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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGATATACAAAGTATTGCTTCTGAGATGGAAGGAAAAACCGAGGAGGAAGTTGAAAGATATGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATGgtatgttacagttacagttacagccaattcttctatggattttgttgattatttaagtgtggaagaaaaatacttagccaaatccaaatgaatgtttata...

Basic information

species Glycine max
transcript GLYMA15G10370.1
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G10370.1 (Glycine max), 5'ss of exon 21
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 21
AATGATATACAAAGTATTGCTTCTGAGATGGAAGGAAAAACCGAGGAGGAAGTTGAAAGATATGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATGgtatgttacagttacagttacagccaattcttctatggatt-ttgttgat-tatttaa-gtgtggaagaa--aaatacttagccaaatccaaat----gaatgtttata-------------------------------------------------------------------
||||| ||| | |  ||  | ||||| ||||| || ||||| || ||||| ||  |  | || || || || ||  | |||||||||||||||||||||||||| ||   || ||  || |    | |  || |||    |  || |||  ||||||| |||| |  ||      || | |     | |||| |    || || ||| |                                                                   
AATGACATAAAGAACATATCCTCTGAAATGGAGGGGAAAACAGAAGAGGAGGTGCAGCGGTACGCTAAAGTTTTCCAGGAAAGATACAAGGAATTAAATGgtatatttt-gtaaccttttctcttactgtttgtattccctactgatgacctatttaatgtgtagctgactttgttattaacttgtaaccaagtaatggattgcttacatgctgagctgagtaatggtcagatacaaaatctgttttgactaaatatgatgtcctcatcctatcag

upper sequence: GLYMA15G10370.1 (Glycine max), 5'ss of exon 21
lower sequence: AT3G06400.3 (Arabidopsis thaliana), 5'ss of exon 21
AATGATATACAAAGTATTGCTTCTGAGATGGAAGGAAAAACCGAGGAGGAAGTTGAAAGATATGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATGgtatgttacag-ttacagttacagccaattct---tctatggattttgttgattatttaagtgtggaagaaaaatacttagccaaatccaaatgaatgtttata---------------
|| || ||| |||| ||||| |||||||||||||| ||||| ||||| ||||||||||||||||| || || ||||||||  | ||||||||  | || |||| || |||  || || |   |    || |    | | |  || ||  | | || ||   |       ||||   ||||  | ||   |  | |   | | |                
AACGACATAAAAAGCATTGCCTCTGAGATGGAAGGGAAAACAGAGGAAGAAGTTGAAAGATATGCCAAAGTATTTAAAGAGCGGTACAAGGAGCTGAACGgtaagtaacacctttcaatgctaagttatgcagtgtttttacatgtttctaagtaattcc-tacctccaaaaagagcttatgctaagtaagtttatcatctttccctctaaatatgtag

upper sequence: GLYMA15G10370.1 (Glycine max), 5'ss of exon 21
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 5'ss of exon 21
AATGATATACAAAGTATTGCTTCTGAGATGGAAGGAAAAACCGAGGAGGAAGTTGAAAGATATGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATGgt-----atgttacagttacagttacagccaat-----tcttctatg-gattttgttgattatttaagtgtggaagaaaaatacttagccaaatccaaatgaatgtttata-
|| || ||| | |||||||| |||||||||||||| ||||| ||||| || |||||| |||||||  | || ||  |||   |||| || ||  | ||||||     |  ||| | |   |  || ||  |||     | | |  || ||    ||||  ||||||    |     |    | | |       |||     ||   || || 
AACGACATAAAGAGTATTGCCTCTGAGATGGAAGGGAAAACTGAGGAAGAGGTTGAACGATATGCTCAAGTTTTCCAAGTGCGATATAAAGAGCTGAATGgttagtaactttagattgttaagtaaagttaatgagtgtttgcagtgcgacaaagttggatatttat-cctaagtaagctctgcctcttgttttcctttgtaaaaattgtag

upper sequence: GLYMA15G10370.1 (Glycine max), 5'ss of exon 21
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 5'ss of exon 21
AATGATATACAAAGTATTGCTTCTGAGATGGAAGGAAAAACCGAGGAGGAAGTTGAAAGATATGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATGgtatgttacagttacagttacagccaattcttctatggattttgttgattatttaagtgtggaagaa---aaatacttagccaaatccaaatgaatgtttata
|||||| || |||||||||||||||| |||||||| || || |||||||||||||| ||||||||||| | ||| |||||||||||||| ||||||||||||| || | | |||    |         |   ||     ||  | ||| | |||       ||         |   |||     |||    |   |  ||   
AATGATGTAAAAAGTATTGCTTCTGAAATGGAAGGGAAGACAGAGGAGGAAGTTGAGAGATATGCAAAAGCCTTCAAAGAAAGATACAAAGAATTAAATGgtaagtgatatttaattctgtgctattgtaaccttacagttgagatgaatgtttggagtcagatatgctgggaagtttatttttatcacgttcctttctt---

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|208266252|gb|GE065455.1|GE065455
EST:     AGTTGAAAGATATGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATG                         ATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTC
genomic: AGTTGAAAGATATGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATGgtatgttaca ... ttgtctgcagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTC
EST: gi|58023312|gb|CX710053.1|CX710053
EST:     AGTTGAAAGATATGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATG                         ATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTC
genomic: AGTTGAAAGATATGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATGgtatgttaca ... ttgtctgcagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTC
EST: gi|10238767|gb|BE807655.1|BE807655
EST:     GAAAGATACAAGGAATTAAATG                         ATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTC
genomic: GAAAGATACAAGGAATTAAATGgtatgttaca ... ttgtctgcagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTC
EST: gi|193422520|gb|FK387599.1|FK387599
EST:     TGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATG                         ATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTC
genomic: TGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATGgtatgttaca ... ttgtctgcagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTC
EST: gi|57575241|gb|CX548216.1|CX548216
EST:     AGTTGAAAGATATGCAAAGGTC-TTAAAGAAAGATACAAGGAATTAAATG                         ATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTC
genomic: AGTTGAAAGATATGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATGgtatgttaca ... ttgtctgcagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTC
EST: gi|192313279|gb|FK005051.1|FK005051
EST:     AGTTGAAAGATATGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATG                         ATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTC
genomic: AGTTGAAAGATATGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATGgtatgttaca ... ttgtctgcagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTC
EST: gi|5666886|gb|AI930922.1|AI930922
EST:     AGTTGAAAGATATGCAAAGGTCTTTAAAGAAAGATACAAGGAACTAAATG                         ATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATCTCTC
genomic: AGTTGAAAGATATGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATGgtatgttaca ... ttgtctgcagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTC
EST: gi|193703234|gb|FK637006.1|FK637006
EST:     AGTTGAAAGATATGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATG                         ATTATGACAGAATTATTAAAAACATTGGAAAGGGGGGAGGCAAGAATTTCT
genomic: AGTTGAAAGATATGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATGgtatgttaca ... ttgtctgcagATTATGACAGAATTATTAAAAACATTG-AAAGGGGGGAGGCAAGAATTTCT
EST: gi|7796461|gb|AW781858.1|AW781858
EST:     AAGATATGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATG                         ATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTC
genomic: AAGATATGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATGgtatgttaca ... ttgtctgcagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGATATACAAAGTATTGCTTCTGAGATGGAAGGAAAAACCGAGGAGGAAGTTGAAAGATATGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATGgtatgttacagttacagttacagccaattcttctatggattttgttgattatttaagtgtggaagaaaaatacttagccaaatccaaatgaatgtttata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaagaaa