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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggaaaagaagcaaaacatgttcttattttcttgtattattcatctctgacccactacaagaatataaaatggttgagtctgcttttacttggattgcagTATAAGGGAAATATGTGGGAAGGAAGATATAGACATTGCTTACAAGCATTTCAAAGCTTTCTATCAAAACTTTTCAAGCGTAGACAAGATGCTGACTGTG

Basic information

species Glycine max
transcript GLYMA20G32790.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32790.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0106g00700.t01 (Vitis vinifera), 3'ss of exon 9
tggaaaagaagcaaaacatgttcttattttcttgtattattcatctctgaccc-actacaagaatataaaatggttgagtctgcttttacttggattgcagTATAAGGGAAATATGTGGGAAGGAAGATATAGACATTGCTTACAAGCATTTCAAAGCTTTCTATCAAAACTTTTCAAGCGTAGACAAGATGCTGACTGTG
||             || ||| ||  ||    |  |||  |  | | ||  |    | |    ||| |       | | | | | ||  |||  |||||||| | || ||  ||||||||||||||||||| ||||||||||||||||||||||| || || || ||||  || ||||| ||||||| ||  |||| ||||
tgctgcttccatttcac-tgtgctgcttgaactacatttattttgtgtgttcttggtgctgatatacagtgatacttaattttccttgtcttatattgcagTGTGAGAGAGGTATGTGGGAAGGAAGATATTGACATTGCTTACAAGCATTTCAAGGCATTTTACCAAACATTCTCAAGTGTAGACAGGAAACTGAATGTG
















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|16347296|gb|BI972891.1|BI972891
EST:     GTTGGCATCCGAACAGCTGACTGTGGAATTGCTCAACTTTCAATGCACAG                         TATAAGGGAAATATGTGGGAAGGAAGATATAGACATTGCTTACAAGCATGT
genomic: GTTGGCATCCGAACAGTTGACTGTGGAATTGCTCAACTTTCAATGCACAGgtataaaatg ... tggattgcagTATAAGGGAAATATGTGGGAAGGAAGATATAGACATTGCTTACAAGCATTT
EST: gi|14258779|gb|BG881687.1|BG881687
EST:     GTTGGCATCCGAACAGTTGACTGTGGAATTGCTCAACTTTCAATGCACAG                         TATAAGGGAAATATGTGGGAAGGAAGATATAGACATTGCTTACAAGCATTT
genomic: GTTGGCATCCGAACAGTTGACTGTGGAATTGCTCAACTTTCAATGCACAGgtataaaatg ... tggattgcagTATAAGGGAAATATGTGGGAAGGAAGATATAGACATTGCTTACAAGCATTT
EST: gi|6718964|gb|AW306611.1|AW306611
EST:     GAACAGTTGACTGTGGAATTGCTCAACTTTCAATGCACAG                         TATAAGGGAAATATGTGGGAAGGAAGATATAGACATTGCTTACAAGCATTT
genomic: GAACAGTTGACTGTGGAATTGCTCAACTTTCAATGCACAGgtataaaatg ... tggattgcagTATAAGGGAAATATGTGGGAAGGAAGATATAGACATTGCTTACAAGCATTT
EST: gi|10232725|gb|BE801613.1|BE801613
EST:     GTTGGCATCCGAACAGTTGACTGTGGAATTGCTCAACTTTCAATGCACAG                         TATAAGGGAAATATGTGGGAAGG
genomic: GTTGGCATCCGAACAGTTGACTGTGGAATTGCTCAACTTTCAATGCACAGgtataaaatg ... tggattgcagTATAAGGGAAATATGTGGGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgacccactacaagaatataaaatggttgagtctgcttttacttggattgcagTATAAGGGAAATATGTGGGAAGGAAGATATAGACATTGCTTACAAGCATTTCAAAGCTTTCTATCAAAACTTTTCAAGCGTAGACAAGATGCTGACTGTG
 ctctgac  putative branch site (score: 3)
                                     cttttactt  putative PPT
          tacaagaatataaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggaaaagaagcaaaacatgttcttattttcttgtattattcatctctgacccactacaagaatataaaatggttgagtctgcttttacttggattgcagTATAAGGGAAATATGTGGGAAGGAAGATATAGACATTGCTTACAAGCATTTCAAAGCTTTCTATCAAAACTTTTCAAGCGTAGACAAGATGCTGACTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- -aaaagaa
- - - - - - - - catgttc
- - - - - - - - - - - - - - - - - - - - - - - - gacccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttgag