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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtatatctgttggacatacatttttttggtgagctatttatttgttatgttcctactaggaacttcataattactttgataattaaatttttagATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTCGTTTATTGGATAAGGAGATCGCTGAGCATGAATTCTCAAAAAACTCTCAAGAAGGAT

Basic information

species Vitis vinifera
transcript Vv14s0171g00490.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 4
---gtcagtatatctgttggac------atacat-ttttttggtgagctatttatttgttatgttccta------ctaggaacttcataattactttgataattaaat--ttttagATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTCGTTTATTGGATAAGGAGATCGCTGAGCATGAATTCTCAAAAAACTCTCAAGAAGGAT
     || |  || | ||| ||       |  ||  | | |  ||  ||   ||  |  ||   |  |       |||  |   ||||  ||  |||     ||   |  ||||||||||||||||| ||||| || || ||| | ||||| || ||||| || |||||||| |||||  | ||||||||||  |  |||||   |   || || |
gttagcactggatttcttgcactgttttgtcaatactctgtaatggtctcactacataatactctgttggttgatctaaaatgatcattctttgtttccctttttcttccttttagATCAAATATGTAAGTGGCTCTTATGATTCTGAGGATGGATTTCGCTTGTTGGATAAAGAGATTTCAGAGCATGAATATTTGAAAAAGAGTGTTGAGGGTT
















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|30128455|gb|CB913794.1|CB913794
EST:     AGGATGCTACATCCGAGCATTCAGAAGAAGTATCTAAATTTTTGCAACTG                         ATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTCGTTTATTG
genomic: AGGATGCTACATCCGAGCATTCAGAAGAAGTATCTAAATTTTTGCAACTGgtcagtatat ... aaatttttagATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTCGTTTATTG
EST: gi|30299156|gb|CB975950.1|CB975950
EST:     AGGATGCTACATCTGAGCATTCAGAAGAAGTATCTAAATTTTTGCAACTG                         ATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTTGTTTATTG
genomic: AGGATGCTACATCCGAGCATTCAGAAGAAGTATCTAAATTTTTGCAACTGgtcagtatat ... aaatttttagATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTCGTTTATTG
EST: gi|110686452|gb|EE064108.1|EE064108
EST:     AGGATGCTACATCCGAGCATTCAGAAGAAGTATCTAAATTTTTGCAACTG                         ATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTCGTTTATTG
genomic: AGGATGCTACATCCGAGCATTCAGAAGAAGTATCTAAATTTTTGCAACTGgtcagtatat ... aaatttttagATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTCGTTTATTG
EST: gi|161717585|gb|FC065623.1|FC065623
EST:     AGGATGCTACATCTGAGCATTCAGAAGAAGTATCTAAATTTTTGCAACTG                         ATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTTGTTTATTG
genomic: AGGATGCTACATCCGAGCATTCAGAAGAAGTATCTAAATTTTTGCAACTGgtcagtatat ... aaatttttagATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTCGTTTATTG
EST: gi|294965944|gb|GW839283.1|GW839283
EST:     AGGATGCTACATCCGAGCATTCAGAAGAAGTATCTAAATTTTTGCAACTG                         ATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTCGTTTATTG
genomic: AGGATGCTACATCCGAGCATTCAGAAGAAGTATCTAAATTTTTGCAACTGgtcagtatat ... aaatttttagATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTCGTTTATTG
EST: gi|37190597|gb|CF609946.1|CF609946
EST:     AGGATGCTACATCTGAGCATTCAGAAGAAGTATCTAAATTTTTGCAACTG                         ATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTCGTTTATTG
genomic: AGGATGCTACATCCGAGCATTCAGAAGAAGTATCTAAATTTTTGCAACTGgtcagtatat ... aaatttttagATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTCGTTTATTG
EST: gi|110364929|gb|EC928538.1|EC928538
EST:     AGGATGCTACATCTGAGCATTCAGAAGAAGTATCTAAATTTTTGCAACTG                         ATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTTGTTTATTG
genomic: AGGATGCTACATCCGAGCATTCAGAAGAAGTATCTAAATTTTTGCAACTGgtcagtatat ... aaatttttagATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTCGTTTATTG
EST: gi|30128024|gb|CB913363.1|CB913363
EST:     AGGATGCTACATCCGAGCATTCAGAAGAAGTATCTAAATTTTTGCAACTG                         ATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTCGTTTATTG
genomic: AGGATGCTACATCCGAGCATTCAGAAGAAGTATCTAAATTTTTGCAACTGgtcagtatat ... aaatttttagATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTCGTTTATTG
EST: gi|161719304|gb|FC068268.1|FC068268
EST:     AGGATGCTACATCTGAGCATTCAGAAGAAGTATCTAAATTTTTGCAACTG                         ATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTTGTTTATTG
genomic: AGGATGCTACATCCGAGCATTCAGAAGAAGTATCTAAATTTTTGCAACTGgtcagtatat ... aaatttttagATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTCGTTTATTG
EST: gi|110372969|gb|EC937167.1|EC937167
EST:     AGGATGCTACATCTGAGCATTCAGAAGAAGTATCTAAATTTTTGCAACTG                         ATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTTGTTTATTG
genomic: AGGATGCTACATCCGAGCATTCAGAAGAAGTATCTAAATTTTTGCAACTGgtcagtatat ... aaatttttagATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTCGTTTATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgttatgttcctactaggaacttcataattactttgataattaaatttttagATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTCGTTTATTGGATAAGGAGATCGCTGAGCATGAATTCTCAAAAAACTCTCAAGAAGGAT
                                  ctttgat  putative branch site (score: 5)
                                                ttttt  putative PPT
                     aacttcataattactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtatatctgttggacatacatttttttggtgagctatttatttgttatgttcctactaggaacttcataattactttgataattaaatttttagATCAAATATGTGAGTGGATCATACGATGCCGAGGACGGTTTTCGTTTATTGGATAAGGAGATCGCTGAGCATGAATTCTCAAAAAACTCTCAAGAAGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG