACCATATATGCGCTCTGAGCTGAAAGATGAAC                         AGAGATTCCGCGAGATATATAACTTTGCTTTTGGGCTGG
genomic: TAAGTTCCGTGAAAAGATACCATATATGCGCTCTGAGCTGAAAGATGAACgtatgggcaa ... gattgtccagAGAAATTCCGCGAGATATATAACTTTGCTTTTGG-CTGG
EST: gi|26057708|gb|CA800622.1|CA800622
EST:     TAAGTTCCGTGAAAAGATACCATATATGCGCTCTGAGCTGAAAGATGAAC                         AGAAATTCCGCGAGATATATAACTTTGCTTTTGGCTGGGCAAAAGAGAAG
genomic: TAAGTTCCGTGAAAAGATACCATATATGCGCTCTGAGCTGAAAGATGAACgtatgggcaa ... gattgtccagAGAAATTCCGCGAGATATATAACTTTGCTTTTGGCTGGGCAAAAGAGAAG
EST: gi|213615205|gb|DB965013.1|DB965013
EST:     TAAGTTCCGTGAAAAGATACCATATATGCGCTCTGAGCTGAAAGATGAAC                         AGAAATTCCGCGAGATATATAACTTTGCTTTTGGCTGGGCAAAAGAGAAG
genomic: TAAGTTCCGTGAAAAGATACCATATATGCGCTCTGAGCTGAAAGATGAACgtatgggcaa ... gattgtccagAGAAATTCCGCGAGATATATAACTTTGCTTTTGGCTGGGCAAAAGAGAAG
EST: gi|6666545|gb|AW278012.1|AW278012
EST:     TAAGTTCCGTGAAAAGATACCATATATGCGCTCTGAGCTGAAAGATGAAC                         AGAAATTCCGCGAGATATATAANCTT-GCTTTTGGCTGGGCAAAAGAGAAG
genomic: TAAGTTCCGTGAAAAGATACCATATATGCGCTCTGAGCTGAAAGATGAACgtatgggcaa ... gattgtccagAGAAATTCCGCGAGATATATAA-CTTTGCTTTTGGCTGGGCAAAAGAGAAG
EST: gi|8283983|gb|BE021542.1|BE021542
EST:     TAAGTTNCGTGAAAAGATACCATATATGCGCTCTGAGCTGAAAGATGAAC                         AGAAATTGCGCGAGATATATAACTTTGC
genomic: TAAGTTCCGTGAAAAGATACCATATATGCGCTCTGAGCTGAAAGATGAACgtatgggcaa ... gattgtccagAGAAATTCCGCGAGATATATAACTTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccagcaatttttgataagctccctgaaatatattcactgtttttgattgtccagAGAAATTCCGCGAGATATATAACTTTGCTTTTGGCTGGGCAAAAGAGAAG
                                         ttttgat  putative branch site (score: 4)
      aatttttgataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgggcaacagtattcagactgcagctcaaaactagttttagtcatacaatttataattcacttgtcactagaaattatctccagcaatttttgataagctccctgaaatatattcactgtttttgattgtccagAGAAATTCCGCGAGATATATAACTTTGCTTTTGGCTGGGCAAAAGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA