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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggggaggtatgccaatgtgcaggtctttgattacttaataatagtcatttctgcttttctccttttctgaaagtggtgcatggttgcatctcatgtctatatgtcctacttattatccttacattgctctcctaaattttatcttgaagGTCCTGTCAGAGTATCCAGAGGCAAAAATGACTACTGATGAACAAAATTCATCATTAGGAGAGACCTACCTGGATTTGGTGAAAAGGTTGGATGAAG

Basic information

species Vitis vinifera
transcript Vv16s0039g02270.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g02270.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G09810.1 (Glycine max), 3'ss of exon 4
gtatggggaggtatgccaatgtgca--------ggtctttgattacttaataatagt-------catttctgcttttctccttttctgaaagtggtgcatggttgcatctcatgtctatatgtcctacttattatccttacatt---gctctcctaaattttatcttgaagGTCCTGTCAGAGTATCCAGAGGCAAAAATGACTACTGATGAACAAAATTCATCATTAGGAGAGACCTACCTGGATTTGGTGAAAAGGTTGGATGAAG
|||||||||||||||| |   ||||          | |||  ||  ||  ||   ||       ||| |  | ||||    ||||        |        |||| | |       ||||     |  || | | ||| | ||    |  |  | ||  || |  |  |||| |||||||||||||| |||||||||||||| | |||  | ||  || ||||||| || ||  ||||| | || ||||| || |  ||||||||||
gtatggggaggtatgctagcatgcattcttatgtattttttgttggttcttagaggtatgctagcatgtaagttttttatatttttgtctcaggtcatgcaattgcttattgaaatcatattattcatataatcttctttctttttcaccatatttaaaattgttatacagGTACTGTCAGAGTATCCTGAGGCAAAAATGACAAGTGAGCAGCAGTATGCATCATTGGGTGAATCCTACATTGAGTTGGTCAACAAATTGGATGAAG
















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|161721212|gb|FC070718.1|FC070718
EST:     GCATGATTGGGACAAACTGAAGAATTTGCTATCCTTCCAGTTGAAGCAG                         GTCCTGTCAGAGTATCCAGAGGCAAAAATGACTACTGATGAACAAAATTCA
genomic: GCATGATTGGGACAAACTGAAGAATTTGCTATCCTTCCAGTTGAAGCAGgtatggggag ... tatcttgaagGTCCTGTCAGAGTATCCAGAGGCAAAAATGACTACTGATGAACAAAATTCA
EST: gi|110719175|gb|EE096848.1|EE096848
EST:     GCATGATTGGGACAAACTGAAGAATTTGCTATCCTTCCAGTTGAAGCAG                         GTCCTGTCAGAGTATCCAGAGGCAAAAATGACTACTGATGAACAAAATTCA
genomic: GCATGATTGGGACAAACTGAAGAATTTGCTATCCTTCCAGTTGAAGCAGgtatggggag ... tatcttgaagGTCCTGTCAGAGTATCCAGAGGCAAAAATGACTACTGATGAACAAAATTCA
EST: gi|27584835|gb|CB007530.1|CB007530
EST:     GCATGATTGGGACAAACTGAAGAATTTGCTATCCTTCCAGTTGAAGCAG                         GTCCTGTCAGAGTATCCAGAGGCAAAAATGACTACTGATGAACAAAATTCA
genomic: GCATGATTGGGACAAACTGAAGAATTTGCTATCCTTCCAGTTGAAGCAGgtatggggag ... tatcttgaagGTCCTGTCAGAGTATCCAGAGGCAAAAATGACTACTGATGAACAAAATTCA
EST: gi|30125898|gb|CB911237.1|CB911237
EST:     GCATGATTGGGACAAACTGAAGAATTTGCTATCCTTCCAGTTGAAGCAGGTATGGGGAG                
genomic: GCATGATTGGGACAAACTGAAGAATTTGCTATCCTTCCAGTTGAAGC----------AGgtatggggag ... t
EST: gi|110686390|gb|EE063974.1|EE063974
EST:     GCATGATTGGGACAAACTGAAGAATTTGCTATCCTTCCAGTTGAAGCAG                         GTCCTGTCAGAGTATCCAGAGGCAAAAATGACTACTGATGAACAAAATTCA
genomic: GCATGATTGGGACAAACTGAAGAATTTGCTATCCTTCCAGTTGAAGCAGgtatggggag ... tatcttgaagGTCCTGTCAGAGTATCCAGAGGCAAAAATGACTACTGATGAACAAAATTCA
EST: gi|110698756|gb|EE076614.1|EE076614
EST:     GCATGATTGGGACAAACTGAAGAATTTGCTATCCTTCCAGTTGAAGCAG                         GTCCTGTCAGAGTATCCAGAGGCAAAAATGACTACTGATGAACAAAATTCA
genomic: GCATGATTGGGACAAACTGAAGAATTTGCTATCCTTCCAGTTGAAGCAGgtatggggag ... tatcttgaagGTCCTGTCAGAGTATCCAGAGGCAAAAATGACTACTGATGAACAAAATTCA
EST: gi|161718060|gb|FC067589.1|FC067589
EST:     GCATG-TTGGGACAAACTGAAGAATTTGCTATCCTTCCAGTTGAAGCAG                         GTCCTGTCAGAGTATCCAGAGGCAAAAATGACTACTGATGAACAAAATTCA
genomic: GCATGATTGGGACAAACTGAAGAATTTGCTATCCTTCCAGTTGAAGCAGgtatggggag ... tatcttgaagGTCCTGTCAGAGTATCCAGAGGCAAAAATGACTACTGATGAACAAAATTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctatatgtcctacttattatccttacattgctctcctaaattttatcttgaagGTCCTGTCAGAGTATCCAGAGGCAAAAATGACTACTGATGAACAAAATTCATCATTAGGAGAGACCTACCTGGATTTGGTGAAAAGGTTGGATGAAG
                                   tcctaaa  putative branch site (score: 2)
                                          ttttatctt  CT-rich tract
                                      taaattttatcttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggggaggtatgccaatgtgcaggtctttgattacttaataatagtcatttctgcttttctccttttctgaaagtggtgcatggttgcatctcatgtctatatgtcctacttattatccttacattgctctcctaaattttatcttgaagGTCCTGTCAGAGTATCCAGAGGCAAAAATGACTACTGATGAACAAAATTCATCATTAGGAGAGACCTACCTGGATTTGGTGAAAAGGTTGGATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA