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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgacagctacaattagttttgttttcctcctgtgactatttaaattccattgccttattttatgatcttacccatttcctgctgcttttttttttttagTGATTCAATACTGAGACATGCATCCAGTGATTTCAAGAAAATGGGCCAGCGCATTTTTGTATTTATTGTAGGTGGAGCTACTCGATCCGAG

Basic information

species Vitis vinifera
transcript Vv13s0019g05000.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA17G14450.1 (Glycine max), 3'ss of exon 18
------ttgacagctacaattagttttgttttcctcctgtgactatttaaattccattgccttattttatgatcttacccatttcctgctgcttttttttttttagTGATTCAATACTGAGACATGCATCCAGTGATTTCAAGAAAATGGGCCAGCGCATTTTTGTATTTATTGTAGGTGGAGCTACTCGATCCGAG
      |||   |  || | |   | | | ||     ||  |      |  | ||||| ||  |  | |  || | |    | |  | |||||  | | |    || || ||  | || | |||||||||||||||||||||||||||||| || || || ||| |||| ||||| |||||||| ||  |||| |||
aataatttgtaggggactactgagtatctgttggaattgcaaactaggacctgccatt-ccaaaactcac-atttaatttgtctttttctgctggtatat----agCGACTCGGTGCTAAAACATGCATCCAGTGATTTCAAGAAAATGGGGCAACGAATATTTATATTCATTGTTGGTGGAGCAACCAGATCTGAG

upper sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA11G03230.1 (Glycine max), 3'ss of exon 18
ttgacagctacaattagttttgttttcctc-ctgtgactatttaaattccattgccttattttatgatct-tacccatttcctgctgcttttttttttttagTGATTCAATACTGAGACATGCATCCAGTGATTTCAAGAAAATGGGCCAGCGCATTTTTGTATTTATTGTAGGTGGAGCTACTCGATCCGAG
 | |   ||| |  |||     |   | || ||||    |||   |    |  | |  ||||  |||| | ||    |||     |   |  |    |  || |||||| | || ||||||||||| |||||||||| ||  ||||| || || ||||||||||| ||||| |||||||| ||  |||| |||
-ttattactatatgtagggaaatacccgtctctgttgaaattgtcaactaagcggcaaatttc-tgatgtgtatatttttatatttttgtgatggcatacagCGATTCAGTGCTTAGACATGCATCGAGTGATTTCAGGAGGATGGGGCAACGAATTTTTGTATTCATTGTTGGTGGAGCAACCAGATCTGAG

upper sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 19
--ttgacagctacaattagttttgttttcctcctg--tgactatttaaattccattgccttattttatgatcttacccatttcctgctgcttttttttttttagTGATTCAATACTGAGACATGCATCCAGTGATTTCAAGAAAATGGGCCAGCGCATTTTTGTATTTATTGTAGGTGGAGCTACTCGATCCGAG
   |   |   | ||| | || |      || |||  |  || ||  |||| |||| ||  |  | |  || | |      ||||  |   |  |  | | ||| |||||  | || | ||| |||||||||||||||||||||||||| ||  | || ||| |||| ||||| |||||||| ||  |||| |||
tgctattatagataataatttgtaggggactactgagtatctgttggaattgcatt-ccaaaactcac-atttaattttcatcctttt--ctgctggtatatagCGATTCGGTGCTAAAACACGCATCCAGTGATTTCAAGAAAATGGGGCAAAGAATATTTATATTCATTGTTGGTGGAGCGACCAGATCTGAG

upper sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA01G42140.2 (Glycine max), 3'ss of exon 14
ttgacagctacaattagttttgttttcctcctgtgactatttaaatt--ccatt--gccttattttatgatct-tacccatttcctgctgcttttttttttttagTGATTCAATACTGAGACATGCATCCAGTGATTTCAAGAAAATGGGCCAGCGCATTTTTGTATTTATTGTAGGTGGAGCTACTCGATCCGAG
     || || ||| |||   |   | |  | ||  || || |||||  | | |  ||   | ||| |||  | ||    |||     |   |  |    |  || |||||| | || ||||||||||| |||||||||| ||  ||||| || || |||||| |||| ||||| |||||||| ||  ||||||||
---ctagatataataagtagggaaatac--cagtctctgttgaaattgtcaactaagcggcactttctgacgtgtatatttttatatttttgtgatgacatacagCGATTCAGTGCTTAGACATGCATCAAGTGATTTCAGGAGGATGGGGCAACGAATTTTTCTATTCATTGTTGGTGGAGCAACCAGATCCGAG

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|30299355|gb|CB976149.1|CB976149
EST:     AGACGGTCCACATGGGCTCGGCCTCGGGGCTCTGATGATGGTTATTCAAG                         TGATTCAATACTGAGACATGCATCCAGTGATTTCAAGAAAATGGGCCAGCG
genomic: AGACGGTCCACATGGGCTCGGCCTCGGGGCTCTGATGATGGTTATTCAAGgtactcttgt ... ttttttttagTGATTCAATACTGAGACATGCATCCAGTGATTTCAAGAAAATGGGCCAGCG
EST: gi|349823502|gb|FQ414912.1|FQ414912
EST:     AGACGGTCCACATGGGCTCGGCCTCGGGGCTCTGATGATGGTTATTCAAG                         TGATTCAATACTGAGACATGCATCCAGTGATTTCAAGAAAATGGGCCAGCG
genomic: AGACGGTCCACATGGGCTCGGCCTCGGGGCTCTGATGATGGTTATTCAAGgtactcttgt ... ttttttttagTGATTCAATACTGAGACATGCATCCAGTGATTTCAAGAAAATGGGCCAGCG
EST: gi|110702370|gb|EE081006.1|EE081006
EST:     AGACGGTCCACATGGGCTCGGCCTCGGGGCTCTGATGATGGTTATTCAAG                         TGATTCAATACTGAGACATGCATCCAGTGATTTCAAGAAAATGGGCCAGCG
genomic: AGACGGTCCACATGGGCTCGGCCTCGGGGCTCTGATGATGGTTATTCAAGgtactcttgt ... ttttttttagTGATTCAATACTGAGACATGCATCCAGTGATTTCAAGAAAATGGGCCAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccattgccttattttatgatcttacccatttcctgctgcttttttttttttagTGATTCAATACTGAGACATGCATCCAGTGATTTCAAGAAAATGGGCCAGCGCATTTTTGTATTTATTGTAGGTGGAGCTACTCGATCCGAG
                    atcttac  putative branch site (score: 3)
                     tcttacccatttcctg  CT-rich tract
          ttattttatgatctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgacagctacaattagttttgttttcctcctgtgactatttaaattccattgccttattttatgatcttacccatttcctgctgcttttttttttttagTGATTCAATACTGAGACATGCATCCAGTGATTTCAAGAAAATGGGCCAGCGCATTTTTGTATTTATTGTAGGTGGAGCTACTCGATCCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - cagctac
- - - - - - - - - - - - -tcctcct
- - - - - - - - - - - - - - - - - - - - - - - -ccattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcttt