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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttaaagacaaatatctagtgtgaaatttgttgcatcctaaattgatttcacacattcatgatcctggaatactcttcgaatttataatttcctgtagATGTGTTGTGAGTGGTTCTGGGAAGATCGCAATGCATGTCTTGGAGAAGCTAATTGCTTATGGTGCTCTTCCCATTTCAGTATCAG

Basic information

species Glycine max
transcript GLYMA08G20930.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20930.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g37760.2 (Oryza sativa), 3'ss of exon 8
tttttaaagacaaatatctagtgtgaaatttgttgcatcctaaattgatttcacaca--ttcatgatcctggaatactcttcga-atttataatttcctgtagATGTGTTGTGAGTGGTTCTGGGAAGATCGCAATGCATGTCTTGGAGAAGCTAATTGCTTATGGTGCTCTTCCCATTTCAGTATCAG
                    || | ||  | | |  ||  ||  ||  ||  | | |  ||  | | | |     |||     |  |  ||   ||| || ||||||||  | ||||||||||| ||||| ||||||||||| ||||| |||||  |  | | ||  ||| ||||  || |||| ||||
--------------------gttttaacatagatctatt-tagtttatttgtatatagttttgtaaccatttgggacttcctaatgtgcatggcttc-tgcagATGTGTGATAAGTGGTTCTGGAAAGATAGCAATGCATGTATTGGAAAAGCTTCTGTCATGTGAAGCTATTCCTGTTACAGTTTCAG

upper sequence: GLYMA08G20930.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G015289_T02 (Zea mays), 3'ss of exon 8
tttttaaagacaaatatctagtgtgaaatttgttgcatcctaaattgatttcacaca--ttcatgatcctggaatactcttcgaatttataatttcctgtagATGTGTTGTGAGTGGTTCTGGGAAGATCGCAATGCATGTCTTGGAGAAGCTAATTGCTTATGGTGCTCTTCCCATTTCAGTATCAG
              | |||    |  | |    |  ||  |   ||| | | |   |   |  || | ||  |||||| | | ||       ||| ||| ||||||||  | || |||||||||||||| ||||||||||| ||||| |||||  |  ||| ||| ||  |||| ||| | || ||||
-------------gtttcttacattga-tccactaaatgtttctttgttataatttagccttttgttactttaatactatgcaaa------gttttctgcagATGTGTGATCAGCGGTTCTGGGAAGATAGCAATGCATGTTTTGGAAAAGCTTTTGCCTTGTGGAGCCATTCCTATTACTGTCTCAG

upper sequence: GLYMA08G20930.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G51720.1 (Arabidopsis thaliana), 3'ss of exon 9
--tttttaaagacaaatatctagtgtgaaatttgttgcatcctaaattgatttcacacattcatgatcctggaatactcttcgaatttataatttcctgtagATGTGTTGTGAGTGGTTCTGGGAAGATCGCAATGCATGTCTTGGAGAAGCTAATTGCTTATGGTGCTCTTCCCATTTCAGTATCAG
  | |||     |  | ||  |   ||||  |   ||  |  |  |    |||   ||  ||||  |  || ||   |   |   | ||||||||  |  |||||||| ||||||||||  |||||||| || ||||||||  | |||||||||||||||| ||| || | |||  || | || ||||
aatatttggcttctcacata-acactgaagctgtgtgacttgtgtacaattttgtgactctcatc-ttatgaaaccataaactcttctataatttatttcagATGTGTCGTGAGTGGTTGCGGGAAGATTGCGATGCATGTTGTAGAGAAGCTAATTGCTTGTGGAGCCCATCCGGTTACTGTTTCAG

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|7924271|gb|AW830297.1|AW830297
EST:     TTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGATTAAG                         ATGTGTTGTGAGTGGTTCTGGGAAGATCGCAATGCATGTCTTGGAGAAGCT
genomic: TTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGATTAAGgtttctattc ... tttcctgtagATGTGTTGTGAGTGGTTCTGGGAAGATCGCAATGCATGTCTTGGAGAAGCT
EST: gi|193386749|gb|FK352082.1|FK352082
EST:     TTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGATTAAG                         ATGTGTTGTGAGTGGTTCTGGGAAGATCGCAATGCATGT
genomic: TTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGATTAAGgtttctattc ... tttcctgtagATGTGTTGTGAGTGGTTCTGGGAAGATCGCAATGCATGT
EST: gi|207749540|gb|GD720958.1|GD720958
EST:     TTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGATTAAG                         ATGTGTTGTGAGTGGTTCTGGGAAGATCGCAATGCATGTCTTGGAGAAGCT
genomic: TTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGATTAAGgtttctattc ... tttcctgtagATGTGTTGTGAGTGGTTCTGGGAAGATCGCAATGCATGTCTTGGAGAAGCT
EST: gi|16997272|gb|BM086644.1|BM086644
EST:     TTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGATTAAG                         ATGTGTTGTGAGTGGTTCTGGGAAGATCGCAATGCATGTCTTGGAGAAGCT
genomic: TTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGATTAAGgtttctattc ... tttcctgtagATGTGTTGTGAGTGGTTCTGGGAAGATCGCAATGCATGTCTTGGAGAAGCT
EST: gi|193653480|gb|FK599478.1|FK599478
EST:     TTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGATTAAG                         ATGTGTTGTGAGTGGTTCTGGGAAGATCGCAATGCATGT
genomic: TTTGCCCAGCTCATGCTTGCTGACATGAATAAAGAACTTAAAGGATTAAGgtttctattc ... tttcctgtagATGTGTTGTGAGTGGTTCTGGGAAGATCGCAATGCATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatttcacacattcatgatcctggaatactcttcgaatttataatttcctgtagATGTGTTGTGAGTGGTTCTGGGAAGATCGCAATGCATGTCTTGGAGAAGCTAATTGCTTATGGTGCTCTTCCCATTTCAGTATCAG
 aattgat  putative branch site (score: 4)
                                             tttcctgt  putative PPT
                                ttcgaatttataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttaaagacaaatatctagtgtgaaatttgttgcatcctaaattgatttcacacattcatgatcctggaatactcttcgaatttataatttcctgtagATGTGTTGTGAGTGGTTCTGGGAAGATCGCAATGCATGTCTTGGAGAAGCTAATTGCTTATGGTGCTCTTCCCATTTCAGTATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - aagacaaa
- - - - - - - - - tagtgtg
- - - - - - - - - - - - - - - - -tgcatcc
- - - - - - - - - - - - - - - - - - - - - - - - - -cacacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgatc