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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTTTTCTACGTTGGCAAAGCCCCCAAGGGCACCAAAACCAATTGGATCATGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAGgtatacagctacacatacacacatccacatactctgtttcttaattgttttacaccttcaattaattagaatgtctaattgcag

Basic information

species Glycine max
transcript GLYMA13G35550.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G35550.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
CGTTTTCTACGTTGGCAAAGCCCCCAAGGGCACCAAAACCAATTGGATCATGCACGAGTATCGCCTCCTCGAC----TCTTCCCGAAAGAACACTGGCACCAAGgtatacagctacacatacacacatccacatactctgtttcttaattgttttacacct-tcaattaattagaatgtcta--attgcag-----------------------------------------------------------
                   ||||||||||||   |||||||| |||||||||||||||||||||||    ||     | |  ||    |  |||   ||||   |        | |   ||   | | |   | |      |    |   |   || |||| || || |       || |||  ||| | |                                                           
------------------GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgtatagc-gtacatctcactcaacatcaggagtaaacctgtcgatcatgctagttgcctatgattcctgaatcgatatatgttgcctgtggaccagcgaatgacgcccgtctaattttgtggctgcag
















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|254339905|gb|GR858030.1|GR858030
EST:     TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAG                         CTTGATGATTGGGTTCTGTGTCGTATATACA-GAAGA-CTCGAGTGCACAG
genomic: TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAGgtatacagct ... ctaattgcagCTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
EST: gi|37997645|gb|CF809234.1|CF809234
EST:     TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAG                         CTTGATGAATTGGGTTCTGTGTCGTATA
genomic: TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAGgtatacagct ... ctaattgcagCTTGATGA-TTGGGTTCTGTGTCGTATA
EST: gi|151400077|gb|EV269891.1|EV269891
EST:     TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAG                         CTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
genomic: TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAGgtatacagct ... ctaattgcagCTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
EST: gi|13481525|gb|BG510868.1|BG510868
EST:     TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAG                         CTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
genomic: TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAGgtatacagct ... ctaattgcagCTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
EST: gi|17023864|gb|BM094898.1|BM094898
EST:     TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAG                         CTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
genomic: TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAGgtatacagct ... ctaattgcagCTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
EST: gi|254316594|gb|GR828131.1|GR828131
EST:     TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAG                         CTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
genomic: TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAGgtatacagct ... ctaattgcagCTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
EST: gi|254349339|gb|GR860137.1|GR860137
EST:     TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAG                         CTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
genomic: TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAGgtatacagct ... ctaattgcagCTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
EST: gi|254349338|gb|GR860136.1|GR860136
EST:     TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAG                         CTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
genomic: TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAGgtatacagct ... ctaattgcagCTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
EST: gi|192295101|gb|FG986820.1|FG986820
EST:     TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAG                         CTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
genomic: TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAGgtatacagct ... ctaattgcagCTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
EST: gi|22541207|gb|BU091050.1|BU091050
EST:     TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAG                         CTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
genomic: TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAGgtatacagct ... ctaattgcagCTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
EST: gi|254343208|gb|GR856912.1|GR856912
EST:     TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAG                         CTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
genomic: TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAGgtatacagct ... ctaattgcagCTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
EST: gi|193700789|gb|FK636454.1|FK636454
EST:     TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAG                         CTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
genomic: TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAGgtatacagct ... ctaattgcagCTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
EST: gi|37996921|gb|CF808510.1|CF808510
EST:     TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAG                         CTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG
genomic: TGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAGgtatacagct ... ctaattgcagCTTGATGATTGGGTTCTGTGTCGTATATACAAGAAGAACTCGAGTGCACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTTTTCTACGTTGGCAAAGCCCCCAAGGGCACCAAAACCAATTGGATCATGCACGAGTATCGCCTCCTCGACTCTTCCCGAAAGAACACTGGCACCAAGgtatacagctacacatacacacatccacatactctgtttcttaattgttttacaccttcaattaattagaatgtctaattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC