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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCAGCAAAGAAAGAGAACAAACTGTGTCAAAGAGCAGTATTGTGACTACTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagcttgatcacagttttctttatgcgcttgtagttgattttgttactgtggaactcttctattcttcaacttgatttaaaaaaaaactactat...

Basic information

species Vitis vinifera
transcript Vv04s0023g03200.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03200.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA16G24130.1 (Glycine max), 5'ss of exon 3
TGTCAGCAAAGAAAGAGAACAAACTGTGTCAAAGAGCAGTATTGTGACTACTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagcttgatcacagtt-ttctttatgcgcttgtagttgattttgttactgtggaactcttctattcttcaacttgatttaaaaaaaaactactat---
|||||||||||||   ||||||||  ||||||  ||||| ||||||||||| |||||||  |||||||||| ||||| ||| |||||||| || || |||||||| |  |   || |   || ||   |||     | |  | || |     | | || ||       |     || |     ||| | | | | |||      
TGTCAGCAAAGAACAGGAACAAACCCTGTCAAGAAGCAGCATTGTGACTACACAAATTCTGCAACTTGGAACATTTTACCCTGCAGAGCCAGAGCACCAGgtttgtttccaaaataatgtttatttactattgatgtttgatagaat--accagtttgaaataggatcaaatcacacc--agattatatagatattacagcgat

upper sequence: Vv04s0023g03200.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G05550.1 (Glycine max), 5'ss of exon 3
TGTCAGCAAAGAAAGAGAACAAACTGTGTCAAAGAGCAGTATTGTGACTACTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagcttgatcacagttttctttatgc--gcttgtagttgattttgttactgtggaactcttctattcttcaacttgatttaaaaaaaaactactat
|||||||||||||   ||||||||   |||||  ||||| |||||||||||||||||||  |||||||||| ||||| ||| |||||||| || || ||||| || |  |   || |   ||      || |    ||| | | |||     ||   |  |        |   |  |     |||| |  ||   ||     
TGTCAGCAAAGAACAGGAACAAACCAGGTCAAGAAGCAGCATTGTGACTACTCAAATTCTGCAACTTGGAACATTTTACCCTGCAGAGCCAGAGCACCAGgtatgtttccaaaataatgtttgatagaataccaatttgaaatagatggaaataggattaagtcacagcagattatacagatatttcagcaatttcttgc--
















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|83274580|gb|DV938677.1|DV938677
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAG                         AAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
EST: gi|77582988|gb|DV220511.1|DV220511
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCATGAACATCAG                         AAATTTGAGCTCAAAAGAAATCCTTTCCTCCTTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
EST: gi|110719878|gb|EE095384.1|EE095384
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAG                         AAATTTGAGCTCAAAAGAAATCCTTTCCTCCTTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
EST: gi|33404892|gb|CF210519.1|CF210519
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAG                         AAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
EST: gi|33404977|gb|CF210604.1|CF210604
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAG                         AAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
EST: gi|71875950|gb|DT025005.1|DT025005
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAG                         AAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
EST: gi|71875949|gb|DT025004.1|DT025004
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAG                         AAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
EST: gi|110719966|gb|EE095534.1|EE095534
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAG                         AAATTTGAGCTCAAAAGAAATCCTTTCCTCCTTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
EST: gi|34545817|gb|CF514049.1|CF514049
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAG                         AAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
EST: gi|161719951|gb|FC069029.1|FC069029
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCATGAACATCAG                         GAATTTGAGCTCAAAAGAAATCCTTTCCTCCTTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
EST: gi|110716777|gb|EE092054.1|EE092054
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAG                         AAATTTGAGCTCAAAAGAAATCCTTTCCTCCTTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
EST: gi|71870654|gb|DT019709.1|DT019709
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCATGAACATCAG                         AAATTTGAGCTCAAAAGAAATCCTTTCCTCCTTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
EST: gi|110406198|gb|EC971761.1|EC971761
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAG                         AAATTTGAGCTCAAAAGAAATCCTTTCCTCCTTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
EST: gi|161716432|gb|FC068424.1|FC068424
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCATGAACATCAG                         AAATTTGAGCTCAAAAGAAATCCTTTCCTCCTTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
EST: gi|34545903|gb|CF514135.1|CF514135
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAG                         AAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
EST: gi|110414444|gb|EC980276.1|EC980276
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAG                         AAATTTGAGCTCAAAAGAAATCCTTTCCTCCTTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
EST: gi|33408384|gb|CF214011.1|CF214011
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCATGAACATCAG                         AAATTTGAGCTCAAAAGAAATCCTTTCCTCCTTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
EST: gi|33408641|gb|CF214268.1|CF214268
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCATGAACATCAG                         AAATTTGAGCTCAAAAGAAATCCTTTCCTCCTTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
EST: gi|110718218|gb|EE094803.1|EE094803
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAG                         AAATTTGAGCTCAAAAGAAATCCTTTCCTCCTTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
EST: gi|161716720|gb|FC067841.1|FC067841
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAG                         AAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
EST: gi|30133186|gb|CB918525.1|CB918525
EST:     CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAG                         AAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG
genomic: CTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagc ... aaatctgcagAAATTTGAGCTCAAAAGAAATCCTTTCCTCATTCAGCTGATGGGGAACTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTCAGCAAAGAAAGAGAACAAACTGTGTCAAAGAGCAGTATTGTGACTACTCAAATTCAACAACTTGGAAAATTTTGCCCAGCAGAGCCTGAACATCAGgtttggtagcttgatcacagttttctttatgcgcttgtagttgattttgttactgtggaactcttctattcttcaacttgatttaaaaaaaaactactat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa