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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatctcactgactatgccaatgatatggtttaaaatgttaggaaggtgattaggtgggtagtgctatttgtgctaattctatgtgtttcgcccttgcagAGGCATTTGCAGTTTGTGAAAACTATTCCCCTCCTGAAGGATTCAATCCAAAAGATCTTCATCGCCTTCTTGAGAAGGTTGGAAGTCCCTCAGGGGTAGA

Basic information

species Glycine max
transcript GLYMA15G07970.4
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G07970.2 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os06g49140.1 (Oryza sativa), 3'ss of exon 9
-----tgatctcactgactatgccaatgatatggtttaaaatgttaggaaggtgattaggtgggtagtgctatttgtgctaat-tctatgtgtttcgcccttgcagAGGCATTTGCAGTTTGTGAAAACTATTCCCCTCCTGAAGGATTCAATCCAAAAGATCTTCATCGCCTTCTTGAGAAGGTTGGAAGTCCCTCAGGGGTAGA
        | ||||| ||| |   |      || ||   | |    ||    ||   |  ||  |     | |   |  | |  | |     | ||       ||||||| |||||||||||||| || ||||| ||||| |||||||| ||   ||||||| |  ||| ||| || ||||| || || | ||| || ||||  ||
aacagatgtttcacttacttt-ttatcttcgtgattcttatttcctggttcctgga-aaatgtttgagagtttccataatcacctttccacatatcaa----acagAGGCGTTTGCAGTTTGTGAGAATTATTCGCCTCCCGAAGGATTTAAGGAAAAAGATTTATATCACCTGCTAGAGAAAGTGGGGACTCCTTCTGGGGCTGA

upper sequence: GLYMA15G07970.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv08s0007g01960.t01 (Vitis vinifera), 3'ss of exon 9
tgatctcactgactatgccaa-tgatatggtttaaaat--gttaggaaggtgattaggtgggtagtgctatttgtgctaattctatgtgtttcgcccttg---cagAGGCATTTGCAGTTTGTGAAAACTATTCCCCTCCTGAAGGATTCAATCCAAAAGATCTTCATCGCCTTCTTGAGAAGGTTGGAAGTCCCTCAGGGGTAGA
     |||  ||  |       |||| |  || | |||    |   ||  ||  |     |  |      |    ||||||||| ||| |||      ||    |||||||||||||||||||||||| ||||| |||||||||||||| |||   |||||| | ||||||||||| || ||||| |||||||| ||||| | |||
-----tcagagaagacatagtctgattttattgacaattgactgacaatttgcctgccctgtgaccctggtcaaagctaattct-tgtattttttttatgatgtagAGGCATTTGCAGTTTGTGAAAATTATTCTCCTCCTGAAGGATTTAATGAGAAAGATTTGCATCGCCTTCTAGAAAAGGTGGGAAGTCCATCAGGAGCAGA
















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|7926380|gb|AW832406.1|AW832406
EST:     CCCTGTAGTGACGTTCGCAAAACCAAAAAGCAGCCGTAATTCCAGCATAG                         AGGCATTTGCAGTTTGTGAAAACTAT
genomic: CCCTGTAGTGACGTTCGCAAAACCAAAAAGCAGCCGTAATTCCAGCATAGgtaaggattt ... gcccttgcagAGGCATTTGCAGTTTGTGAAAACTAT
EST: gi|193636813|gb|FK580840.1|FK580840
EST:     CCCTGTAGTGACGTTCGCAAAACCAAAAAGCAGCCGTAATTCCAGCATAG                         AGGCATTTGCAGTTTGTGAAAACTATTCCCCTCCTGAAGGATTCAATCCAA
genomic: CCCTGTAGTGACGTTCGCAAAACCAAAAAGCAGCCGTAATTCCAGCATAGgtaaggattt ... gcccttgcagAGGCATTTGCAGTTTGTGAAAACTATTCCCCTCCTGAAGGATTCAATCCAA
EST: gi|151411265|gb|EV281076.1|EV281076
EST:     CCCTGTAGTGACGTTCGCAAAACCAAAAAGCAGCCGTAATTCCAGCATAG                         AG-CATTTGCAGTTTGTGAAAACTATTCCCCTCCTGAAAGATTCAATCCAA
genomic: CCCTGTAGTGACGTTCGCAAAACCAAAAAGCAGCCGTAATTCCAGCATAGgtaaggattt ... gcccttgcagAGGCATTTGCAGTTTGTGAAAACTATTCCCCTCCTGAAGGATTCAATCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgattaggtgggtagtgctatttgtgctaattctatgtgtttcgcccttgcagAGGCATTTGCAGTTTGTGAAAACTATTCCCCTCCTGAAGGATTCAATCCAAAAGATCTTCATCGCCTTCTTGAGAAGGTTGGAAGTCCCTCAGGGGTAGA
                          tgctaat  putative branch site (score: 2)
                                         tttcgccctt  putative PPT
                             taattctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatctcactgactatgccaatgatatggtttaaaatgttaggaaggtgattaggtgggtagtgctatttgtgctaattctatgtgtttcgcccttgcagAGGCATTTGCAGTTTGTGAAAACTATTCCCCTCCTGAAGGATTCAATCCAAAAGATCTTCATCGCCTTCTTGAGAAGGTTGGAAGTCCCTCAGGGGTAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - ctcactg
- - - - - - ctatgcc
- - - - - - - - - - -tgatatg
- - - - - - - - - - - - - - - - - - - - - - -ggtgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - aggtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgtg