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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctaaattgaactggcttgaaatataatcttggtttattttttgacatataactgatcataaccatgctgttcccgttactgataattacgtgaatgttttggaacgtagGTCAAACTACAAGACTCCGCTTAAAGGGTTATACTTATGCGGAAGTGGGGCACATCCTGGTGGTGGTGTTATGGGAGCACCTGGACGTAATGCTGCTCGT

Basic information

species Glycine max
transcript GLYMA02G06340.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G06340.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv04s0023g01790.t01 (Vitis vinifera), 3'ss of exon 15
gtaagctaaattgaactggcttgaaatataatcttggtttattttttgacatataactgatcataaccatgctgttcccgttactgataattacgtgaatgttttggaacgtagGTCAAACTACAAGACTCCGCTTAAAGGGTTATACTTATGCGGAAGTGGGGCACATCCTGGTGGTGGTGTTATGGGAGCACCTGGACGTAATGCTGCTCGT
                  |  |     |  |  |    |  |||||| |  || | ||  | | |||  |  |||     | | | ||  ||  || | |  | ||||    ||||||   || | ||||||  | | |||| | || || ||||| |||||  ||||||||||||||||||| ||||| || ||||| |||||  |||| |  
------------------gtatttctcaccacttatagtagtttttttatgtagatct--ttagaactttaatgt-----tgagtaatcctt--gttattcctgtgga-tacagGTCAGGTTATAGGACTCCAGTGAGAGGGCTGTATTTGTGCGGCAGTGGAACACATCCTGGTGGTGGTGTGATGGGGGCGCCTGGTCGTAACTCTGCGCAA

upper sequence: GLYMA02G06340.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv04s0023g01780.t01 (Vitis vinifera), 3'ss of exon 15
gtaagctaaattgaactggcttg-aaatataatcttggtttattttttgacatataactgatcata-accatgctgttcccgttactgataattacgtgaatgttttggaacgtagGTCAAACTACAAGACTCCGCTTAAAGGGTTATACTTATGCGGAAGTGGGGCACATCCTGGTGGTGGTGTTATGGGAGCACCTGGACGTAATGCTGCTCGT
||||  | | ||  ||||  ||| || | ||   ||    | ||          |   ||   |   |  |  |  ||   ||   ||    ||  |||||    ||||||   |||||||||||||  ||||| ||  | ||| | || || ||||| |||||||| |||||||| |||||||| ||||| || ||||| |||||||| ||   |
gtaa--ttatttttactgaattgcaagtttagatttttcctgttcccccgtgattgtgtgggaaagtaagaaacaatttatgtctttg---ttttggtgaaa---ttggaatacagGTCAAACTACAGAACTCCACTGCAGGGGCTTTATTTGTGCGGGAGTGGGGCTCATCCTGGGGGTGGTGTGATGGGTGCCCCTGGTCGTAATGCCGCGTCT
















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|13240122|gb|BG359431.1|BG359431
EST:     CCCTTTTCCTCATGCGACCTGCAAAGGGATG                         GTCAAACTACAAGACTCCG-TTAAAGGGTTATACTTATGCGGAAGTGGGGC
genomic: CCCTTTTCCTCATGCGACCTGCAAAGGGATGgtaagctaaa ... tggaacgtagGTCAAACTACAAGACTCCGCTTAAAGGGTTATACTTATGCGGAAGTGGGGC
EST: gi|24135342|gb|BU925852.1|BU925852
EST:     GGTGCTATGGGGTTGGATTCCCTTTTCCTCATGCGACCTGCAAAGGGATG                         GTCAAACTACAAGACTCCGCTTAAAGGGTTATACTTATGCGGAAGTGGGGC
genomic: GGTGCTATGGGGTTGGATTCCCTTTTCCTCATGCGACCTGCAAAGGGATGgtaagctaaa ... tggaacgtagGTCAAACTACAAGACTCCGCTTAAAGGGTTATACTTATGCGGAAGTGGGGC
EST: gi|57574137|gb|CX547112.1|CX547112
EST:     GGTGCTATGGGGTTGGATTCCCTTTTCCTCATGCGACCTGCAAAGGGATG                         GTCAAACTACAAGACTCCGCTTAAAGGGTTATACTTATGCGGAAGTGGGGC
genomic: GGTGCTATGGGGTTGGATTCCCTTTTCCTCATGCGACCTGCAAAGGGATGgtaagctaaa ... tggaacgtagGTCAAACTACAAGACTCCGCTTAAAGGGTTATACTTATGCGGAAGTGGGGC
EST: gi|57574232|gb|CX547207.1|CX547207
EST:     GGTGCTATGGGGTTGGATTCCCTTTTCCTCATGCGACCTGCAAAGGGATG                         GTCAAACTACAAGACTCCGCTTAAAGGGTTATACTTATGCGGAAGTGGGGC
genomic: GGTGCTATGGGGTTGGATTCCCTTTTCCTCATGCGACCTGCAAAGGGATGgtaagctaaa ... tggaacgtagGTCAAACTACAAGACTCCGCTTAAAGGGTTATACTTATGCGGAAGTGGGGC
EST: gi|51335571|gb|CO979437.1|CO979437
EST:     GGTGCTATGGGGTTGGATTCCCTTTTCCTCATGCGACCTGCAAAGGGATG                         GTCAAACTACAAGACTCCGCTTAAAGGGTTATACTTATGCGGAAGTGGGGC
genomic: GGTGCTATGGGGTTGGATTCCCTTTTCCTCATGCGACCTGCAAAGGGATGgtaagctaaa ... tggaacgtagGTCAAACTACAAGACTCCGCTTAAAGGGTTATACTTATGCGGAAGTGGGGC
EST: gi|193339448|gb|FK304795.1|FK304795
EST:     GGTGCTATGGGGTTGGATTCCCTTTTCCTCATGCGACCTGCAAAGGGATG                         GTCAAACTACAAGACTCCGCTTAAAGGGTTATACTTATGCGGAAGTGGGGC
genomic: GGTGCTATGGGGTTGGATTCCCTTTTCCTCATGCGACCTGCAAAGGGATGgtaagctaaa ... tggaacgtagGTCAAACTACAAGACTCCGCTTAAAGGGTTATACTTATGCGGAAGTGGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcataaccatgctgttcccgttactgataattacgtgaatgttttggaacgtagGTCAAACTACAAGACTCCGCTTAAAGGGTTATACTTATGCGGAAGTGGGGCACATCCTGGTGGTGGTGTTATGGGAGCACCTGGACGTAATGCTGCTCGT
                      tactgat  putative branch site (score: 2)
                         tgataatta  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctaaattgaactggcttgaaatataatcttggtttattttttgacatataactgatcataaccatgctgttcccgttactgataattacgtgaatgttttggaacgtagGTCAAACTACAAGACTCCGCTTAAAGGGTTATACTTATGCGGAAGTGGGGCACATCCTGGTGGTGGTGTTATGGGAGCACCTGGACGTAATGCTGCTCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT