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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgacatgtgttcacaccaggttgtacaaaactgcatttacttcatgcttttagaagaatactgtgtgatgaaaacaattctgtggatttgtttcttttagGTTGTTAATTATGTTGTGGAAAAGATGGTCCTTGACAAACCAATGGATAGTGTAAACCCTGATGGAACATTTGCCCCGGGCCTCCCTGGTGGGCAGTCAC

Basic information

species Vitis vinifera
transcript Vv14s0030g01350.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0030g01350.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA19G43070.1 (Glycine max), 3'ss of exon 16
tgacatgtgttcacaccaggttgtacaaaactgcatttacttcatgcttttagaagaatactgtgtgatgaaaacaa--ttctgtggatttgtttcttttagGTTGTTAATTATGTTGTGGAAAAGATGGTCCTTGACAAACCAATGGATAGTGTAAACCCTGATGGAACATTTGCCCCGGGCCTCCCTGGTGGGCAGTCAC
| |  |  | |       |  || |      || |||      |   |    || | ||  ||  | || ||   ||  |||  |   |||| ||  |||||||||||||||||||  | || |||||||| |||||||||||  |||| ||  |||   |||| || |   ||||||| || ||  ||||    |||||||
ttagtttagcttttgt--gcatgcatgtgtgtggattctgaaaacagtagatgatgcattttgaattatcaacttaactttcctttattttggttggtttagGTTGTTAATTATGTAATAGAGAAGATGGTGCTTGACAAACCTTTGGACAGCTTAAGTGCTGAAGGTAGTATTGCCCCTGGTCTTACTGGGTCACAGTCAC

upper sequence: Vv14s0030g01350.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AT3G05090.2 (Arabidopsis thaliana), 3'ss of exon 16
tgacatgtgttcacaccaggttgtacaaaactgca--tttacttcatgcttttagaagaatactgtgtgatgaaaacaattctgtggatttgtttcttttagGTTGTTAATTATGTTGTGGAAAAGATGGTCCTTGACAAACCAATGGATAGTGTAAACCCTGATGGAACATTTGCCCCGGGCCTCCCTGGTGGGCAGTCAC
                     || |   | ||| |  ||||  |  |  ||||    | |  || ||| ||  ||    |||| |  || | | | |   |||||   ||||| |||||||||||||||||||||||||| ||  |||||||| ||     ||||| | ||  ||   | ||    |    |  ||      
--------------------gtgcatttatctgtaattttaagttgtagttttgcttgcactctctgttattcaatggcttct-taaatgtctatgt---agGTTACCAATTACGTTGTGGAAAAGATGGTCCTTGACAATCCGTTGGATAGTCTAGCTATTGATGCAGCAAGTGTTTCAGGAGGACAACCTCAGCCACTGT
















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|33402527|gb|CF208154.1|CF208154
EST:     TCCTTACTCAAGGGAAACTGAGTGCACCTCGTATATTGAGAATTCATAAA                         GTTGTTAATTATGTTGTGGAAAAGATGGTCCTTGACAAACCAATGGATAGT
genomic: TCCTTACTCAAGGGAAACTGAGTGCACCTCGTATATTGAGAATTCATAAAgtaagttttt ... tttcttttagGTTGTTAATTATGTTGTGGAAAAGATGGTCCTTGACAAACCAATGGATAGT
EST: gi|294965578|gb|GW837177.1|GW837177
EST:     TCCTTACTCAAGGGAAACTGAGTGCACCTCGTATATTGAGAATTCATAAA                         GTTGTTAATTATGTTGTGGAAAAGATGGTCCTTGACAAACCAATGGATAAT
genomic: TCCTTACTCAAGGGAAACTGAGTGCACCTCGTATATTGAGAATTCATAAAgtaagttttt ... tttcttttagGTTGTTAATTATGTTGTGGAAAAGATGGTCCTTGACAAACCAATGGATAGT
EST: gi|33402504|gb|CF208131.1|CF208131
EST:     TCCTTACTCAAGGGAAACTGAGTGCACCTCGTATATTGAGAATTCATAAA                         GTTGTTAATTATGTTGTGGAAAAGATGGTCCTTGACAAACCAATGGATAGT
genomic: TCCTTACTCAAGGGAAACTGAGTGCACCTCGTATATTGAGAATTCATAAAgtaagttttt ... tttcttttagGTTGTTAATTATGTTGTGGAAAAGATGGTCCTTGACAAACCAATGGATAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttttagaagaatactgtgtgatgaaaacaattctgtggatttgtttcttttagGTTGTTAATTATGTTGTGGAAAAGATGGTCCTTGACAAACCAATGGATAGTGTAAACCCTGATGGAACATTTGCCCCGGGCCTCCCTGGTGGGCAGTCAC
                                         tttgtttctttt  CT-rich tract
                                        atttgtttctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgacatgtgttcacaccaggttgtacaaaactgcatttacttcatgcttttagaagaatactgtgtgatgaaaacaattctgtggatttgtttcttttagGTTGTTAATTATGTTGTGGAAAAGATGGTCCTTGACAAACCAATGGATAGTGTAAACCCTGATGGAACATTTGCCCCGGGCCTCCCTGGTGGGCAGTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- -catgtgt
- - - - - -cacacca
- - - - - - - - - - - - acaaaac
- - - - - - - - - - - - - - - - -catttac
- - - - - - - - - - - - - - - - - - - - - - - - - -agaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaacaa