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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attatttgatttggtgtattacacccccccctcccccccccccccccacacacacacacactattttagcaatttgacattattatgattattcttacagATTTTGATTTTGGATGAGGCTGATAGACTCTTAGATATGGGATTCCAGAAGCAGATAACTTCTATTATATCTCTCTTGCCTAAGCTTCGGAGAACTGGTC

Basic information

species Glycine max
transcript GLYMA11G35640.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G35640.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g07080.1 (Oryza sativa), 3'ss of exon 2
attatttgatttggtgtattacacccccccctcccccccccccccccacacacacacacactattttagcaatttgacattat-tatgattattctta-cagATTTTGATTTTGGATGAGGCTGATAGACTCTTAGATATGGGATTCCAGAAGCAGATAACTTCTATTATATCTCTCTTGCCTAAGCTTCGGAGAACTGGTC
 |  |||     |   |   | |  |     |    |       |    | |  || |    |  |    || |||   || | ||||  | |||  | |||||||||||  ||||||| |||||||| || || ||| | ||||||||||||||||| || || ||||| ||    ||||| |||||  ||||||| || |
gtggttttggaagcaattgaaaattcatgtgttgttcttttgtgcttgaa-atgcaaatctgacat----aaattgttgttgtgtatgtgttttcgaagcagATTTTGATCCTGGATGAAGCTGATAGGCTGTTGGATTTAGGATTCCAGAAGCAGATTACGTCGATTATTTCGAAGTTGCCAAAGCTGAGGAGAACAGGGC

upper sequence: GLYMA11G35640.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G125947_T01 (Zea mays), 3'ss of exon 2
--attatttgatttggtgta-----ttacacccccccctcccccccccccccccacacacacacacactattttagcaatttgacattattatgattattctta-----cagATTTTGATTTTGGATGAGGCTGATAGACTCTTAGATATGGGATTCCAGAAGCAGATAACTTCTATTATATCTCTCTTGCCTAAGCTTCGGAGAACTGGTC
    | |  ||      | |      |       ||  | |  |            | |        |  || |   |  |  |  |  || ||  |||   |      |||||||||||  | |||||||||||||| ||||| ||||||||||||||||| || || |  |  ||  | ||  | ||||| |||||  |||| ||||| |
gtggtttcagagacaacggaaccctctgtgtgatccttttctgcttaatttggtgaaaatgttgtggcatttatgttagctccatttgtttttgtgtatgtgtgggaagcagATTTTGATCCTAGATGAGGCTGATAGGCTCTTGGATATGGGATTCCAGAAACATATTAACTTCATACTTTCAATGTTGCCAAAGCTGAGGAGGACTGGGC

upper sequence: GLYMA11G35640.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G367714_T01 (Zea mays), 3'ss of exon 4
attatttgatttggtgtattac---acccccccctcccccccccccccccacacacacacacactattttagcaatt----tgacattatt-----atgattattctta-----cagATTTTGATTTTGGATGAGGCTGATAGACTCTTAGATATGGGATTCCAGAAGCAGATAACTTCTATTATATCTCTCTTGCCTAAGCTTCGGAGAACTGGTC
      || |||     |  ||   |||| |        ||    |  |   |   |   | | | || | ||| ||    |  |   |||      ||  |||   |      |||||||||||  | |||||||||||||| ||||| ||||||||||||||||| || || |  |   |  | ||  | ||||| |||||  |||| ||||| |
-----gtggtttcagagacaacggaaccctctgtgtgatccttttctgctgaatttagtgaaaatgttgtggcatttatgttagctccatttgtttttgtgtatgtgtgggaagcagATTTTGATCCTAGATGAGGCTGATAGGCTCTTGGATATGGGATTCCAGAAACATATTAACTTCGTACTTTCAATGTTGCCAAAGCTGAGGAGGACTGGGC

upper sequence: GLYMA11G35640.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G303752_T01 (Zea mays), 3'ss of exon 2
--attatttgatttggtgta-----ttacacccccccctcccccccccccccccacacacacacacactattttagcaatttgacattattatgattattctta-----cagATTTTGATTTTGGATGAGGCTGATAGACTCTTAGATATGGGATTCCAGAAGCAGATAACTTCTATTATATCTCTCTTGCCTAAGCTTCGGAGAACTGGTC
    | |  ||      | |     |||      ||  |    |            | |        |  || |   |  |  |  |  || ||  ||| | |      |||||||||||  | |||||||||||||| ||||| ||||||||||||||||| || || |  |  ||  | ||  | ||||| |||||  |||| ||||| |
gtggtttcagagacaacggaaccctttatgtgatccttttatgctgaatttggtgaaaatgttgtggcatttatgttagctccatttgtttttgtgtatgcatgggaagcagATTTTGATCCTAGATGAGGCTGATAGGCTCTTGGATATGGGATTCCAGAAACATATTAACTTCATACTTTCAATGTTGCCAAAGCTGAGGAGGACTGGGC

upper sequence: GLYMA11G35640.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0067g01900.t01 (Vitis vinifera), 3'ss of exon 2
---attatttgatttggtgtattacacccccccctcccccccccccccccacacacacacacactattttagcaatttgacattattatgattattcttacagATTTTGATTTTGGATGAGGCTGATAGACTCTTAGATATGGGATTCCAGAAGCAGATAACTTCTATTATATCTCTCTTGCCTAAGCTTCGGAGAACTGGTC
   |||   |  |   | |||| | | ||             ||            | | | | ||  ||   | |     ||| || |  |  ||   |||||||||||||||||| ||||||||||| || ||||||||||||||||||||||| || ||||| || ||  ||| | | || |||||||| ||||||||||
gaaatttcctcttgctgagtatgatatccttttggatttttaccaagtttgtttcaaaata-attaaatttatactcctgaatttttgt--tggttggaacagATTTTGATTTTGGACGAGGCTGATAGGCTTTTAGATATGGGATTCCAGAAGCAAATTACTTCCATCATTGCTCGCCTACCAAAGCTTCGCAGAACTGGTC

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|208267505|gb|GE064146.1|GE064146
EST:     TATATGACATAATGAATCGGATGGATGTTTTGGATCTTAAAAACCTTGAG                         ATTTTGATTTTGGATGAGGCTGATAGACTCTTAGATATGGGATTCCAGAAG
genomic: TATATGACATAATGAATCGGATGGATGTTTTGGATCTTAAAAACCTTGAGgtatgtgttt ... attcttacagATTTTGATTTTGGATGAGGCTGATAGACTCTTAGATATGGGATTCCAGAAG
EST: gi|41146019|gb|CK606230.1|CK606230
EST:     TATATGACATAATGAATCGGATGGATGTTTTGGATCTTAAAAACCTTGAG                         ATTTCGATTTTGGA
genomic: TATATGACATAATGAATCGGATGGATGTTTTGGATCTTAAAAACCTTGAGgtatgtgttt ... attcttacagATTTTGATTTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccacacacacacacactattttagcaatttgacattattatgattattcttacagATTTTGATTTTGGATGAGGCTGATAGACTCTTAGATATGGGATTCCAGAAGCAGATAACTTCTATTATATCTCTCTTGCCTAAGCTTCGGAGAACTGGTC
                          atttgac  putative branch site (score: 4)
                                           ttattctt  putative PPT
                         aatttgacattattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attatttgatttggtgtattacacccccccctcccccccccccccccacacacacacacactattttagcaatttgacattattatgattattcttacagATTTTGATTTTGGATGAGGCTGATAGACTCTTAGATATGGGATTCCAGAAGCAGATAACTTCTATTATATCTCTCTTGCCTAAGCTTCGGAGAACTGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - tgatttg
- - - - - - - - - - - -ccccccc
- - - - - - - - - - - - - - - ctccccc
- - - - - - - - - - - - - - - - - - - - - - - -acacaca