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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcacttttcctcattctttcccaaaaggcaaaaactaaacagaaaattcagagccctgttttcagagttatcacacgaaatatgggtacttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAGATATTAAACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTC

Basic information

species Vitis vinifera
transcript Vv08s0007g05350.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g05350.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os07g46520.1 (Oryza sativa), 3'ss of exon 1
--tttcacttttcctcattctttcccaaaaggcaaaaactaaacagaaaattcagagccctgttttcagagttatcacacgaaatatgggtacttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAGATATTAAACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTC
    || |||||    || ||     |   |     || ||  || |      |  | | | ||      | |  | |  ||  |   |||  || || ||| | || ||||  ||||| || || ||||| ||  | || || ||    ||||| || |  |||||||| ||||||||||| ||||| ||||||||||| |
aagctctctttttgcgatgctgggatatgtgtgcgcaattatgcatatggaatat-gtcttcttcatgtggcttactcctgatgtcctggtgtttgtt-cagGTATACAGAACAATTGGCGAAAAGTATGGAGTCAACTACTCAGAGGATGAGATCTTGATGAGATACAGGAGGGCTTATGCGCAGCCATGGGGTAGATCGC

upper sequence: Vv08s0007g05350.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G28600.1 (Glycine max), 3'ss of exon 1
tttcacttttcctcattctttcc-caaaaggcaaaaactaaacagaaaattcagagccctgttttcagagttatcacacgaaatatgggtacttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAGATATTAAACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTC
 | |    |||    | |   || |   |  |  |||||||        || | | |   ||  |    ||| |         |     |  || | | |||| |||||||||||||| ||||| ||||| |||||||||||||||   |||||| |   |||||| ||||| || ||||  ||||| ||||| | |||||
gtgcgtgcttcgatgtgcgcgccacgtgaaactgaaactaattctgt--ttaaaaacggcgtcgtttacgttttt-tgttttttgcttttttttttggtagATATATAGAAAGATTGGAGAGAAGTATGGAGTGGAGTATTCGGAAGATGAGATACTGTTCAGATATAGAAGAGCGTATGGTCAGCCTTGGGGAAAATCTC

upper sequence: Vv08s0007g05350.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G31340.1 (Glycine max), 3'ss of exon 1
------------------tttcacttttcctcattctt---tcccaaaaggca-aaaactaaacagaaaattcagagccctgttttcagagttatcacacgaaatatgggtacttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAGATATTAAACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTC
                  |   |||    || |||||    |   ||  | |   ||||| |    |  ||  |  |   |  |||  |  || |         |||   |  || | | |||| |||||||||||||| ||||| ||||| ||||||||||||||    |||||| |   |||||||||||| || ||||  ||||| ||||| | |||||
gtgcgcgctacgtgaaactgagactgaaactaattctgttattttaacggacgtgaaactgattctattatataacggtgtcgtttacgttttttgtttttcgctatt--tttttttggtagATATATAGAAAGATTGGGGAGAAGTATGGAGTGGAGTATTCGGAGGATGAGATACTGTTCAGATACAGAAGAGCGTATGGTCAGCCTTGGGGAAAATCTC

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|32267815|gb|CD716974.1|CD716974
EST:     TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|110731628|gb|EE106216.1|EE106216
EST:     TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACTGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|30299817|gb|CB976611.1|CB976611
EST:     TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|110395612|gb|EC961279.1|EC961279
EST:     TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|110429697|gb|EC996199.1|EC996199
EST:     CTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACTGAG
genomic: CTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|161719017|gb|FC067637.1|FC067637
EST:     TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|26258618|gb|CA809681.1|CA809681
EST:     TGGTTGATGCCGTCGGTACCCTTCCTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|33403789|gb|CF209416.1|CF209416
EST:     TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|110725316|gb|EE101677.1|EE101677
EST:     TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACTGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|161712968|gb|FC062094.1|FC062094
EST:     TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|110730112|gb|EE106820.1|EE106820
EST:     TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACTGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|110713079|gb|EE088696.1|EE088696
EST:     TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACTGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|71877278|gb|DT026333.1|DT026333
EST:     TGGATGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|26266814|gb|CA817877.1|CA817877
EST:     TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|294965827|gb|GW837310.1|GW837310
EST:     TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACTGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|26257149|gb|CA808212.1|CA808212
EST:     TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGCGGAGTATTCGGAAACCGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|110731791|gb|EE106512.1|EE106512
EST:     TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACTGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|110688614|gb|EE067366.1|EE067366
EST:     TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|294966056|gb|GW837423.1|GW837423
EST:     TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACTGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|110713855|gb|EE090151.1|EE090151
EST:     TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGTCCATGGCTCAG                         ATCTATAGAAAGATCGGTGAGAAATATGGGGTGGAGTATTCGGAAACTGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|71877965|gb|DT027020.1|DT027020
EST:     TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|161715593|gb|FC068349.1|FC068349
EST:     TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG
EST: gi|110712773|gb|EE088110.1|EE088110
EST:     TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAG                         ATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACTGAG
genomic: TGGTTGATGCCGTCGGTACTCTTCTTGTTCCCTCACAGCCCATGGCTCAGgtttgcattt ... cttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattcagagccctgttttcagagttatcacacgaaatatgggtacttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAGATATTAAACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTC
                                           tacttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcacttttcctcattctttcccaaaaggcaaaaactaaacagaaaattcagagccctgttttcagagttatcacacgaaatatgggtacttattgcagATCTATAGAAAGATTGGTGAGAAATATGGGGTGGAGTATTCGGAAACCGAGATATTAAACAGATACAGAAGGGCTTATGCACAGCCCTGGGGTAGATCTC

- - - - -tcctcat
- - - - - - - - -ctttccc
- - - - - - - - - - - - aaaaggc
- - - - - - - - - - - - - - - - -aaactaa
- - - - - - - - - - - - - - - - - - - - - agaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcacacg