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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttaactttaatttgatgctgggtttcggaaatcatactaataatcttttgtttttcctcttcttttgtcttttttacccctcttttcttttgaatttaGGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAATGGCTCAACATGGCGTT

Basic information

species Vitis vinifera
transcript Vv10s0003g02790.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g02790.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G25740.2 (Glycine max), 3'ss of exon 1
-------------------------------------------------------------------------------ttttaactttaatttgatgctgggtttcg--gaaatcatactaataatcttttgtttttcctcttcttttgtcttt-------tttacccctcttttcttttgaatttaGGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAATGGCTCAACATGGCGTT----------------------------------
                                                                               ||||   |||  |   | |   |   ||   | ||||   |  | ||     |  ||| |  || |||| |  ||        || |    |  |   | |    || ||||||||||||| || ||||| |||||||| |||||| |||||||| | ||||||   ||||| |                                    
gtacgttcccattcccattctcattctcgttagccaattaacgaaattttcgagtgactagtttcttctggctttgctattttctttttcttccaacgaaagcactcaatggaatctctcataaaactagcttctttgcaactcctttgggtttcataattgttaattgattatcattgtctggttcagGCTGATCCTGAGTTGGAAGCAATCAGACAGAGAAGGTTGCAGGAGCTTATGGCTGGCCATGGTGGCGTGGTTAGAGAATCAGAGATCATTCGTTTTACTT

upper sequence: Vv10s0003g02790.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G25740.1 (Glycine max), 3'ss of exon 1
-------------------------------------------------------------------------------ttttaactttaatttgatgctgggtttcg--gaaatcatactaataatcttttgtttttcctcttcttttgtcttttttacccctcttttcttttga-------atttaGGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAATGGCTCAACATGGCGTT---
                                                                               ||||   |||  |   | |   |   ||   | ||||   |  | ||     |  ||| |  || |||| |  ||  | |    |  ||  || | |        || ||||||||||||| || ||||| |||||||| |||||| |||||||| | ||||||   ||||| |     
gtacgttcccattcccattctcattctcgttagccaattaacgaaattttcgagtgactagtttcttctggctttgctattttctttttcttccaacgaaagcactcaatggaatctctcataaaactagcttctttgcaactcctttgggtttcataattgttaattgattatcattgtctggttcagGCTGATCCTGAGTTGGAAGCAATCAGACAGAGAAGGTTGCAGGAGCTTATGGCTGGCCATGGTGGCGTG

upper sequence: Vv10s0003g02790.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G29850.2 (Arabidopsis thaliana), 3'ss of exon 1
ttttaactttaatttgatgctgggtttcggaaatcatactaataatcttttgtttttcctcttcttttgtcttttttacccctcttttcttttgaatt-taGGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAATGGCTCAACATGGCGTT
  | | ||| | | | ||| | |     |  |||    ||   ||| ||       | |  || | |  |  | ||||| ||| ||   |  ||   | ||||||||||||||| |||||||||| ||||| || || ||||| ||| | ||||||| ||| ||| | 
--taatcttcagtataatgttagccaaagataattcatcttcaaatgttaaaacactgcatttttatgtttatatttactccttttacttcctgttctgtagGCTGATCCTGAACTAGAAGCTATTAGACAGAGGAGAATGCAAGAGCTCATGGCTCGACAAGGCATG

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|30298572|gb|CB975366.1|CB975366
EST:     CATCCGTGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAAT-                         GGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
genomic: CATCCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAATGgtaatccatt ... tttgaatttaGGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
EST: gi|28970247|gb|CB349280.1|CB349280
EST:     CATCCGTGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAAT-                         GGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
genomic: CATCCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAATGgtaatccatt ... tttgaatttaGGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
EST: gi|29783283|gb|CB349364.2|CB349364
EST:     CATCCGTGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAAT-                         GGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
genomic: CATCCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAATGgtaatccatt ... tttgaatttaGGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
EST: gi|110392495|gb|EC957959.1|EC957959
EST:     CATCCGTGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAAT-                         GGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
genomic: CATCCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAATGgtaatccatt ... tttgaatttaGGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
EST: gi|110416972|gb|EC982990.1|EC982990
EST:     CCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAAT-                         GGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
genomic: CCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAATGgtaatccatt ... tttgaatttaGGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
EST: gi|87586667|gb|DY474848.1|DY474848
EST:     CATCCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAAT-                         GGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
genomic: CATCCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAATGgtaatccatt ... tttgaatttaGGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
EST: gi|352764365|gb|FQ471332.1|FQ471332
EST:     CATCCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAAT-                         GGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
genomic: CATCCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAATGgtaatccatt ... tttgaatttaGGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
EST: gi|71879748|gb|DT028803.1|DT028803
EST:     CATCCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAAT-                         GGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
genomic: CATCCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAATGgtaatccatt ... tttgaatttaGGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
EST: gi|110385381|gb|EC949901.1|EC949901
EST:     CATCCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAAT-                         GGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
genomic: CATCCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAATGgtaatccatt ... tttgaatttaGGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
EST: gi|351028143|gb|FQ426044.1|FQ426044
EST:     CATCCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAAT-                         GGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
genomic: CATCCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAATGgtaatccatt ... tttgaatttaGGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
EST: gi|28960498|gb|CB340254.1|CB340254
EST:     CATCCGTGATCAAGATCACCTCTCCCCTTACTCCATCTCTTGGAAAAAT-                         GGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
genomic: CATCCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAATGgtaatccatt ... tttgaatttaGGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
EST: gi|22013208|gb|BQ798242.1|BQ798242
EST:     CATCCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAAT-                         GGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
genomic: CATCCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAATGgtaatccatt ... tttgaatttaGGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
EST: gi|110390216|gb|EC955116.1|EC955116
EST:     CCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAAT-                         GGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
genomic: CCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAATGgtaatccatt ... tttgaatttaGGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
EST: gi|22012545|gb|BQ797579.1|BQ797579
EST:     CATCCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAAT-                         GGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT
genomic: CATCCGGGATCAAGATCACCTCTCTCCTTACTCCATCTCTTGGAAAAATGgtaatccatt ... tttgaatttaGGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttgtttttcctcttcttttgtcttttttacccctcttttcttttgaatttaGGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAATGGCTCAACATGGCGTT
       tttttcctcttctttt  CT-rich tract
                                       ttttcttttgaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttaactttaatttgatgctgggtttcggaaatcatactaataatcttttgtttttcctcttcttttgtcttttttacccctcttttcttttgaatttaGGCTGATCCTGAATTAGAAGCTATCAGACAAAGAAGGATGCAGGAGTTAATGGCTCAACATGGCGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - -gatgctg
- - - - - - - - - - - - - - - aaatcat