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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcttaaaaacttttttttatgtttgaatcattggcagtattttggtgtttaatgtcattatagtttgttgacatgtttaaatctaaaaaatttgcagTATTATTTAGAGAAGAATCTTGATGCTAGGGAAAGAGAACTTGAACGCGAGGCAGAGCTTGATAGCAAAGCTCCTAAAGTGAAAGCCAAATCTAAGATGT

Basic information

species Glycine max
transcript GLYMA06G15200.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G15200.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0031g01640.t01 (Vitis vinifera), 3'ss of exon 7
----ttttcttaaaaacttttttttatgtttgaatcattggcagtattttggtgtttaatgtcattatagtttgttgacatgtttaaatctaaaaaatttgcagTATTATTTAGAGAAGAATCTTGATGCTAGGGAAAGAGAACTTGAACGCGAGGCAGAGCTTGATAGCAAAGCTCCTAAAGTGAAAGCCAAATCTAAGATGT
      | | | || |     |   ||| | |   || ||| | |     | || | | | |  ||   | ||  |||    || |||| |||     |  ||||||||| | |||||||| || ||||| || | |||||| ||||||||||||||||||||||||   || || |||||||| ||||||||||| |||||||
tcttcctgcctgaatatcaagtccaatgctagtg-cagtggaattgcccagttgctgagtttatttcctggttcctgattgtttgaaatttaatg---tcacagTATTATCTGGAGAAGAACCTCGATGCAAGAGCAAGAGAGCTTGAACGCGAGGCAGAGCTTGATGAGAAGGCCCCTAAAGTAAAAGCCAAATCCAAGATGT
















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|193322215|gb|FK284965.1|FK284965
EST:     TGATAGAAATTAAAGATGGCACTATACAGGATTATGCAGGTGATTACGAT                         TATTATTTAGAGAAGAATCTTGATGCT
genomic: TGATAGAAATTAAAGATGGCACTATACAGGATTATGCAGGTGATTACGATgtaagttaat ... aaatttgcagTATTATTTAGAGAAGAATCTTGATGCT
EST: gi|193518984|gb|FK472789.1|FK472789
EST:     TGATAGAAATTAAAGATGGCACTATACAGGATTATGCAGGTGATTACGAT                         TATTATTTAGAGAAGAATCTTGATGCTAGGGAAAGAG
genomic: TGATAGAAATTAAAGATGGCACTATACAGGATTATGCAGGTGATTACGATgtaagttaat ... aaatttgcagTATTATTTAGAGAAGAATCTTGATGCTAGGGAAAGAG
EST: gi|27446272|gb|CA953395.1|CA953395
EST:     TGATAGAAATTAAAGATGGCACTATACAGGATTATGCAGGTGATTACGAT                         TATTATTTAGAGAAGAATCTTGATGCTAGGGAAAGAGAACTTGAACGCGAG
genomic: TGATAGAAATTAAAGATGGCACTATACAGGATTATGCAGGTGATTACGATgtaagttaat ... aaatttgcagTATTATTTAGAGAAGAATCTTGATGCTAGGGAAAGAGAACTTGAACGCGAG
EST: gi|308099193|gb|HO761426.1|HO761426
EST:     TGATAGAAATTAAAGATGGCACTATACAGGATTATGCAGGTGATTACGAT                         TATTATTTAGAGAAGAATCTTGATGCTAGGGAAAGAGAACTTGAACGCGAG
genomic: TGATAGAAATTAAAGATGGCACTATACAGGATTATGCAGGTGATTACGATgtaagttaat ... aaatttgcagTATTATTTAGAGAAGAATCTTGATGCTAGGGAAAGAGAACTTGAACGCGAG
EST: gi|193528209|gb|FK487743.1|FK487743
EST:     TGATAGAAATTAAAGATGGCACTATACAGGATTATGCAGGTGATTACGAT                         TATTATTTAGAGAAGAATCTTGATGCTAGGGAAAGAGAACTTGAACGCGAG
genomic: TGATAGAAATTAAAGATGGCACTATACAGGATTATGCAGGTGATTACGATgtaagttaat ... aaatttgcagTATTATTTAGAGAAGAATCTTGATGCTAGGGAAAGAGAACTTGAACGCGAG
EST: gi|214007287|gb|DB986223.1|DB986223
EST:     TGATAGAAATTAAAGATGACATTATACAGGATTATGCAGGTGATTACGAT                         TATTATTTAGAGAAGAATCTTGATGCTAGGGAAAGAGAACTTGAACGCGAG
genomic: TGATAGAAATTAAAGATGGCACTATACAGGATTATGCAGGTGATTACGATgtaagttaat ... aaatttgcagTATTATTTAGAGAAGAATCTTGATGCTAGGGAAAGAGAACTTGAACGCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtgtttaatgtcattatagtttgttgacatgtttaaatctaaaaaatttgcagTATTATTTAGAGAAGAATCTTGATGCTAGGGAAAGAGAACTTGAACGCGAGGCAGAGCTTGATAGCAAAGCTCCTAAAGTGAAAGCCAAATCTAAGATGT
                                      atctaaa  putative branch site (score: 3)
                            acatgtttaaatctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcttaaaaacttttttttatgtttgaatcattggcagtattttggtgtttaatgtcattatagtttgttgacatgtttaaatctaaaaaatttgcagTATTATTTAGAGAAGAATCTTGATGCTAGGGAAAGAGAACTTGAACGCGAGGCAGAGCTTGATAGCAAAGCTCCTAAAGTGAAAGCCAAATCTAAGATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - taaaaac
- - - - - - - - - - -atgtttg
- - - - - - - - - - - - - - - - - - - - - -tttggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgac