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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttttgtgatgttatccctctttttggacaacttggttatgtgattgcatgatttttgatcatgacacaaattttcccttttataactgtagACCATCAGCTATATGGCAGAGCGTGTTGTTGGGCATGGATCTTTTGGAGTAGTGTTCCAG

Basic information

species Vitis vinifera
transcript Vv07s0005g02100.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G01280.1 (Glycine max), 3'ss of exon 3
gtaagtttttgtgatgttatccctctt-tttggacaacttggttatgtgattgcatg---atttttgatcatg-acacaaatttt-------cccttttataactgtagACCATCAGCTATATGGCAGAGCGTGTTGTTGGGCATGGATCTTTTGGAGTAGTGTTCCAG
||  |||| ||  || |||    | ||  ||| ||||     || | || ||||||    ||  ||  | ||| |  |  ||| |       |  ||| || | || |||| || ||||||||||| ||||| ||||||||  ||||||| ||||| ||||| ||||||
gtctgtttgtgatatcttaaatttgttacttgaacaatcaatttgtctgtttgcatttgcatggttacttatgcatgcttattgtgatgcaacattttcatgattgcagACAATAAGCTATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG
















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|161705537|gb|FC055340.1|FC055340
EST:     GTCATATAATTGTAACAACTATTGGAGGGAAAAATGGCCAGCCAAAGCAG                         ACCATCAGCTATATGGCAGAGCGTGT
genomic: GTCATATAATTGTAACAACTATTGGAGGGAAAAATGGCCAGCCAAAGCAGgtaagttttt ... ataactgtagACCATCAGCTATATGGCAGAGCGTGT
EST: gi|161717738|gb|FC065945.1|FC065945
EST:     GTCATATAATTGTAACAACTATTGGAGGGAAAAATGGCCAGCCAAAGCAG                         ACCATCAGCTATATGGCAGAGCGTGTTGTTGGGCATGGATCTTTTGGAGTA
genomic: GTCATATAATTGTAACAACTATTGGAGGGAAAAATGGCCAGCCAAAGCAGgtaagttttt ... ataactgtagACCATCAGCTATATGGCAGAGCGTGTTGTTGGGCATGGATCTTTTGGAGTA
EST: gi|71862885|gb|DT011940.1|DT011940
EST:     GTCATATAATTGTAACAACTATTGGAGGGAAAAATGGCCAGCCAAAGCAG                         ACCATCAGCTATATGGCAGAGCGTGTTGTTGGGCATGGATCTTTTGGAGTA
genomic: GTCATATAATTGTAACAACTATTGGAGGGAAAAATGGCCAGCCAAAGCAGgtaagttttt ... ataactgtagACCATCAGCTATATGGCAGAGCGTGTTGTTGGGCATGGATCTTTTGGAGTA
EST: gi|110703118|gb|EE079682.1|EE079682
EST:     GTCATATAATTGTAACAACTATTGGAGGGAAAAATGGCCAGCCAAAGCAG                         ACCATCAGCTATATGGCAGAGCGTGTTGTTGGGCATGGATCTTTTGGAGTA
genomic: GTCATATAATTGTAACAACTATTGGAGGGAAAAATGGCCAGCCAAAGCAGgtaagttttt ... ataactgtagACCATCAGCTATATGGCAGAGCGTGTTGTTGGGCATGGATCTTTTGGAGTA
EST: gi|110685785|gb|EE062810.1|EE062810
EST:     GTCATATAATTGTAACAACTATTGGAGGGAAAAATGGCCAGCCAAAGCAG                         ACCATCAGCTATATGGCAGAGCGTGTTGTTGGGCATGGATCTTTTGGAGTA
genomic: GTCATATAATTGTAACAACTATTGGAGGGAAAAATGGCCAGCCAAAGCAGgtaagttttt ... ataactgtagACCATCAGCTATATGGCAGAGCGTGTTGTTGGGCATGGATCTTTTGGAGTA
EST: gi|71875370|gb|DT024425.1|DT024425
EST:     GTCATATAATTGTAACAACTATTGGAGGGAAAAATGGCCAGCCAAAGCAG                         ACCATCAGCTATATGGCAGAGCGTGTTGTTGGGCATGGATCTTTTGGAGTA
genomic: GTCATATAATTGTAACAACTATTGGAGGGAAAAATGGCCAGCCAAAGCAGgtaagttttt ... ataactgtagACCATCAGCTATATGGCAGAGCGTGTTGTTGGGCATGGATCTTTTGGAGTA
EST: gi|71875374|gb|DT024429.1|DT024429
EST:     GTCATATAATTGTAACAACTATTGGAGGGAAAAATGGCCAGCCAAAGCAG                         ACCATCAGCTATATGGCAGAGCGTGTTGTTGGGCATGGATCTTTTGGAGTA
genomic: GTCATATAATTGTAACAACTATTGGAGGGAAAAATGGCCAGCCAAAGCAGgtaagttttt ... ataactgtagACCATCAGCTATATGGCAGAGCGTGTTGTTGGGCATGGATCTTTTGGAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtgattgcatgatttttgatcatgacacaaattttcccttttataactgtagACCATCAGCTATATGGCAGAGCGTGTTGTTGGGCATGGATCTTTTGGAGTAGTGTTCCAG
                                           ttataac  putative branch site (score: 2)
                                  ttttcccttttat  CT-rich tract
                                         ttttataact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttttgtgatgttatccctctttttggacaacttggttatgtgattgcatgatttttgatcatgacacaaattttcccttttataactgtagACCATCAGCTATATGGCAGAGCGTGTTGTTGGGCATGGATCTTTTGGAGTAGTGTTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG