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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttaatctttttgccttgtttaaaggttgcctcattgacaatttgccatggaatgtaatgtaataatagttagttttcatattttccttttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGCTATCTTGTGTAGAGGCTTTATCTGCTGCTTTGACAATATG

Basic information

species Glycine max
transcript GLYMA05G31550.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G31550.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G10070.1 (Arabidopsis thaliana), 3'ss of exon 6
tatttaatctttttgccttgtttaaaggttgcctcattgacaatttgccatggaatgtaatgtaataatagttagttttcatattttccttttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGCTATCTTGTGTAGAGGCTTTATCTGCTGCTTTGACAATATG
                      |||    |  |   || ||   |    ||| |     || |      | |  ||||  |  || |  | |  ||||||| |||||| | |||||||| |||||||||||||||||  | |||||| || |||| ||||| |||||||||||||| ||||| | | ||||
---------------------gtaagaacttacgacttaactgataaatatgtatccagatctctaggaaat--gtttctaatttcttttatggttgcagTACCATGGTTAGTAGCAGCTAATCCAGTAAATTATGGAAGACCATGTGAGTTATCATGTGTGGAGGCTTTATCTGCCGCTTTAATACTATG

upper sequence: GLYMA05G31550.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0031g01200.t01 (Vitis vinifera), 3'ss of exon 6
tatttaatctttttgcct-tgtttaaaggttgcctcattgacaatttgccatggaatgtaatgtaata-atagttagttttcatattttccttttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGCTATCTTGTGTAGAGGCTTTATCTGCTGCTTTGACAATATG
    |||| |  |  ||| || |   ||  ||    |||| ||  || |  | |  | |  |  |  |  |  | |   |  | | ||   |   |||||||| |||||||| || |||||||| ||||||||||||||||| |||||| |||| |||||||| || || |||||||| |||||    |||||
agagtaatgtgctcacctgtgatctcagaatgga--attgtcacattccttttgtttatcttagagcatgtcttcataatagaaaattgtgtggaattgcagTACCATGGCTGGTGGCAGCAAACCCAGTAAATTATGGTCGACCATGTGAGCTCTCTTGTGTGGAAGCATTATCTGCAGCTTTATTTATATG

upper sequence: GLYMA05G31550.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ23130 (Selaginella moellendorffii), 3'ss of exon 3
tatttaatctttttgccttgtttaaaggttgcctcattgacaatttgccatggaatgtaatgtaataatagtt--agttttcatattttccttttat-tgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGCTATCTTGTGTAGAGGCTTTATCTGCTGCTTTGACAATATG
                                                 | |  || |  | |  |  |  |     ||||  | |||| ||| ||  |||||||||||||||||| || || ||||||  ||||||||| ||||| ||  ||||||| || ||||| ||| |  | || ||  ||   || ||
-----------------------------------------------gtaagttatttcctctctttgttctccagatttttttctttttcttgtacatgcagTGCCATGGCTTGTTGCTGCCAATCCAACAAATTATGGCCGGCCTTGCAAGCTATCGTGCGTAGAAGCTCTTACCGCGGCACTGGTTATTTG

upper sequence: GLYMA05G31550.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ20187 (Selaginella moellendorffii), 3'ss of exon 3
tatttaatctttttgccttgtttaaaggttgcctcattgacaatttgccatggaatgtaatgtaataatagtt-agttttcatattttccttttat-tgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGCTATCTTGTGTAGAGGCTTTATCTGCTGCTTTGACAATATG
                                                 | |  || |  | |  |  |  |  || |||  | |||| ||| ||  |||||||||||||||||| || || ||||||  ||||||||| ||||| ||  ||||||| || ||||| ||| |  | || ||  ||   || ||
-----------------------------------------------gtaagttatttcctctctttgttctccagattttttctttttcttgtacatgcagTGCCATGGCTTGTTGCTGCCAATCCAACAAATTATGGCCGGCCTTGCAAGCTATCGTGCGTAGAAGCTCTTACCGCGGCACTGGTTATTTG

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|19346470|gb|BM891350.1|BM891350
EST:     CTTAGATGATGTGCCTTTCATGAGGCTGCGCTGTGCTGCTCCTCGCCTCT                         TGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
genomic: CTTAGATGATGTGCCTTTCATGAGGCTGCGCTGTGCTGCTCCTCGCCTCTgtatgaactt ... tttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
EST: gi|193603153|gb|FK557120.1|FK557120
EST:     CTTAGATGATGTGCCTTTCATGAGGCTGCGCTGTGCTGCTCCTCGCCTCT                         TGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAG
genomic: CTTAGATGATGTGCCTTTCATGAGGCTGCGCTGTGCTGCTCCTCGCCTCTgtatgaactt ... tttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAG
EST: gi|208179337|gb|GD974040.1|GD974040
EST:     CTTAGATGATGTGCCTTTCATGAGGCTGCGCTGTGCTGCTCCTCGCCTCT                         TGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
genomic: CTTAGATGATGTGCCTTTCATGAGGCTGCGCTGTGCTGCTCCTCGCCTCTgtatgaactt ... tttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccatggaatgtaatgtaataatagttagttttcatattttccttttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGCTATCTTGTGTAGAGGCTTTATCTGCTGCTTTGACAATATG
                              ttttcatattttcctt  CT-rich tract
        aatgtaatgtaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttaatctttttgccttgtttaaaggttgcctcattgacaatttgccatggaatgtaatgtaataatagttagttttcatattttccttttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGCTATCTTGTGTAGAGGCTTTATCTGCTGCTTTGACAATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - ttttgcc
- - - - - - - - - - - - - - -tgcctca
- - - - - - - - - - - - - - - - - - - - - - - -ccatgga