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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtataaaatggatatatagtgacattatgactattgtcatttggaaagtatttgttttttagtaattatggattattgataatttttcactttggacagGACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAG

Basic information

species Glycine max
transcript GLYMA17G05390.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G05390.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os02g32570.2 (Oryza sativa), 3'ss of exon 11
tgtataaaatggatatatagtgacattatga-ctattg-tcatttggaaagtatttgttttttagtaattatggattattgataatttttcactttggacagGACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAG
   | |  ||  || | | |||  ||  ||| ||| |  |  ||||    ||     | || |    || ||   |   |  ||||  |    ||    ||||| || |||||||||||||||||||| ||||||||| | ||||| || ||||| ||||| ||||||||||  ||| |||| | | | || || || |||
aaaacattatacatttcttgtgctatagtgatctactaattttttgccgtgttagcatattcttagcatcatttgtgtatcgtaatcat--gtttccttcagGATCCTTGGTGGAATCCTGCTGTTGAAGAACAAGCTATCATGCGGATCCATCGAATTGGTCAAACAAAGAGTGTTTCCATCAAAAGATTCATCGTCAAG

upper sequence: GLYMA17G05390.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G057504_T01 (Zea mays), 3'ss of exon 7
tgtataaaatggatatatagtgacattatgactattgtcatttggaaagtatttgttttttagtaattatggattattgataatttttc------actttggac--agGACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAG
        |  |  ||||||||   |  |  ||  | |  | ||  |   |||   ||||   |   |     || ||  | | | |        |  || | |  ||||||| ||||||||||||||||| || ||||||||||| ||||| || ||||| ||||| ||||| ||||  ||| | || ||| | || || ||||||
--------acagtaatatagtgtactgttagcttcttttttatgctagccattatcttttagctgccttccacttgtttgtgagtgtcttatgagatgtttgccgaagGACCCTTGGTGGAATCCTGCTGTGGAAGAACAAGCTGTCATGCGCATCCATCGAATTGGTCAAACGAAGACTGTTTCTATCAGAAGATTCATCGTGAAG

upper sequence: GLYMA17G05390.1 (Glycine max), 3'ss of exon 18
lower sequence: AT5G22750.1 (Arabidopsis thaliana), 3'ss of exon 18
----tgtataaaatggatatatagtgacattatgactattgtcatttggaaagtatttgttttttagtaattatggat-tattgataatttt-tcactttggacagGACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAG
      | |    |  | |  | ||||    |||| || ||     |  ||| ||   |||||  || | ||   | | ||  || ||     | |  |   | |||| ||||||||||| || || || |||||||||||||||||||||||||||||||| || ||||| ||| | ||    || ||| | || || || |||
gccaccttttgtttcaaaagcttgtga----atgagtactgcacaatacaaaatag--gttttaaagaagtttcagttgtaaagaaaaccaagttatgtcctatagGATCCATGGTGGAACCCAGCGGTAGAGGAACAAGCTGTTATGCGTATTCATCGTATAGGGCAAACTAAGGAAGTCAAAATCAGAAGATTCATCGTTAAG

upper sequence: GLYMA17G05390.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv06s0061g01190.t01 (Vitis vinifera), 3'ss of exon 18
tgtataaaatggatatatagtgacattatga-ctattgtcatttggaaagtatttgttttttagtaattatg-gattattgataatttttcac--------tttggacagGACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAG
             |||   ||  |    ||  || ||  ||| |  ||  | ||| || || ||||| |  | | ||  | ||||||| |||         | |    |||| |||||||||||||| ||||| |||||||||||||||||||| ||||||||||||||||||||||| | |||    || |  ||||| |||||||||
----------tagtattccgtctctcactgttctgtttccatgttcaatatgtttcttgttaagtaactgagtgtttgataataatttctcatgggcattttctttgaagGATCCATGGTGGAATCCAGCTGTAGAGGAACAAGCTGTTATGCGGATTCATCGTATTGGACAAACAAAAAGGGTAATGATCAAGCGGTTCATTGTGAAG

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|193352415|gb|FK316811.1|FK316811
EST:     CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTCTTGTCATG                         GACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
genomic: CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATGgtacgtgcaa ... ctttggacagGACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
EST: gi|208062975|gb|GD860877.1|GD860877
EST:     CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATG                         GACC-ATGGTGGAATCCTGC
genomic: CTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATGgtacgtgcaa ... ctttggacagGACCCATGGTGGAATCCTGC
EST: gi|208340160|gb|GE133202.1|GE133202
EST:     TGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATG                         GACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT
genomic: TGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATGgtacgtgcaa ... ctttggacagGACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagtatttgttttttagtaattatggattattgataatttttcactttggacagGACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAG
                             tattgat  putative branch site (score: 3)
                                      tttttcacttt  putative PPT
     atttgttttttagtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtataaaatggatatatagtgacattatgactattgtcatttggaaagtatttgttttttagtaattatggattattgataatttttcactttggacagGACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG