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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgatgcatgtaaaaattagcatgatgaaaaaaaatgttcattcaaagcaaatatacttgtgatatcctgatcagtgacaacatggaattctttgtgcagAAAGCGCCTGTTCACTATGATTAATGATTTGCCTACAATATTTGAGGTTGTAACTGGATCTGCAAAGAAACAGACAAAGGAGAAGTCATCAGAGAACAAT

Basic information

species Glycine max
transcript GLYMA09G07970.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G07970.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0016g01500.t01 (Vitis vinifera), 3'ss of exon 3
atgatgcatgtaaaaattagcatgatgaaaaaaaatgttcattcaaagcaaatatacttgtgatatcctgatcagtgacaacatggaattctttgtgcagAAAGCGCCTGTTCACTATGATTAATGATTTGCCTACAATATTTGAGGTTGTAACTGGATCTGCAAAGAAACAGACAAAGGAGAAGTCATCAGAGAACAAT
 | |   |||       ||  | | ||   || | |    | |   |     |||  |   | | |  | |  |   |     ||||||| ||  ||||| || || || |||| ||||||||||||| | || ||||||||||||||||| |||||| |||||||||||||   |||||||||||||||||     || 
cttaaatatgcttgttatatgaggctgctgaacattaccaaattggatgctgtattttatagttttattcaataaaaaattgctggaatttttaatgcagGAAACGTCTTTTCAATATGATTAATGATCTTCCAACAATATTTGAGGTTGTGACTGGAGCTGCAAAGAAACAAGTAAAGGAGAAGTCATCAGTTTCGAAC
















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|298191570|gb|HO039049.1|HO039049
EST:     TCAGTGGCTTTCTACTTTGGGGCAAGATTTGGTTTTGATAAAGCTGACAG                         AAAGCGCCTGTTCACTATGATTAATGATTTGCCTACAATATTTGAGGTTGT
genomic: TCAGTGGCTTTCTACTTTGGGGCAAGATTTGGTTTTGATAAAGCTGACAGgtataatagt ... ctttgtgcagAAAGCGCCTGTTCACTATGATTAATGATTTGCCTACAATATTTGAGGTTGT
EST: gi|151412383|gb|EV282195.1|EV282195
EST:     TCAGTGGCTTTCTACTTTGGGGCAAGATTTGGTTTTGATAAAGCTGACAG                         AAAGCGCCTGTTCACTATGATTAATGATTTGCCTACAATATTTGAGGTTGT
genomic: TCAGTGGCTTTCTACTTTGGGGCAAGATTTGGTTTTGATAAAGCTGACAGgtataatagt ... ctttgtgcagAAAGCGCCTGTTCACTATGATTAATGATTTGCCTACAATATTTGAGGTTGT
EST: gi|192323928|gb|FK018649.1|FK018649
EST:     TCAGTGGCTTTCTACTTTGGGGCAAGATTTGGTTTTGATAAAGCTGACAG                         AAAGCGCCTGTTCACTATGATTAATGATTTGCCTACAATATTTGAGGTTGT
genomic: TCAGTGGCTTTCTACTTTGGGGCAAGATTTGGTTTTGATAAAGCTGACAGgtataatagt ... ctttgtgcagAAAGCGCCTGTTCACTATGATTAATGATTTGCCTACAATATTTGAGGTTGT
EST: gi|192299703|gb|FG990027.1|FG990027
EST:     TCAGTGGCTTTCTACTTTGGGGCAAGATTTGGTTTTGATAAAGCTGACAG                         AAAGCGCCTGTTCACTATGATTAATGATTTGCCTACAATATTTGAGGTTGT
genomic: TCAGTGGCTTTCTACTTTGGGGCAAGATTTGGTTTTGATAAAGCTGACAGgtataatagt ... ctttgtgcagAAAGCGCCTGTTCACTATGATTAATGATTTGCCTACAATATTTGAGGTTGT
EST: gi|12689413|gb|BG155810.1|BG155810
EST:     TCAGTGGCTTTCTACTTTGGGGCAAGATTTGGTTTTGATAAAGCTGACAG                         AAAGCGCCTGTTCACTATGATTAATGATTTGCCTACAATATTTGAGGTTGT
genomic: TCAGTGGCTTTCTACTTTGGGGCAAGATTTGGTTTTGATAAAGCTGACAGgtataatagt ... ctttgtgcagAAAGCGCCTGTTCACTATGATTAATGATTTGCCTACAATATTTGAGGTTGT
EST: gi|151401139|gb|EV270953.1|EV270953
EST:     TCAGTGGCTTTCTACTTTGGGGCAAGATGTGGTTTTGATAAAGCTGACAG                         AAAGCGCCTGTTCACTATGATTAATGATTTGCCTACAATATTTGAGGTTGT
genomic: TCAGTGGCTTTCTACTTTGGGGCAAGATTTGGTTTTGATAAAGCTGACAGgtataatagt ... ctttgtgcagAAAGCGCCTGTTCACTATGATTAATGATTTGCCTACAATATTTGAGGTTGT
EST: gi|151411128|gb|EV280939.1|EV280939
EST:     TCAGTGGCTTTCTACTTTGGGGCAAGATTTGGTTTTGATAAAGCTGACAG                         AAAGCGCCTGTTCACTATGATTAATGATTTGCCTACAATATTTGAGGTTGT
genomic: TCAGTGGCTTTCTACTTTGGGGCAAGATTTGGTTTTGATAAAGCTGACAGgtataatagt ... ctttgtgcagAAAGCGCCTGTTCACTATGATTAATGATTTGCCTACAATATTTGAGGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcaaatatacttgtgatatcctgatcagtgacaacatggaattctttgtgcagAAAGCGCCTGTTCACTATGATTAATGATTTGCCTACAATATTTGAGGTTGTAACTGGATCTGCAAAGAAACAGACAAAGGAGAAGTCATCAGAGAACAAT
                    tcctgat  putative branch site (score: 3)
                                           ttctttgt  putative PPT
     aatatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgatgcatgtaaaaattagcatgatgaaaaaaaatgttcattcaaagcaaatatacttgtgatatcctgatcagtgacaacatggaattctttgtgcagAAAGCGCCTGTTCACTATGATTAATGATTTGCCTACAATATTTGAGGTTGTAACTGGATCTGCAAAGAAACAGACAAAGGAGAAGTCATCAGAGAACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - -gcatgta
- - - - - - - - - -gcatgat
- - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - -cattcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -acttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagtgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catggaa