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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgatttctacagaatccacatcattccattgcaatatagttactatgtgaatcgttcatctaacttaaatgtgtttttgtaatagGTTGCTACTGACAAGTGTATTATGGCACTTCTTTTCCTTATTGTCATTGGAGTAATTGCAATCATTATTGTAAAG

Basic information

species Glycine max
transcript GLYMA17G15990.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G15990.1 (Glycine max), 3'ss of exon 8
lower sequence: AT2G35190.1 (Arabidopsis thaliana), 3'ss of exon 7
gttgatttctacagaatccacatcattccattgcaatatagttact----atgtgaa--------tcgttcatctaacttaaa---tgtgtttttgtaat-agGTTGCTACTGACAAGTGTATTATGGCACTTCTTTTCCTTATTGTCATTGGAGTAATTGCAATCATTATTGTAAAG
|||  | ||   |   |||  ||   | | ||  |  ||  |||||    || || |        | || | | | |||||     |||  || | | || ||||||| |||||||| |||||||||||| ||||||||||||| |||||||| || || |||||||| || || |||
gttagtctcataaatctccttatttcttctttatatcatcattacttgttatctgcagctccttcttgtccctttcacttactctctgtccttcttttatcagGTTGCCACTGACAAATGTATTATGGCATTTCTTTTCCTTATCGTCATTGGTGTCATAGCAATCATCATCGTCAAG
















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|58022209|gb|CX708950.1|CX708950
EST:     ATTTCTCTATAAAGAAAGCCTCTAAATTGGTCAAGGAAATCGGTAGGCAG                         GTTGCTACTGACAAGTGTATTATGGCACTTCTTTTCCTTATTGTCATTGGA
genomic: ATTTCTCTATAAAGAAAGCCTCTAAATTGGTCAAGGAAATCGGTAGGCAGgttgatttct ... tttgtaatagGTTGCTACTGACAAGTGTATTATGGCACTTCTTTTCCTTATTGTCATTGGA
EST: gi|58022411|gb|CX709152.1|CX709152
EST:     TTTCTCTATAAAGAAAGCCTCTAAATT-GTCAAAGGAAATCGGTAGGCAG                         GTTGCTACTGACAAGTGTATTATGGCACTTCTTTTCCTTATTGTCATTGGA
genomic: TTTCTCTATAAAGAAAGCCTCTAAATTGGTC-AAGGAAATCGGTAGGCAGgttgatttct ... tttgtaatagGTTGCTACTGACAAGTGTATTATGGCACTTCTTTTCCTTATTGTCATTGGA
EST: gi|192306339|gb|FG996897.1|FG996897
EST:     ATTTCTCTATAAAGAAAGCCTCTAAATTGGTCAAGGAAATCGGTAGACAG                         GTTGCTACTGACAAGTGTATTATGGCACTTCTTTTCCTTATTGTCATTGGA
genomic: ATTTCTCTATAAAGAAAGCCTCTAAATTGGTCAAGGAAATCGGTAGGCAGgttgatttct ... tttgtaatagGTTGCTACTGACAAGTGTATTATGGCACTTCTTTTCCTTATTGTCATTGGA
EST: gi|151412161|gb|EV281973.1|EV281973
EST:     ATTTCTCTATAAAGAAAGCCTCTAAATTGGTCAAGGAAACCGGTAGGCAG                         GTTGCTACTGACAAGTGTATTATGGCACTTCTTTTCCTTATTGTCATTGGA
genomic: ATTTCTCTATAAAGAAAGCCTCTAAATTGGTCAAGGAAATCGGTAGGCAGgttgatttct ... tttgtaatagGTTGCTACTGACAAGTGTATTATGGCACTTCTTTTCCTTATTGTCATTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaatatagttactatgtgaatcgttcatctaacttaaatgtgtttttgtaatagGTTGCTACTGACAAGTGTATTATGGCACTTCTTTTCCTTATTGTCATTGGAGTAATTGCAATCATTATTGTAAAG
                           atctaac  putative branch site (score: 2)
                                         tgttttt  putative PPT
                                  ttaaatgtgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgatttctacagaatccacatcattccattgcaatatagttactatgtgaatcgttcatctaacttaaatgtgtttttgtaatagGTTGCTACTGACAAGTGTATTATGGCACTTCTTTTCCTTATTGTCATTGGAGTAATTGCAATCATTATTGTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG