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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggggagcgaataatttcttctgtatctactgtttttcatgcaccttaataataaagttatttgatatatataactgcatattcaaacttccctctgtcagGCACCATCGCGCAGTTGTTTGGAGCTGGTGAAGGTGAATGTTCTGTTATCATGCTATGGACATATGTTTTGGCCTCAGTTGCAGTCACTTTTTGGACAAC

Basic information

species Glycine max
transcript GLYMA11G09390.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G09390.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv04s0044g01880.t01 (Vitis vinifera), 3'ss of exon 11
ggggagcgaata-atttcttctgtatctactgtttttcatgcaccttaataataaagttatttgatatatataactgcatattcaaacttccctctgtcagGCACCATCGCGCAGTTGTTTGGAGCTGGTGAAGGTGAATGTTCTGTTATCATGCTATGGACATATGTTTTGGCCTCAGTTGCAGTCACTTTTTGGACAAC
 |   |  |||| |  |      ||  |    | |    ||    || |||  |||   |||   || |   |  ||  || |            || ||||||| ||| ||||| |||||||||| || ||  | ||||||||||| |||||||| ||||||||||  ||||| ||||||||  ||||  ||||| | ||
-gtatggaaatacacctgaaacataattctattataatttgggtgttgatagaaaaaggattaattagaggcagttgtgtaatg-----------tggcagGCACAATCACGCAGCTGTTTGGAGCAGGCGAGAGCGAATGTTCTGTCATCATGCTGTGGACATATGCCTTGGCGTCAGTTGCCCTCACGCTTTGGTCCAC

upper sequence: GLYMA11G09390.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv04s0044g01870.t01 (Vitis vinifera), 3'ss of exon 9
ggggagcgaataatttcttctgtatctactgtttttcatgcaccttaat---aataaagttatttgatatatataactgcatattcaaacttccc--tctgtcagGCACCATCGCGCAGTTGTTTGGAGCTGGTGAAGGTGAATGTTCTGTTATCATGCTATGGACATATGTTTTGGCCTCAGTTGCAGTCACTTTTTGGACAAC
         ||||||||    || |         || | |  | ||  |   | || | ||   |  |  |||| |     |     |||| ||   |||  ||||||| ||    |||||||||||||| |||||  |||||||||||||||||||||| ||||||||||  ||||| |||||| || ||||  ||||| ||||
-----tttgataatttcactggtttaagaaagagttgaagttcgttccttggattatatttgcctttttaatatgaaaatttgactcaactccctaatcttgcagGCACAATTATCCAGTTGTTTGGAGCGGGTGAGAGTGAATGTTCTGTTATCATGCTGTGGACATATGGCTTGGCATCAGTTTCACTCACCCTTTGGTCAAC
















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|4295191|gb|AI442298.1|AI442298
EST:     TCAGTTTGTGCTTCTCCTTCAATATGCACTTCCACCTGCAATGGCTATAG                         GCACCATCGCGCAGTTGTTTGGAGCTGGTGAAGGTGAATGTTCTGTTATCA
genomic: TCAGTTTGTGCTTCTCCTTCAATATGCACTTCCACCTGCAATGGCTATAGgtataataat ... cctctgtcagGCACCATCGCGCAGTTGTTTGGAGCTGGTGAAGGTGAATGTTCTGTTATCA
EST: gi|51341651|gb|CO982968.1|CO982968
EST:     TCAGTTTGTGGTTCTCCTTCAATATGCACTTCCACCTGCAATGGCTATAG                         GCACCATCGCGCAGTTGTTTGGAGCTGGTGAAGGTGAATGTTCTGTTATCA
genomic: TCAGTTTGTGCTTCTCCTTCAATATGCACTTCCACCTGCAATGGCTATAGgtataataat ... cctctgtcagGCACCATCGCGCAGTTGTTTGGAGCTGGTGAAGGTGAATGTTCTGTTATCA
EST: gi|192315779|gb|FK008489.1|FK008489
EST:     TCAGTTTGTGCTTCTCCTTCAATATGCACTTCCACCTGCAATGGCTATAG                         GCACCATCGCGCAGTTGTTTGGAGCTGGTGAAG-TGAATGTTCTGTTATCA
genomic: TCAGTTTGTGCTTCTCCTTCAATATGCACTTCCACCTGCAATGGCTATAGgtataataat ... cctctgtcagGCACCATCGCGCAGTTGTTTGGAGCTGGTGAAGGTGAATGTTCTGTTATCA
EST: gi|192315780|gb|FK008490.1|FK008490
EST:     TCAGTTTGTGCTTCTCCTTCAATATGCACTTCCACCTGCAATGGCTATAG                         GCACCATCGCGCAGTTGTTTGGAGCTGGTGAAAGTGAATGTTCTGTTATCA
genomic: TCAGTTTGTGCTTCTCCTTCAATATGCACTTCCACCTGCAATGGCTATAGgtataataat ... cctctgtcagGCACCATCGCGCAGTTGTTTGGAGCTGGTGAAGGTGAATGTTCTGTTATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taataataaagttatttgatatatataactgcatattcaaacttccctctgtcagGCACCATCGCGCAGTTGTTTGGAGCTGGTGAAGGTGAATGTTCTGTTATCATGCTATGGACATATGTTTTGGCCTCAGTTGCAGTCACTTTTTGGACAAC
                      atataac  putative branch site (score: 3)
                                         cttccctctgtc  putative PPT
     ataaagttatttgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggggagcgaataatttcttctgtatctactgtttttcatgcaccttaataataaagttatttgatatatataactgcatattcaaacttccctctgtcagGCACCATCGCGCAGTTGTTTGGAGCTGGTGAAGGTGAATGTTCTGTTATCATGCTATGGACATATGTTTTGGCCTCAGTTGCAGTCACTTTTTGGACAAC

-gggagcg
- - - - - - - -tcttctg
- - - - - - - - - - - - tctactg
- - - - - - - - - - - - - - - - - - catgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaaact