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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtggccttggatttgaggatgttatttcctgcaaactattgtatttttcttgtttgaccaatttttgtgatattttatctttggtcccttagATGGCTTGGAAAGATAACACTGGAGACTTACATCTCCCAGATCCATATATGGTTAAG

Basic information

species Vitis vinifera
transcript Vv05s0077g00620.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g00620.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA17G04070.1 (Glycine max), 3'ss of exon 12
----------------------------------------------------------------------------------------------gtaagtggccttggatttgaggatgttatttcctgcaaactattgtatttttcttgtttgaccaatttttgtgatattttatctttggtcccttagATGGCTTGGAAAGATAACACTGGAGACTTACATCTCCCAGATCCATATATGGTTAAG
                                                                                               |   | ||       |     ||   | || || ||   | || ||    |  |  || |  || |  | | | | | | |||    ||   |||||||||||| ||||| |||||||||||||||||||||||||||||||| ||||||||
gtaagttgtctttgtagaagtagaatcttttattcatctctcttttgttcccttctctttcacacatggacatgccttcttatttaatgagctaatttattgctaaatgctgtcaaattgaactttcttcactttgttttaaggctggtaattcattaactaattttacaatgtttctactttcttctagATGGCTTGGGAAGATTACACTGGAGACTTACATCTCCCAGATCCATATCTGGTTAAG

upper sequence: Vv05s0077g00620.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA07G36550.1 (Glycine max), 3'ss of exon 12
----gtaagtggccttggatttgaggatgttatttcctgcaaactattgtatttttcttgtttgaccaatttttgtgatattttatctttggtcccttagATGGCTTGGAAAGATAACACTGGAGACTTACATCTCCCAGATCCATATATGGTTAAG
     |   | ||       |     || | | || || ||   | || |     |  |  ||    || |  | | ||  | | |||    ||   ||| |||||||| ||||| |||||||||||||| ||||||||||||||||| ||||||||
gctattttattgctaaatgctgtcaaatttaaatttcttcactttgttttgaggctggtaattagttaactaattttatgatgtttctactttcttgtagTTGGCTTGGGAAGATTACACTGGAGACTTATATCTCCCAGATCCATATCTGGTTAAG

upper sequence: Vv05s0077g00620.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT3G06550.3 (Arabidopsis thaliana), 3'ss of exon 12
gtaagtggccttggatttgaggatgttatttcctgcaaactattgtatttttcttgtttgaccaatttttgtgatat---tttatctttggtcccttagATGGCTTGGAAAGATAACACTGGAGACTTACATCTCCCAGATCCATATATGGTTAAG
               |  |   |   || |||  |  ||    | | ||| || | ||  | | ||||||   | |    ||| |   ||  |  | || |||||||||||||||||||||||||| || ||||||||| | ||||||||| | ||
--------------gtaagtaaaaaataattca-gtcaatagatatgtttatcctcttataacgattttttcaagaaaaatttgttcatgaactttcagGTGGCTTGGAAAGATAACACTGGAGACATATATCTCCCAGTTTCATATATGGCTCAG

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|110715867|gb|EE094404.1|EE094404
EST:     TTGCGGAATCTCACACAACAATTTCGTTGCTACTCCTTGACCCTTTTTGC                         ATGGCTTGGAAAGATAACACTGGAGACTTACATCTCCCAGATCCATATATG
genomic: TTGCGGAATCTCACACAACAATTTCGTTGCTACTCCTTGACCCTTTTTGCgtaagtggcc ... ggtcccttagATGGCTTGGAAAGATAACACTGGAGACTTACATCTCCCAGATCCATATATG
EST: gi|351025158|gb|FQ433575.1|FQ433575
EST:     TTGCGGAATCTCACACAACAATTTCGTTGCTACTCCTTGACCCTTTTTGC                         ATGGCTTGGAAAGATAACACTGGAGACTTACATCTCCCAGATCCATATATG
genomic: TTGCGGAATCTCACACAACAATTTCGTTGCTACTCCTTGACCCTTTTTGCgtaagtggcc ... ggtcccttagATGGCTTGGAAAGATAACACTGGAGACTTACATCTCCCAGATCCATATATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtatttttcttgtttgaccaatttttgtgatattttatctttggtcccttagATGGCTTGGAAAGATAACACTGGAGACTTACATCTCCCAGATCCATATATGGTTAAG
              gtttgac  putative branch site (score: 4)
                                               tccctt  putative PPT
                      aatttttgtgatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtggccttggatttgaggatgttatttcctgcaaactattgtatttttcttgtttgaccaatttttgtgatattttatctttggtcccttagATGGCTTGGAAAGATAACACTGGAGACTTACATCTCCCAGATCCATATATGGTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA