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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaatattcttagcttgaatcaaattgttatatcaaagttggtgactcactgacgaagactgatatttcagGTTAATCCTGTGAGGGCTAAAGAACTTACAAATATCCGTGCTGCTACCAAAGATGATAATGTGAAGCTGACTCCCCCGCGCCTT

Basic information

species Glycine max
transcript GLYMA12G14080.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G14080.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G128688_T01 (Zea mays), 3'ss of exon 16
gtaagaaatattcttagcttgaatcaaattgttatatcaaagttggtgactcactgacgaagactgatattt--cagGTTAATCCTGTGAGGGCTAAAGAACTTACAAATATCCGTGCTGCTACCAAAGATGATAATGTGAAGCTGACTCCCCCGCGCCTT
    | |  ||  | |  |  ||   |     ||| ||    |   |   |   ||| |   |    | |||  ||||| |||||||||||  |||||||||||||||||||||| ||  ||   || ||||| |||||     || |||| || ||  | 
----gtatgatggtcaaatacaaatcacggcctatttctttctctttctatacttgaagttaatgtctctttggcagGTGAATCCTGTGAGAACTAAAGAACTTACAAATATCCGAGCCCCTGGAAAGGATGAAAATGTCCGTTTGTCTCCACCCCGATTG

upper sequence: GLYMA12G14080.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv12s0028g02640.t01 (Vitis vinifera), 3'ss of exon 16
---gtaagaaatattcttagcttgaatcaaat-tgttatatcaaagtt-ggtgactca-ctgacgaagactgatattt--cagGTTAATCCTGTGAGGGCTAAAGAACTTACAAATATCCGTGCTGCTACCAAAGATGATAATGTGAAGCTGACTCCCCCGCGCCTT
      ||||||     |  ||   ||  ||| |||| | |      | ||||||| | ||  | |  | ||   ||   ||| | || || || |||||||| |||||||| ||||| || |||||| |||| ||||| ||||||||||| ||||| || || |||
gtaaggagaaatgactcttcctcacatttaatgtgttgtgttggttctaggtgactgaacttgctattattgtggttaaacagATCAACCCAGTAAGGGCTAAGGAACTTACCAATATACGCGCTGCTTCCAAGGATGAGAATGTGAAGCTAACTCCTCCTCGTCTT
















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|193485145|gb|FK450717.1|FK450717
EST:     CGTATGATGGAATGATAGTTGGAGAACATTCACGGGATACAGATCTTGAT                         GTTAATCCTGTGAGGGCTAAAGAACTTACAAATATCCGTGCTGCTACCAAA
genomic: CGTATGATGGAATGATAGTTGGAGAACATTCACGGGATACAGATCTTGATgtaagaaata ... gatatttcagGTTAATCCTGTGAGGGCTAAAGAACTTACAAATATCCGTGCTGCTACCAAA
EST: gi|193686123|gb|FK625474.1|FK625474
EST:     CGTATGATGGAATGATAGTTGGAGAACATTCACGGGATACAGATCTTGAT                         GTTAATCCTGTGAGGGCTAAAGAACTTACAAATATCCGTGCTGCTACCAAA
genomic: CGTATGATGGAATGATAGTTGGAGAACATTCACGGGATACAGATCTTGATgtaagaaata ... gatatttcagGTTAATCCTGTGAGGGCTAAAGAACTTACAAATATCCGTGCTGCTACCAAA
EST: gi|193646733|gb|FK592240.1|FK592240
EST:     CGTATGATGGAATGATAGTTGGAGAACATTCACGGGATACAGATCTTGAT                         GTTAATCCTGTGAGGGCTAAAGAACTTACAAATATCCGTGCTGCTACCAAA
genomic: CGTATGATGGAATGATAGTTGGAGAACATTCACGGGATACAGATCTTGATgtaagaaata ... gatatttcagGTTAATCCTGTGAGGGCTAAAGAACTTACAAATATCCGTGCTGCTACCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatcaaattgttatatcaaagttggtgactcactgacgaagactgatatttcagGTTAATCCTGTGAGGGCTAAAGAACTTACAAATATCCGTGCTGCTACCAAAGATGATAATGTGAAGCTGACTCCCCCGCGCCTT
     aaattgttatatcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaatattcttagcttgaatcaaattgttatatcaaagttggtgactcactgacgaagactgatatttcagGTTAATCCTGTGAGGGCTAAAGAACTTACAAATATCCGTGCTGCTACCAAAGATGATAATGTGAAGCTGACTCCCCCGCGCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA