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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgattggaaattttaactggtccttcttactttttgagggtgatatgatggtaagttttgaaattttctgatcttctaagctttagccattttaaacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTCGGAAACAAAGAAAACTCTGGCAAG

Basic information

species Glycine max
transcript GLYMA14G16070.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G16070.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g48160.3 (Oryza sativa), 3'ss of exon 4
-----------------------------ctgattggaaattttaa--ctggtccttcttactttttgagggtgatatgatggtaagtttt--------------gaaattttctgatcttctaagctttagccatttta-------aacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTCGGAAACAAAGAAAACTCTGGCAAG
                             | | | || |||  |    |||| | | | |  ||| |||   |  | |     || | |||               | |  | |  ||   ||    |||     | ||          |||||||| || || |||||||| |||||||| |||||||| |||||||||||||| || ||||||
gtaccaagcattccatttcaggtttttttcagttgggcaatgctgtttctgggcttccctgttttctgaactttctgttgctatatgcttttctgattacaccaaaacagctgccaattgactgctatttgtatttcttgtctatatgccagAAACCGGAGTCATGGAGGCTTGCTTGTCAGACTATTGTTGGAAACAAAGAAAATTCCGGCAAG

upper sequence: GLYMA14G16070.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G470653_T01 (Zea mays), 3'ss of exon 4
ctgattggaaattttaactggtcc-ttcttactttttgag-ggtgatatgatggtaagttttgaaattttctgatcttctaagctttagccattttaaacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTCGGAAACAAAGAAAACTCTGGCAAG
    | || | |    ||||| |    | |||  ||      |   |  | || |  || || |     |  | || | | | ||       |      |||||||| || || |||||||| ||||| || |||||||| || |||||||| ||||||||||||
---gtaggcattggacactggacagcgcgtacagttcactcagcactcagttgctctgtcttaattcaataagctcgtttgatctccc-ttgtccccggcagAAACCAGACTCATGGAGGCTAGCTTGCCAGACTATTGTAGGCAACAAAGAGAACTCTGGCAAG

upper sequence: GLYMA14G16070.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G481261_T01 (Zea mays), 3'ss of exon 5
ctgattggaaattttaactggtccttcttactttttgagggtgatatgatggtaagttttgaaattttctgatcttctaagctttagccattttaaacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTCGGAAACAAAGAAAACTCTGGCAAG
      | |    ||    |   ||    |       | | | |        | ||||  |   | |  | |     |     |      | |    |||||||| || || |||||||| ||||| || |||||||| || |||||||| ||||||||||||
------gtaggcattg---gacactggacagcgcgcaatgttcactcagcactcagtt--gctctgtcttaactcgtttgatctcccttgtctctggcagAAACCAGACTCATGGAGGCTAGCTTGCCAGACTATTGTAGGCAACAAAGAGAACTCTGGCAAG

upper sequence: GLYMA14G16070.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0008g04240.t01 (Vitis vinifera), 3'ss of exon 4
ctgattggaaattttaactggtccttcttactttttgagggtgatatgatggtaagtttt----gaaattttctgat-cttctaag------ctttagccattttaaacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTCGGAAACAAAGAAAACTCTGGCAAG
       ||  | | | ||  ||| |||         |   | |||||| | |  ||| |    ||| ||  || || |||||         |||| |   |  |  ||||||||| |||||||||||||| ||||| ||||||||||| ||||| ||||| ||||||||||||
---gcatgatctctgatcttctccctctggacac---acaatcatatgaagtttcgttctctcagaatttgcctaatgcttcttcatcacttctttggttttgatgtacagAAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAG

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|12691095|gb|BG157431.1|BG157431
EST:     GATATCTTAAGAAG                         AAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTCGGAAACAAAGAA
genomic: GATATCTTAAGAAGgcatgctccc ... ttttaaacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTCGGAAACAAAGAA
EST: gi|31475388|gb|CD417416.1|CD417416
EST:     GGATTTTTTAAATTGAAAGAACAAACACTGAATTCAGATATCTTAAGAAG                         AAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTCGGAAACAAAGAA
genomic: GGATCTTTTAAA-TGAAAGAACAAACACTGAATTCAGATATCTTAAGAAGgcatgctccc ... ttttaaacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTCGGAAACAAAGAA
EST: gi|51338261|gb|CO982127.1|CO982127
EST:     AGATATCTTAAGAAG                         AAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTCGGAAACAAAGAA
genomic: AGATATCTTAAGAAGgcatgctccc ... ttttaaacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTCGGAAACAAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatggtaagttttgaaattttctgatcttctaagctttagccattttaaacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTCGGAAACAAAGAAAACTCTGGCAAG
                     ttctgat  putative branch site (score: 3)
                                          ccatttt  putative PPT
       taagttttgaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgattggaaattttaactggtccttcttactttttgagggtgatatgatggtaagttttgaaattttctgatcttctaagctttagccattttaaacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTCGGAAACAAAGAAAACTCTGGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
ctgattg
- - - - - - - - - - - ccttctt
- - - - - - - - - - - - - - - - - - gagggtg
- - - - - - - - - - - - - - - - - - - - - - - -gatggta